<?xml version="1.0"?>
<feed xmlns="http://www.w3.org/2005/Atom" xml:lang="en">
	<id>https://wiki.phagocytes.ca/api.php?action=feedcontributions&amp;feedformat=atom&amp;user=Akipp4</id>
	<title>Heit Lab Wiki - User contributions [en]</title>
	<link rel="self" type="application/atom+xml" href="https://wiki.phagocytes.ca/api.php?action=feedcontributions&amp;feedformat=atom&amp;user=Akipp4"/>
	<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php/Special:Contributions/Akipp4"/>
	<updated>2026-05-11T19:51:18Z</updated>
	<subtitle>User contributions</subtitle>
	<generator>MediaWiki 1.40.1</generator>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Gibson_Assembly&amp;diff=255</id>
		<title>Gibson Assembly</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Gibson_Assembly&amp;diff=255"/>
		<updated>2025-01-17T19:55:37Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Gibson Assembly, also known as enzymatic or chew-back assembly, is a powerful tool used for DNA cloning. It allows you to manipulate almost any fragment of DNA in any location, alleviating the need to plan projects around restriction sites.&lt;br /&gt;
&lt;br /&gt;
=Overview and Background Info=&lt;br /&gt;
Gibson Assembly uses sequence homology between fragments of DNA to join them together. A Gibson Assembly reaction mixture uses 3 enzymes: 5'--&amp;gt;3' exonuclease, high-fidelity polymerase and ligase. Together, these enzymes '''''chew back''''' the 5' end of DNA fragments (allowing fragments with sequence homology to anneal), '''''fill in''''' any gaps created by the chew-back, and '''''seal''''' the nicks in the annealed fragment. While it can be used to generate linear assemblies, Gibson is most commonly used to manipulate circular plasmids, for transformation and propagation in bacteria. Fragments for Gibson Assembly must have 15-500 bp of homology. This can be done through synthesis of entire fragments, or by amplification with &amp;quot;overhanging&amp;quot; primers&lt;br /&gt;
&amp;lt;p&amp;gt;[[File:ga.png]]&amp;lt;/p&amp;gt;&lt;br /&gt;
&lt;br /&gt;
=Protocol=&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
1. Prepare DNA required for the reaction, typically linearize vector (see restriction digest) and PCR amplification of insert(s) (see PCR)&lt;br /&gt;
&lt;br /&gt;
2. In a PCR tube, prepare reaction mix as indicated below&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
| &lt;br /&gt;
|'''2-3 Fragments'''&lt;br /&gt;
|'''4-6 Fragments'''&lt;br /&gt;
|-&lt;br /&gt;
|Recommended DNA Molar Ratio (Vector:Insert)&lt;br /&gt;
|1:2&lt;br /&gt;
|1:1&lt;br /&gt;
|-&lt;br /&gt;
|Starting amount of vector&lt;br /&gt;
|50 – 100 ng&lt;br /&gt;
|50 – 100 ng&lt;br /&gt;
|-&lt;br /&gt;
|Amount of insert&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; |depends on molar ratio&lt;br /&gt;
|-&lt;br /&gt;
|2X HiFi DNA Assembly Master Mix&lt;br /&gt;
|10 µL&lt;br /&gt;
|10 µL&lt;br /&gt;
|-&lt;br /&gt;
|ddH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O&lt;br /&gt;
|x (up to 20 uL)&lt;br /&gt;
|x (up to 20 uL)&lt;br /&gt;
|}&lt;br /&gt;
3. Incubate the sample in a thermocycler at 50°C for 15-30 mins for 2-3 fragments or 60 mins for 4-6 fragments&lt;br /&gt;
&lt;br /&gt;
4. Transform into component E. coli &lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;br /&gt;
NEBuilder HiFi DNA Assembly Master Mix Instruction Manual &lt;br /&gt;
&lt;br /&gt;
https://nebcloner.neb.com/#!/products/search/E2621&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Gibson_Assembly&amp;diff=254</id>
		<title>Gibson Assembly</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Gibson_Assembly&amp;diff=254"/>
		<updated>2025-01-17T19:06:10Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: /* Materials */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Gibson Assembly, also known as enzymatic or chew-back assembly, is a powerful tool used for DNA cloning. It allows you to manipulate almost any fragment of DNA in any location, alleviating the need to plan projects around restriction sites.&lt;br /&gt;
&lt;br /&gt;
=Overview and Background Info=&lt;br /&gt;
Gibson Assembly uses sequence homology between fragments of DNA to join them together. A Gibson Assembly reaction mixture uses 3 enzymes: 5'--&amp;gt;3' exonuclease, high-fidelity polymerase and ligase. Together, these enzymes '''''chew back''''' the 5' end of DNA fragments (allowing fragments with sequence homology to anneal), '''''fill in''''' any gaps created by the chew-back, and '''''seal''''' the nicks in the annealed fragment. While it can be used to generate linear assemblies, Gibson is most commonly used to manipulate circular plasmids, for transformation and propagation in bacteria. Fragments for Gibson Assembly must have 15-500 bp of homology. This can be done through synthesis of entire fragments, or by amplification with &amp;quot;overhanging&amp;quot; primers&lt;br /&gt;
&amp;lt;p&amp;gt;[[File:ga.png]]&amp;lt;/p&amp;gt;&lt;br /&gt;
&lt;br /&gt;
=Protocol=&lt;br /&gt;
&lt;br /&gt;
==Reaction==&lt;br /&gt;
If using NEBuilder HiFi:&lt;br /&gt;
*Add 10 μL of DNA (+ water) to 10μL of 2xNEBuilder HiFi&lt;br /&gt;
If using homemade Master Mix:&lt;br /&gt;
*Add 5 or 10 μL of DNA (+ water, depending on indicated concentration of Master Mix) directly to tube containing 15 μL aliquot of master mix&lt;br /&gt;
&lt;br /&gt;
Incubate at 50˚C for 45-75 mins ('''if Master Mix contains T7 DNA Ligase''': incubate for additional 15-30 mins at 25˚C or room temp).&amp;lt;br /&amp;gt;&lt;br /&gt;
Transform 1-4 μL into competent bacteria, or store mixture at -20˚C.&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Restriction_Digest&amp;diff=253</id>
		<title>Restriction Digest</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Restriction_Digest&amp;diff=253"/>
		<updated>2025-01-17T18:56:49Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
'''Protocol'''&lt;br /&gt;
&lt;br /&gt;
# Check the NEB (or other supplier) website to confirm enzyme compatibility &lt;br /&gt;
# In a PCR tube add the reaction components according to the table listed below&lt;br /&gt;
# Mix reaction gently and spin down briefly with benchtop centrifuge&lt;br /&gt;
# Incubate at 37°C for 30 min if time-saver qualified, 60 minutes if not&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Example Reaction'''&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|'''Component'''&lt;br /&gt;
|'''Volume'''&lt;br /&gt;
|-&lt;br /&gt;
|ddH2O&lt;br /&gt;
|Up to 50 µL&lt;br /&gt;
|-&lt;br /&gt;
|10X rCutSmart Buffer&lt;br /&gt;
|5 µL&lt;br /&gt;
|-&lt;br /&gt;
|DNA&lt;br /&gt;
|x (1 µg)&lt;br /&gt;
|-&lt;br /&gt;
|Enzyme 1&lt;br /&gt;
|1 µL&lt;br /&gt;
|-&lt;br /&gt;
|Enzyme 2&lt;br /&gt;
|1 µL&lt;br /&gt;
|}	&lt;br /&gt;
&lt;br /&gt;
'''Notes'''&lt;br /&gt;
&lt;br /&gt;
- NEB High-Fidelity (HF) enzymes are ordered whenever possible, they all use rCutSmart reaction buffer and are usually time-saver qualified&lt;br /&gt;
&lt;br /&gt;
- NEB has the option to select your specific enzymes and generate a detailed protocol&lt;br /&gt;
-	Heat inactivation may be recommended if there are additional steps in the workflow without a DNA purification step&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''References, related resources, and acknowledgments'''&lt;br /&gt;
&lt;br /&gt;
https://nebcloner.neb.com/#!/redigest&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Restriction_Digest&amp;diff=252</id>
		<title>Restriction Digest</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Restriction_Digest&amp;diff=252"/>
		<updated>2025-01-17T18:52:51Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: Created page with &amp;quot; Protocol  1. Check the NEB (or other supplier) website to confirm enzyme compatibility  2.  In a PCR tube add the reaction components according to the table listed below 3.  Incubate at 37°C for 30 min if time-saver qualified, 60 minutes if not  Example Reaction	  Component	Volume ddH2O	Up to 50 µL 10X rCutSmart Buffer	5 µL DNA	x (1 µg) Enzyme 1	1 µL Enzyme 2	1 µL  Notes -	NEB High-Fidelity (HF) enzymes are ordered whenever possible, they all use rCutSmart reactio...&amp;quot;&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
Protocol &lt;br /&gt;
1. Check the NEB (or other supplier) website to confirm enzyme compatibility &lt;br /&gt;
2.  In a PCR tube add the reaction components according to the table listed below&lt;br /&gt;
3.  Incubate at 37°C for 30 min if time-saver qualified, 60 minutes if not&lt;br /&gt;
&lt;br /&gt;
Example Reaction	&lt;br /&gt;
&lt;br /&gt;
Component	Volume&lt;br /&gt;
ddH2O	Up to 50 µL&lt;br /&gt;
10X rCutSmart Buffer	5 µL&lt;br /&gt;
DNA	x (1 µg)&lt;br /&gt;
Enzyme 1	1 µL&lt;br /&gt;
Enzyme 2	1 µL&lt;br /&gt;
&lt;br /&gt;
Notes&lt;br /&gt;
-	NEB High-Fidelity (HF) enzymes are ordered whenever possible, they all use rCutSmart reaction buffer and are usually time-saver qualified Hi&lt;br /&gt;
-	NEB has the option to select your specific enzymes and generate a detailed protocol&lt;br /&gt;
-	Heat inactivation may be recommended if there are additional steps in the workflow without a DNA purification step&lt;br /&gt;
&lt;br /&gt;
References, related resources, and acknowledgments&lt;br /&gt;
-	https://nebcloner.neb.com/#!/redigest&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=251</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=251"/>
		<updated>2025-01-17T18:50:46Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: /* DNA/Cloning */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
*[[Restriction Digest]]&lt;br /&gt;
|&lt;br /&gt;
|'''Transfections and Transductions'''&lt;br /&gt;
* [[J774 Cell Transfection]]&lt;br /&gt;
* [[Raw Cell Transfection]]&lt;br /&gt;
* [[THP1 Culture and Differentiation]]&lt;br /&gt;
* [[Neon® Transfection System]]&lt;br /&gt;
* [[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
*[[Transduction of THP-1s]]&lt;br /&gt;
*[[Nucleofector]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Primary Macrophage Culture|Primary Murine Macrophages]]&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
&lt;br /&gt;
'''Bead Preparation'''&lt;br /&gt;
&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
*[[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|'''Bacteria Work'''&lt;br /&gt;
&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
|&lt;br /&gt;
==== Protein Work ====&lt;br /&gt;
*[[Bradford Assay]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
|&lt;br /&gt;
|'''Microscopy'''&lt;br /&gt;
*[[3D Printed PDMS Chambers]]&lt;br /&gt;
*[[Acid Washing Coverslips]]&lt;br /&gt;
*[[Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Immunostaining|Fluorescent Immunostaining]]&lt;br /&gt;
*[[FRET in FIJI]]&lt;br /&gt;
*[[Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Immuno-FISH]]&lt;br /&gt;
*[[Live Cell FRET]] [[Nucleofector|(depreciated)]]&lt;br /&gt;
*[[Reducing Photobleaching]]&lt;br /&gt;
*[[Single Particle Tracking]]&lt;br /&gt;
*[[Staining for GSD]]&lt;br /&gt;
*[[Traction Force Microscopy]]&lt;br /&gt;
*[[3D Printed Microscopy Chambers]]&lt;br /&gt;
&lt;br /&gt;
*[[Micropatterning Proteins]]&lt;br /&gt;
*[[Frustrated Phagocytosis]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====General Protocol Sites====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols&lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols&lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols&lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols&lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses.&lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat&lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols&lt;br /&gt;
|&lt;br /&gt;
====Free Science Ebooks====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
=Useful Links=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Molecular Biology Databases====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
=====Microscopy Tools===== &lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Journal Resources====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
====''In Vivo'' Tools====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
====Protease Tools====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Genomics Resources====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
====Chemical Tools====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
====Lipid Tools====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=250</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=250"/>
		<updated>2025-01-17T18:50:24Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: /* DNA/Cloning */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
*[[Digest]]&lt;br /&gt;
|&lt;br /&gt;
|'''Transfections and Transductions'''&lt;br /&gt;
* [[J774 Cell Transfection]]&lt;br /&gt;
* [[Raw Cell Transfection]]&lt;br /&gt;
* [[THP1 Culture and Differentiation]]&lt;br /&gt;
* [[Neon® Transfection System]]&lt;br /&gt;
* [[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
*[[Transduction of THP-1s]]&lt;br /&gt;
*[[Nucleofector]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Primary Macrophage Culture|Primary Murine Macrophages]]&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
&lt;br /&gt;
'''Bead Preparation'''&lt;br /&gt;
&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
*[[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|'''Bacteria Work'''&lt;br /&gt;
&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
|&lt;br /&gt;
==== Protein Work ====&lt;br /&gt;
*[[Bradford Assay]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
|&lt;br /&gt;
|'''Microscopy'''&lt;br /&gt;
*[[3D Printed PDMS Chambers]]&lt;br /&gt;
*[[Acid Washing Coverslips]]&lt;br /&gt;
*[[Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Immunostaining|Fluorescent Immunostaining]]&lt;br /&gt;
*[[FRET in FIJI]]&lt;br /&gt;
*[[Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Immuno-FISH]]&lt;br /&gt;
*[[Live Cell FRET]] [[Nucleofector|(depreciated)]]&lt;br /&gt;
*[[Reducing Photobleaching]]&lt;br /&gt;
*[[Single Particle Tracking]]&lt;br /&gt;
*[[Staining for GSD]]&lt;br /&gt;
*[[Traction Force Microscopy]]&lt;br /&gt;
*[[3D Printed Microscopy Chambers]]&lt;br /&gt;
&lt;br /&gt;
*[[Micropatterning Proteins]]&lt;br /&gt;
*[[Frustrated Phagocytosis]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====General Protocol Sites====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols&lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols&lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols&lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols&lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses.&lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat&lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols&lt;br /&gt;
|&lt;br /&gt;
====Free Science Ebooks====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
=Useful Links=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Molecular Biology Databases====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
=====Microscopy Tools===== &lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Journal Resources====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
====''In Vivo'' Tools====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
====Protease Tools====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Genomics Resources====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
====Chemical Tools====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
====Lipid Tools====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=249</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=249"/>
		<updated>2025-01-17T18:49:55Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
*[[Digests|Restriction Digests]]&lt;br /&gt;
|&lt;br /&gt;
|'''Transfections and Transductions'''&lt;br /&gt;
* [[J774 Cell Transfection]]&lt;br /&gt;
* [[Raw Cell Transfection]]&lt;br /&gt;
* [[THP1 Culture and Differentiation]]&lt;br /&gt;
* [[Neon® Transfection System]]&lt;br /&gt;
* [[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
*[[Transduction of THP-1s]]&lt;br /&gt;
*[[Nucleofector]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Primary Macrophage Culture|Primary Murine Macrophages]]&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
&lt;br /&gt;
'''Bead Preparation'''&lt;br /&gt;
&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
*[[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|'''Bacteria Work'''&lt;br /&gt;
&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
|&lt;br /&gt;
==== Protein Work ====&lt;br /&gt;
*[[Bradford Assay]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
|&lt;br /&gt;
|'''Microscopy'''&lt;br /&gt;
*[[3D Printed PDMS Chambers]]&lt;br /&gt;
*[[Acid Washing Coverslips]]&lt;br /&gt;
*[[Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Immunostaining|Fluorescent Immunostaining]]&lt;br /&gt;
*[[FRET in FIJI]]&lt;br /&gt;
*[[Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Immuno-FISH]]&lt;br /&gt;
*[[Live Cell FRET]] [[Nucleofector|(depreciated)]]&lt;br /&gt;
*[[Reducing Photobleaching]]&lt;br /&gt;
*[[Single Particle Tracking]]&lt;br /&gt;
*[[Staining for GSD]]&lt;br /&gt;
*[[Traction Force Microscopy]]&lt;br /&gt;
*[[3D Printed Microscopy Chambers]]&lt;br /&gt;
&lt;br /&gt;
*[[Micropatterning Proteins]]&lt;br /&gt;
*[[Frustrated Phagocytosis]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====General Protocol Sites====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols&lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols&lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols&lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols&lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses.&lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat&lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols&lt;br /&gt;
|&lt;br /&gt;
====Free Science Ebooks====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
=Useful Links=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Molecular Biology Databases====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
=====Microscopy Tools===== &lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Journal Resources====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
====''In Vivo'' Tools====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
====Protease Tools====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Genomics Resources====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
====Chemical Tools====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
====Lipid Tools====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Digests&amp;diff=248</id>
		<title>Digests</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Digests&amp;diff=248"/>
		<updated>2025-01-17T18:48:45Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: Undo revision 244 by Akipp4 (talk)&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|'''Protocol''' &lt;br /&gt;
|}&lt;br /&gt;
1. Check the NEB (or other supplier) website to confirm enzyme compatibility &lt;br /&gt;
&lt;br /&gt;
2. In a PCR tube add the reaction components according to the table listed below&lt;br /&gt;
&lt;br /&gt;
3. Mix contents gently and spin down using the small benchtop centrifuge &lt;br /&gt;
&lt;br /&gt;
3. Incubate at 37°C for 30 min if time-saver qualified, 60 minutes if not &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|'''Example  Reaction                                                                                                                              ''' &lt;br /&gt;
|}&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|'''Component'''&lt;br /&gt;
|'''Volume'''&lt;br /&gt;
|-&lt;br /&gt;
|ddH2O&lt;br /&gt;
|Up to 50 µL&lt;br /&gt;
|-&lt;br /&gt;
|10X rCutSmart Buffer&lt;br /&gt;
|5 µL&lt;br /&gt;
|-&lt;br /&gt;
|DNA&lt;br /&gt;
|x (1 µg)&lt;br /&gt;
|-&lt;br /&gt;
|Enzyme 1&lt;br /&gt;
|1 µL&lt;br /&gt;
|-&lt;br /&gt;
|Enzyme 2&lt;br /&gt;
|1 µL&lt;br /&gt;
|} &lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|'''Notes'''&lt;br /&gt;
|}&lt;br /&gt;
-         NEB High-Fidelity (HF) enzymes are ordered whenever possible, they all use rCutSmart reaction buffer and are usually time-saver qualified Hi&lt;br /&gt;
&lt;br /&gt;
-         NEB has the option to select your specific enzymes and generate a detailed protocol&lt;br /&gt;
&lt;br /&gt;
-         Heat inactivation may be recommended if there are additional steps in the workflow without a DNA purification step&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|'''References, related resources, and acknowledgments'''&lt;br /&gt;
|}&lt;br /&gt;
-         &amp;lt;nowiki&amp;gt;https://nebcloner.neb.com/#!/redigest&amp;lt;/nowiki&amp;gt;&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=247</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=247"/>
		<updated>2025-01-17T18:45:55Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: /* DNA/Cloning */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
*[[Restriction Digests]]&lt;br /&gt;
|&lt;br /&gt;
|'''Transfections and Transductions'''&lt;br /&gt;
* [[J774 Cell Transfection]]&lt;br /&gt;
* [[Raw Cell Transfection]]&lt;br /&gt;
* [[THP1 Culture and Differentiation]]&lt;br /&gt;
* [[Neon® Transfection System]]&lt;br /&gt;
* [[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
*[[Transduction of THP-1s]]&lt;br /&gt;
*[[Nucleofector]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Primary Macrophage Culture|Primary Murine Macrophages]]&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
&lt;br /&gt;
'''Bead Preparation'''&lt;br /&gt;
&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
*[[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|'''Bacteria Work'''&lt;br /&gt;
&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
|&lt;br /&gt;
==== Protein Work ====&lt;br /&gt;
*[[Bradford Assay]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
|&lt;br /&gt;
|'''Microscopy'''&lt;br /&gt;
*[[3D Printed PDMS Chambers]]&lt;br /&gt;
*[[Acid Washing Coverslips]]&lt;br /&gt;
*[[Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Immunostaining|Fluorescent Immunostaining]]&lt;br /&gt;
*[[FRET in FIJI]]&lt;br /&gt;
*[[Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Immuno-FISH]]&lt;br /&gt;
*[[Live Cell FRET]] [[Nucleofector|(depreciated)]]&lt;br /&gt;
*[[Reducing Photobleaching]]&lt;br /&gt;
*[[Single Particle Tracking]]&lt;br /&gt;
*[[Staining for GSD]]&lt;br /&gt;
*[[Traction Force Microscopy]]&lt;br /&gt;
*[[3D Printed Microscopy Chambers]]&lt;br /&gt;
&lt;br /&gt;
*[[Micropatterning Proteins]]&lt;br /&gt;
*[[Frustrated Phagocytosis]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====General Protocol Sites====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols&lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols&lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols&lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols&lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses.&lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat&lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols&lt;br /&gt;
|&lt;br /&gt;
====Free Science Ebooks====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
=Useful Links=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Molecular Biology Databases====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
=====Microscopy Tools===== &lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Journal Resources====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
====''In Vivo'' Tools====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
====Protease Tools====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Genomics Resources====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
====Chemical Tools====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
====Lipid Tools====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=246</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=246"/>
		<updated>2025-01-17T18:43:48Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: /* DNA/Cloning */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
*[[ Restriction Digests]]&lt;br /&gt;
|&lt;br /&gt;
|'''Transfections and Transductions'''&lt;br /&gt;
* [[J774 Cell Transfection]]&lt;br /&gt;
* [[Raw Cell Transfection]]&lt;br /&gt;
* [[THP1 Culture and Differentiation]]&lt;br /&gt;
* [[Neon® Transfection System]]&lt;br /&gt;
* [[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
*[[Transduction of THP-1s]]&lt;br /&gt;
*[[Nucleofector]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Primary Macrophage Culture|Primary Murine Macrophages]]&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
&lt;br /&gt;
'''Bead Preparation'''&lt;br /&gt;
&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
*[[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|'''Bacteria Work'''&lt;br /&gt;
&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
|&lt;br /&gt;
==== Protein Work ====&lt;br /&gt;
*[[Bradford Assay]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
|&lt;br /&gt;
|'''Microscopy'''&lt;br /&gt;
*[[3D Printed PDMS Chambers]]&lt;br /&gt;
*[[Acid Washing Coverslips]]&lt;br /&gt;
*[[Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Immunostaining|Fluorescent Immunostaining]]&lt;br /&gt;
*[[FRET in FIJI]]&lt;br /&gt;
*[[Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Immuno-FISH]]&lt;br /&gt;
*[[Live Cell FRET]] [[Nucleofector|(depreciated)]]&lt;br /&gt;
*[[Reducing Photobleaching]]&lt;br /&gt;
*[[Single Particle Tracking]]&lt;br /&gt;
*[[Staining for GSD]]&lt;br /&gt;
*[[Traction Force Microscopy]]&lt;br /&gt;
*[[3D Printed Microscopy Chambers]]&lt;br /&gt;
&lt;br /&gt;
*[[Micropatterning Proteins]]&lt;br /&gt;
*[[Frustrated Phagocytosis]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====General Protocol Sites====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols&lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols&lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols&lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols&lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses.&lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat&lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols&lt;br /&gt;
|&lt;br /&gt;
====Free Science Ebooks====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
=Useful Links=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Molecular Biology Databases====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
=====Microscopy Tools===== &lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Journal Resources====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
====''In Vivo'' Tools====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
====Protease Tools====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Genomics Resources====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
====Chemical Tools====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
====Lipid Tools====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=245</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=245"/>
		<updated>2025-01-17T18:43:27Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: /* DNA/Cloning */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[ Restriction Digests]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
|&lt;br /&gt;
|'''Transfections and Transductions'''&lt;br /&gt;
* [[J774 Cell Transfection]]&lt;br /&gt;
* [[Raw Cell Transfection]]&lt;br /&gt;
* [[THP1 Culture and Differentiation]]&lt;br /&gt;
* [[Neon® Transfection System]]&lt;br /&gt;
* [[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
*[[Transduction of THP-1s]]&lt;br /&gt;
*[[Nucleofector]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Primary Macrophage Culture|Primary Murine Macrophages]]&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
&lt;br /&gt;
'''Bead Preparation'''&lt;br /&gt;
&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
*[[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|'''Bacteria Work'''&lt;br /&gt;
&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
|&lt;br /&gt;
==== Protein Work ====&lt;br /&gt;
*[[Bradford Assay]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
|&lt;br /&gt;
|'''Microscopy'''&lt;br /&gt;
*[[3D Printed PDMS Chambers]]&lt;br /&gt;
*[[Acid Washing Coverslips]]&lt;br /&gt;
*[[Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Immunostaining|Fluorescent Immunostaining]]&lt;br /&gt;
*[[FRET in FIJI]]&lt;br /&gt;
*[[Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Immuno-FISH]]&lt;br /&gt;
*[[Live Cell FRET]] [[Nucleofector|(depreciated)]]&lt;br /&gt;
*[[Reducing Photobleaching]]&lt;br /&gt;
*[[Single Particle Tracking]]&lt;br /&gt;
*[[Staining for GSD]]&lt;br /&gt;
*[[Traction Force Microscopy]]&lt;br /&gt;
*[[3D Printed Microscopy Chambers]]&lt;br /&gt;
&lt;br /&gt;
*[[Micropatterning Proteins]]&lt;br /&gt;
*[[Frustrated Phagocytosis]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====General Protocol Sites====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols&lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols&lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols&lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols&lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses.&lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat&lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols&lt;br /&gt;
|&lt;br /&gt;
====Free Science Ebooks====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
=Useful Links=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Molecular Biology Databases====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
=====Microscopy Tools===== &lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Journal Resources====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
====''In Vivo'' Tools====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
====Protease Tools====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Genomics Resources====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
====Chemical Tools====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
====Lipid Tools====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Digests&amp;diff=244</id>
		<title>Digests</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Digests&amp;diff=244"/>
		<updated>2025-01-17T18:42:37Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: updated protocoll to reflect neb enzymes&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|'''Protocol''' &lt;br /&gt;
|}&lt;br /&gt;
1. Check the NEB (or other supplier) website to confirm enzyme compatibility &lt;br /&gt;
&lt;br /&gt;
2. In a PCR tube add the reaction components according to the table listed below&lt;br /&gt;
&lt;br /&gt;
3. Mix contents gently and spin down using the small benchtop centrifuge &lt;br /&gt;
&lt;br /&gt;
3. Incubate at 37°C for 15-30 min if time-saver qualified, 60 minutes if not &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|'''Example  Reaction                                                                                                                              ''' &lt;br /&gt;
|}&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|'''Component'''&lt;br /&gt;
|'''Volume'''&lt;br /&gt;
|-&lt;br /&gt;
|ddH2O&lt;br /&gt;
|Up to 50 µL&lt;br /&gt;
|-&lt;br /&gt;
|10X rCutSmart Buffer&lt;br /&gt;
|5 µL&lt;br /&gt;
|-&lt;br /&gt;
|DNA&lt;br /&gt;
|x (1 µg)&lt;br /&gt;
|-&lt;br /&gt;
|Enzyme 1&lt;br /&gt;
|1 µL&lt;br /&gt;
|-&lt;br /&gt;
|Enzyme 2&lt;br /&gt;
|1 µL&lt;br /&gt;
|} &lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|'''Notes'''&lt;br /&gt;
|}&lt;br /&gt;
-         NEB High-Fidelity (HF) enzymes are ordered whenever possible, they all use rCutSmart reaction buffer and are usually time-saver qualified Hi&lt;br /&gt;
&lt;br /&gt;
-         NEB has the option to select your specific enzymes and generate a detailed protocol&lt;br /&gt;
&lt;br /&gt;
-         Heat inactivation may be recommended if there are additional steps in the workflow without a DNA purification step&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|'''References, related resources, and acknowledgments'''&lt;br /&gt;
|}&lt;br /&gt;
-         &amp;lt;nowiki&amp;gt;https://nebcloner.neb.com/#!/redigest&amp;lt;/nowiki&amp;gt;&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Digests&amp;diff=243</id>
		<title>Digests</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Digests&amp;diff=243"/>
		<updated>2025-01-17T18:40:38Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: /* Protocol */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|'''Protocol''' &lt;br /&gt;
|}&lt;br /&gt;
1. Check the NEB (or other supplier) website to confirm enzyme compatibility &lt;br /&gt;
&lt;br /&gt;
2. In a PCR tube add the reaction components according to the table listed below&lt;br /&gt;
&lt;br /&gt;
3. Mix contents gently and spin down using the small benchtop centrifuge &lt;br /&gt;
&lt;br /&gt;
3. Incubate at 37°C for 30 min if time-saver qualified, 60 minutes if not &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|'''Example  Reaction                                                                                                                              ''' &lt;br /&gt;
|}&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|'''Component'''&lt;br /&gt;
|'''Volume'''&lt;br /&gt;
|-&lt;br /&gt;
|ddH2O&lt;br /&gt;
|Up to 50 µL&lt;br /&gt;
|-&lt;br /&gt;
|10X rCutSmart Buffer&lt;br /&gt;
|5 µL&lt;br /&gt;
|-&lt;br /&gt;
|DNA&lt;br /&gt;
|x (1 µg)&lt;br /&gt;
|-&lt;br /&gt;
|Enzyme 1&lt;br /&gt;
|1 µL&lt;br /&gt;
|-&lt;br /&gt;
|Enzyme 2&lt;br /&gt;
|1 µL&lt;br /&gt;
|} &lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|'''Notes'''&lt;br /&gt;
|}&lt;br /&gt;
-         NEB High-Fidelity (HF) enzymes are ordered whenever possible, they all use rCutSmart reaction buffer and are usually time-saver qualified Hi&lt;br /&gt;
&lt;br /&gt;
-         NEB has the option to select your specific enzymes and generate a detailed protocol&lt;br /&gt;
&lt;br /&gt;
-         Heat inactivation may be recommended if there are additional steps in the workflow without a DNA purification step&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|'''References, related resources, and acknowledgments'''&lt;br /&gt;
|}&lt;br /&gt;
-         &amp;lt;nowiki&amp;gt;https://nebcloner.neb.com/#!/redigest&amp;lt;/nowiki&amp;gt;&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Coomassie_Staining&amp;diff=235</id>
		<title>Coomassie Staining</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Coomassie_Staining&amp;diff=235"/>
		<updated>2024-08-02T16:54:15Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;These procedures are adapted from the procedure at [http://www.nationaldiagnostics.com/article_info.php/articles_id/80 National Diagnostics].&lt;br /&gt;
&lt;br /&gt;
= Method 1: Standard (sensitive) Coomassie&amp;lt;br&amp;gt; =&lt;br /&gt;
&lt;br /&gt;
This is the classical Coomassie stain, and is highly sensitive, detecting as little as 0.1ug/band.&amp;amp;nbsp; To improve detection a thin gel, run at lower voltage, is preferred as the bands ill be more concentrated under these running conditions.&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===== Protocol&amp;lt;br&amp;gt; =====&lt;br /&gt;
&lt;br /&gt;
#Fix gel for 30min to overnight using the fixative solution.&amp;lt;br&amp;gt; &lt;br /&gt;
#Stain gel using the fixative solution containing 0.25% Coomassie R &lt;br /&gt;
#*Stain in a minimal-volume tray &lt;br /&gt;
#*Cover with ~1.5cm staining solution&amp;lt;br&amp;gt; &lt;br /&gt;
#*Gently shake 2 - 4hrs, until gel is the same colour as the dye (prior to this, gel will appear as a lighter area)   &lt;br /&gt;
#Destain 4 - 24hrs in destaining solution.&amp;amp;nbsp; Bands will appear in 1 - 2hrs; destain until background is light-amber or clear&amp;lt;br&amp;gt; &lt;br /&gt;
#Store gels in 7% glacial acetic acid.&amp;lt;br&amp;gt; &lt;br /&gt;
&lt;br /&gt;
===== Recipes&amp;lt;br&amp;gt; =====&lt;br /&gt;
&lt;br /&gt;
====== Fixative&amp;lt;br&amp;gt; ======&lt;br /&gt;
&lt;br /&gt;
*50% methanol&amp;lt;br&amp;gt; &lt;br /&gt;
*10% glacial acetic acid&amp;lt;br&amp;gt; &lt;br /&gt;
*40% ddH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O&amp;lt;br&amp;gt; &lt;br /&gt;
&lt;br /&gt;
====== Destain&amp;lt;br&amp;gt; ======&lt;br /&gt;
&lt;br /&gt;
*5% Methanol&amp;lt;br&amp;gt; &lt;br /&gt;
*7.5% glacial acetic acid&amp;lt;br&amp;gt; &lt;br /&gt;
*87.5% ddH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Method 1b: Fast Version of Classic Stain&amp;lt;br&amp;gt; =&lt;br /&gt;
&lt;br /&gt;
This is a slightly altered version of the standard method, which is completed much more quickly.&amp;amp;nbsp; However, the sensitivity is less with this method and distortions of the gel are a possibility.&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
#Rinse gel once in ddH2O &lt;br /&gt;
#Immerse in staining solution from above protocol, bring to a boil in the microwave (40sec - 1min)&amp;lt;br&amp;gt; &lt;br /&gt;
#Shake for 5 - 10min &lt;br /&gt;
#Rinse 2X in ddH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O &lt;br /&gt;
#Cover gel with 2cm destain solution from above protocol&amp;lt;br&amp;gt; &lt;br /&gt;
#Knot 4 kimwipes together and place around gel in destain - DO&amp;amp;nbsp;NOT&amp;amp;nbsp;PLACE&amp;amp;nbsp;ON&amp;amp;nbsp;GEL&amp;lt;br&amp;gt; &lt;br /&gt;
#Bring to a boil on microwave (40sec - 1min).&amp;lt;br&amp;gt; &lt;br /&gt;
#Incubate on shaker an additional 10min&amp;lt;br&amp;gt; &lt;br /&gt;
#Discard kimwpies and replace with 4 fresh knotted kimwipes&amp;lt;br&amp;gt; &lt;br /&gt;
#Incubate on shaker an additional 10min to over night.&amp;amp;nbsp; A second round of microwaving can be used to speed the process.&amp;lt;br&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Method 2: Rapid Coomassie Blue R-250&amp;lt;br&amp;gt; =&lt;br /&gt;
&lt;br /&gt;
This method is faster than the classical method, but is 2 - 5 times less sensitive.&lt;br /&gt;
&lt;br /&gt;
#Fix gel in 25% isopropyl alcohol, 10% glacial acetic acid (remainder ddH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O), 30 - 60 minutes.&amp;lt;br&amp;gt; &lt;br /&gt;
#Stain gel in 10% Acetic Acid in ddH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O, containing 60 mg/L of Coomassie Blue R-250.&amp;lt;br&amp;gt; &lt;br /&gt;
#Bands will appear in 30 minutes. Allow staining to proceed until desired band intensity is reached.&amp;lt;br&amp;gt; &lt;br /&gt;
#No de-stain is required.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt; &lt;br /&gt;
&lt;br /&gt;
= Method 3: Rapid Coomassie Blue G-250&amp;lt;br&amp;gt; =&lt;br /&gt;
&lt;br /&gt;
This method is the easiest, but is the least sensitive.&amp;amp;nbsp; Simply soak gel in staining solution; bands should appear in 15 min, and increase in intensity over several hours.&amp;amp;nbsp; Staining solution is stable for several weeks at room temp.&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===== Staining Solution:&amp;lt;br&amp;gt; =====&lt;br /&gt;
&lt;br /&gt;
#dissolve 0.2g dye in 100 ml ddH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O (this will require warming to approximately 50°C). &lt;br /&gt;
#Cool and add 100 ml 2N H2S04. &lt;br /&gt;
#Incubate at room temperature 3 hours to overnight, then filter. &lt;br /&gt;
#To filtered solution, CAREFULLY add 22.2 ml 10N KOH &lt;br /&gt;
#Then add 28.7g TCA. Allow to stand &amp;amp;gt; 3 hours &lt;br /&gt;
#Filter again if necessary to obtain an amber-brown solution without blue precipitate.&amp;lt;br&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Method 4: Coomassie Staining of PVDF Membrane&amp;lt;br&amp;gt; =&lt;br /&gt;
&lt;br /&gt;
===== Method 1&amp;lt;br&amp;gt; =====&lt;br /&gt;
&lt;br /&gt;
From &amp;lt;ref&amp;gt;http://world-2dpage.expasy.org/swiss-2dpage/docs/protocols/protocols.fm9.html&amp;lt;/ref&amp;gt;&amp;lt;ref&amp;gt;http://www.ncbi.nlm.nih.gov/pubmed?term=1281090&amp;lt;/ref&amp;gt;.&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
#After transfer wash blot in ddH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O, 2-3 X 5min&amp;lt;br&amp;gt; &lt;br /&gt;
#Stain PVDF membrane with 0.1% Coomassie R-250 in 50% methanol for 15 min.&amp;lt;br&amp;gt; &lt;br /&gt;
#Destain with 40% methanol, 10% acetic acid.&amp;amp;nbsp; Change destain as needed. &lt;br /&gt;
#Rinse with ddH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O and dry &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===== Method 2 (rapid) =====&lt;br /&gt;
&lt;br /&gt;
From &amp;lt;ref&amp;gt;http://www.ecu.edu/cs-dhs/biochemistry/upload/PVDF-Coomassie-Protein-Staining.pdf&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
#Wash 1X 5min in TBS-T &lt;br /&gt;
#Stain using 50% methanol, 7% acetic acid, 0.1% coomassie R-250; on rocker, 5min. &lt;br /&gt;
#Destain with 50% methanol, 7% acetic acid, ~5min (until solution is saturated with dye) &lt;br /&gt;
#Replace with 90% methanol, 1% acetic acid; agitate by hand until bands are desired colour - &amp;lt;u&amp;gt;DO&amp;amp;nbsp;NOT&amp;amp;nbsp;OVER-RINSE&amp;lt;/u&amp;gt; &lt;br /&gt;
#Wash with water and dry &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===== Method 3 (sequencing)&amp;lt;br&amp;gt; =====&lt;br /&gt;
&lt;br /&gt;
From &amp;lt;ref name=&amp;quot;Biosync&amp;quot;&amp;gt;http://www.biosyn.com/faq.aspx?qid=310&amp;lt;/ref&amp;gt;.&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
#Rinse membrane 2-3X in ddH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O, 5 min per rinse&amp;lt;br&amp;gt; &lt;br /&gt;
#Soak in 100% methanol, 10 min&amp;lt;br&amp;gt; &lt;br /&gt;
#Stain PVDF membrane with 0.1% Coomassie R-250 in 40% methanol for no longer than ONE MINUTE usually 15 to 20 seconds will suffice&amp;lt;br&amp;gt; &lt;br /&gt;
#Destain with 40% methanol, change destain as needed&amp;lt;br&amp;gt; &lt;br /&gt;
#Wash 5x ddH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O&amp;lt;br&amp;gt; &lt;br /&gt;
#Dry membrane&amp;lt;br&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= References =&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Antibiotics&amp;diff=166</id>
		<title>Antibiotics</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Antibiotics&amp;diff=166"/>
		<updated>2022-03-01T15:20:17Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: /* Ampicillin */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Protocol ==&lt;br /&gt;
&lt;br /&gt;
==== Ampicillin&amp;lt;br&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Preparation of 5 mL of 100 mg/mL:&lt;br /&gt;
&lt;br /&gt;
#Add 0.5 g of ampicillin into a 12 mL tube.&lt;br /&gt;
#Add 2.5 mL of ddH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O into the tube and mix gently by tapping the side of the tube.&lt;br /&gt;
#Add 2.5 mL of 100% ethanol and mix the tube again.&lt;br /&gt;
#Filter with a 0.22 μm syringe filter&lt;br /&gt;
#Aliquot out 1 mL into each of 5 microcentrifuge tubes.&lt;br /&gt;
#Label the tubes as 1000x ampicillin and write the date.&lt;br /&gt;
#Place tubes in the antibiotics box in the -20 °C freezer.&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Note: Ampicillin stock will only be good for approximately 6 months.&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Kanamycin&amp;lt;br&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Preparation of 5 mL of 50 mg/mL&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
#Add 0.25 g of kanamycin into a 12 mL tube.&amp;lt;br&amp;gt;&lt;br /&gt;
#Add 5 mL ddH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O into the tube and mix by shaking tube.&amp;lt;br&amp;gt;&lt;br /&gt;
#Aliquot out 1 mL into each of 5 microcentrifuge tubes.&amp;lt;br&amp;gt;&lt;br /&gt;
#Label the tubes as 1000x kanamycin and write the date.&amp;lt;br&amp;gt;&lt;br /&gt;
#Place the tubes in the antibiotics box in the -20 °C freezer.&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Note: Kanamycin tubes must be kept in the fridge after being removed from the freezer. &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Agarose_Gels&amp;diff=162</id>
		<title>Agarose Gels</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Agarose_Gels&amp;diff=162"/>
		<updated>2022-02-25T15:15:22Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: /* For a 0.7% gel: */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==== Protocol&amp;lt;br&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
===== For a 0.8% gel: =====&lt;br /&gt;
&lt;br /&gt;
#Set up gel-casting dock. &lt;br /&gt;
#To a 250mL Erlenmeyer flask add 0.24 g of agarose (1 heaping green scoop) and 30 mL of 1X TAE.&lt;br /&gt;
#Microwave (30sec/15sec/15sec) – want the mixture to boil twice and become clear, swirl around.&lt;br /&gt;
#Allow the mixture to cool until you can place your hand on the bottom of the flask, add 3 uL of RedSafe DNA dye.&lt;br /&gt;
#Pour hot mixture into gel-casting dock and place comb. Make sure no bubbles are formed. The gel will cast in about 45 mins at room temp or 15 minutes in the fridge.&lt;br /&gt;
#Remove the comb.&lt;br /&gt;
#When taking out the gel, untighten the knob to release the top and bottom half of the casting dock, but hold them together with your hand. Carefully slide the gel out.&lt;br /&gt;
#Place the gel into the gel-running dock and cover fully with running buffer. The running buffer for a gel: 0.5X TAE =&amp;amp;gt; (5 mL 50X TAE + 500 mL dH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O). Make sure the DNA is running towards the positive end!&lt;br /&gt;
#Add ladder. For the small wells, add 2 μL of ladder; for the large wells, add 8 µL of ladder. The ladder can be found in the ladders box in the -20°C freezer.&lt;br /&gt;
#Add the appropriate amount of 6x loading dye to the samples and then load into separate wells. &lt;br /&gt;
#Run the gel at 100V for 45 minutes (35 minutes for smaller DNA &amp;amp;lt;1 kB)&lt;br /&gt;
#Place the gel on the UV imaging plate and place the plate into the gel imaging doc.&lt;br /&gt;
#Turn the computer on and sign in.&lt;br /&gt;
#Open the program &amp;quot;Image Lab&amp;quot; and press select, then &amp;quot;nucleic acid&amp;quot;, then &amp;quot;ethidium bromide&amp;quot;.&lt;br /&gt;
#Press &amp;quot;run protocol&amp;quot;, alternatively press the green button on the GelDoc once Image Lab is open.&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Agarose_Gels&amp;diff=161</id>
		<title>Agarose Gels</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Agarose_Gels&amp;diff=161"/>
		<updated>2022-02-25T15:07:14Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: Undo revision 160 by Akipp4 (talk)&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==== Protocol&amp;lt;br&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
===== For a 0.7% gel:&amp;lt;br&amp;gt; =====&lt;br /&gt;
&lt;br /&gt;
#Set up gel-casting dock. &lt;br /&gt;
#Add 0.14 g of agarose to a 250mL Erlenmeyer flask. &lt;br /&gt;
#Add 400 µL of 50X TAE and 20 ml of ddH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O (from machine). Microwave (30sec/15sec/15sec) – want the mixture to boil twice and become clear, swirl around. &lt;br /&gt;
#Pour hot mixture into gel-casting dock and place comb. Make sure no bubbles are formed. The gel will cast in 10-15 minutes in the fridge. &lt;br /&gt;
#Remove the comb.&amp;lt;br&amp;gt; &lt;br /&gt;
#When taking out the gel, untighten the knob to release the top and bottom half of the casting dock, but hold them together with your hand. Carefully slide the gel out.&amp;lt;br&amp;gt; &lt;br /&gt;
#Place the gel into the gel-running dock and cover fully with running buffer. The running buffer for a gel: 0.5X TAE =&amp;amp;gt; (5 mL 50X TAE + 500 mL dH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O). Make sure the DNA is running towards the positive end!&amp;lt;br&amp;gt; &lt;br /&gt;
#Add ladder. For the small wells, add 2 μL of ladder; for the large wells, add 8 µL of ladder. The master-mix is located in the blue box in the -20°C freezer.&amp;lt;br&amp;gt; &lt;br /&gt;
#Add the appropriate amount of 6x loading dye to the samples and then load into separate wells. &lt;br /&gt;
#Run the gel at 100V for 45 minutes (35 minutes for smaller DNA &amp;amp;lt;1 kB). &lt;br /&gt;
#Stain the gel with ethidium bromide by adding the gel in the container labelled &amp;quot;Ethidium Bromide&amp;quot; and pour in all of the ethidium bromide from the 5x container. Put the container on the shaker for 5-10 minutes. Pour the ethidium bromide back into the container after use.&amp;lt;br&amp;gt; &lt;br /&gt;
#Rinse the gel twice with tap water and let the gel soak in water for 5-10 minutes. &lt;br /&gt;
#Pour the water out into the sink.&amp;lt;br&amp;gt; &lt;br /&gt;
#Place the gel on the UV imaging plate and place the plate into the gel imaging doc. &lt;br /&gt;
#Turn the computer on and sign in. &lt;br /&gt;
#Open the program &amp;quot;Image Lab&amp;quot; and press select, then &amp;quot;nucleic acid&amp;quot;, then &amp;quot;ethidium bromide&amp;quot;.&amp;lt;br&amp;gt; &lt;br /&gt;
#Press &amp;quot;run protocol&amp;quot;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Agarose_Gels&amp;diff=160</id>
		<title>Agarose Gels</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Agarose_Gels&amp;diff=160"/>
		<updated>2022-02-25T15:05:59Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: /* For a 0.7% gel: */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==== Protocol ====&lt;br /&gt;
'''For a 0.8% gel:'''&lt;br /&gt;
&lt;br /&gt;
1.    Set up gel-casting dock.&lt;br /&gt;
&lt;br /&gt;
2.    To a 250mL Erlenmeyer flask add 0.24 g of agarose (1 heaping green scoop) and 30 mL of 1X TAE&lt;br /&gt;
&lt;br /&gt;
3.    Microwave (30sec/15sec/15sec) – want the mixture to boil twice and become clear, swirl around.&lt;br /&gt;
&lt;br /&gt;
4.    Allow the mixture to cool until you can place your hand on the bottom of the flask, add 3 uL of RedSafe DNA dye&lt;br /&gt;
&lt;br /&gt;
5.    Pour hot mixture into gel-casting dock and place comb. Make sure no bubbles are formed. The gel will cast in about 45 mins at room temp or 15 minutes in the fridge.&lt;br /&gt;
&lt;br /&gt;
6.    Remove the comb.&lt;br /&gt;
&lt;br /&gt;
7.    When taking out the gel, untighten the knob to release the top and bottom half of the casting dock, but hold them together with your hand. Carefully slide the gel out.&lt;br /&gt;
&lt;br /&gt;
8.    Place the gel into the gel-running dock and cover fully with running buffer. The running buffer for a gel: 0.5X TAE =&amp;gt; (10 mL 50X TAE + 990 mL dH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O). Make sure the DNA is running towards the positive end!&lt;br /&gt;
&lt;br /&gt;
9.    Add ladder. For the small wells, add 2 μL of ladder; for the large wells, add 6 µL of ladder. The ladder can be found in the ladders box in the -20°C freezer.&lt;br /&gt;
&lt;br /&gt;
10. Add the appropriate amount of 6x loading dye to the samples and then load into separate wells.&lt;br /&gt;
&lt;br /&gt;
11. Run the gel at 100V for 45 minutes (35 minutes for smaller DNA &amp;lt;1 kB).&lt;br /&gt;
&lt;br /&gt;
12. Place the gel on the UV imaging plate and place the plate into the gel imaging doc.&lt;br /&gt;
&lt;br /&gt;
13. Turn the computer on and sign in.&lt;br /&gt;
&lt;br /&gt;
14. Open the program &amp;quot;Image Lab&amp;quot; and press select, then &amp;quot;nucleic acid&amp;quot;, then &amp;quot;ethidium bromide&amp;quot;.&lt;br /&gt;
&lt;br /&gt;
15. Press &amp;quot;run protocol&amp;quot;, alternatively press the green button on the GelDoc after opening Image Lab.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=159</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=159"/>
		<updated>2022-02-25T15:04:40Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[Digests]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
|&lt;br /&gt;
|'''Transfections and Transductions'''&lt;br /&gt;
* [[J774 Cell Transfection]]&lt;br /&gt;
* [[Raw Cell Transfection]]&lt;br /&gt;
* [[Neon® Transfection System]]&lt;br /&gt;
* [[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
*[[Transduction of THP-1s]]&lt;br /&gt;
*[[Nucleofector]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Primary Macrophage Culture|Primary Murine Macrophages]]&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
&lt;br /&gt;
'''Bead Preparation'''&lt;br /&gt;
&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
*[[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|'''Bacteria Work'''&lt;br /&gt;
&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
|&lt;br /&gt;
==== Protein Work ====&lt;br /&gt;
*[[Bradford Assay]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
|&lt;br /&gt;
|'''Microscopy'''&lt;br /&gt;
*[[3D Printed PDMS Chambers]]&lt;br /&gt;
*[[Acid Washing Coverslips]]&lt;br /&gt;
*[[Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Immunostaining|Fluorescent Immunostaining]]&lt;br /&gt;
*[[FRET in FIJI]]&lt;br /&gt;
*[[Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Immuno-FISH]]&lt;br /&gt;
*[[Live Cell FRET]] [[Nucleofector|(depreciated)]]&lt;br /&gt;
*[[Reducing Photobleaching]]&lt;br /&gt;
*[[Single Particle Tracking]]&lt;br /&gt;
*[[Staining for GSD]]&lt;br /&gt;
*[[Traction Force Microscopy]]&lt;br /&gt;
&lt;br /&gt;
*&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====General Protocol Sites====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols&lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols&lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols&lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols&lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses.&lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat&lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols&lt;br /&gt;
|&lt;br /&gt;
====Free Science Ebooks====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
=Useful Links=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Molecular Biology Databases====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
=====Microscopy Tools===== &lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Journal Resources====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
====''In Vivo'' Tools====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
====Protease Tools====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Genomics Resources====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
====Chemical Tools====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
====Lipid Tools====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=158</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=158"/>
		<updated>2022-02-23T20:25:04Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[Digests]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
|&lt;br /&gt;
|'''Transfections and Transductions'''&lt;br /&gt;
* [[J774 Cell Transfection]]&lt;br /&gt;
* [[Raw Cell Transfection]]&lt;br /&gt;
* [[Neon® Transfection System]]&lt;br /&gt;
* [[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
*[[Transduction of THP-1s]]&lt;br /&gt;
*[[Nucleofector]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Primary Macrophage Culture|Primary Murine Macrophages]]&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
&lt;br /&gt;
'''Bead Preparation'''&lt;br /&gt;
&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
*[[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|'''Bacteria Work'''&lt;br /&gt;
&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
|&lt;br /&gt;
==== Protein Work ====&lt;br /&gt;
*[[Bradford Assay]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
|&lt;br /&gt;
|'''Microscopy'''&lt;br /&gt;
*[[3D Printed PDMS Chambers]]&lt;br /&gt;
*[[Acid Washing Coverslips]]&lt;br /&gt;
*[[Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Immunostaining|Fluorescent Immunostaining]]&lt;br /&gt;
*[[FRET in FIJI]]&lt;br /&gt;
*[[Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Immuno-FISH]]&lt;br /&gt;
*[[Live Cell FRET]] [[Nucleofector|(depreciated)]]&lt;br /&gt;
*[[Reducing Photobleaching]]&lt;br /&gt;
*[[Single Particle Tracking]]&lt;br /&gt;
*[[Staining for GSD]]&lt;br /&gt;
*[[Traction Force Microscopy]]&lt;br /&gt;
&lt;br /&gt;
*&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====General Protocol Sites====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols&lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols&lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols&lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols&lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses.&lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat&lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols&lt;br /&gt;
|&lt;br /&gt;
====Free Science Ebooks====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
=Useful Links=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Molecular Biology Databases====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
=====Microscopy Tools===== &lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Journal Resources====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
====''In Vivo'' Tools====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
====Protease Tools====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Genomics Resources====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
====Chemical Tools====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
====Lipid Tools====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=157</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=157"/>
		<updated>2022-02-23T20:16:00Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: /* Index of Protocols */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[Digests]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
|&lt;br /&gt;
|'''Transfections and Transductions'''&lt;br /&gt;
* [[J774 Cell Transfection]]&lt;br /&gt;
* [[Raw Cell Transfection]]&lt;br /&gt;
* [[Neon® Transfection System]]&lt;br /&gt;
* [[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
*[[Transduction of THP-1s]]&lt;br /&gt;
*[[Nucleofector]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Primary Macrophage Culture|Primary Murine Macrophages]]&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
&lt;br /&gt;
'''Bead Preparation'''&lt;br /&gt;
&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
*[[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|'''Bacteria Work'''&lt;br /&gt;
&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
|&lt;br /&gt;
==== Protein Work ====&lt;br /&gt;
*[[Bradford Assay]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
|&lt;br /&gt;
|'''Microscopy'''&lt;br /&gt;
*[[Nucleofector|3D Printed PDMS Chambers]]&lt;br /&gt;
*[[Nucleofector|Acid Washing Coverslips]]&lt;br /&gt;
*[[Nucleofector|Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Nucleofector|Fluorescent Immunostaining]]&lt;br /&gt;
*[[Nucleofector|FRET in FIJI]]&lt;br /&gt;
*[[Nucleofector|Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Nucleofector|Immuno-FISH]]&lt;br /&gt;
*[[Nucleofector|Live Cell FRET]] [[Nucleofector|(depreciated)]]&lt;br /&gt;
*[[Nucleofector|Reducing Photobleaching]]&lt;br /&gt;
*[[Nucleofector|Single Particle Tracking]]&lt;br /&gt;
*[[Nucleofector|Staining for GSD]]&lt;br /&gt;
*[[Nucleofector|Traction Force Microscopy]]&lt;br /&gt;
&lt;br /&gt;
*&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====General Protocol Sites====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols&lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols&lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols&lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols&lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses.&lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat&lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols&lt;br /&gt;
|&lt;br /&gt;
====Free Science Ebooks====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
=Useful Links=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Molecular Biology Databases====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
=====Microscopy Tools===== &lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Journal Resources====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
====''In Vivo'' Tools====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
====Protease Tools====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Genomics Resources====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
====Chemical Tools====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
====Lipid Tools====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=156</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=156"/>
		<updated>2022-02-23T20:15:06Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: /* Index of Protocols */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[Digests]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
|&lt;br /&gt;
|'''Transfections and Transductions'''&lt;br /&gt;
* [[J774 Cell Transfection]]&lt;br /&gt;
* [[Raw Cell Transfection]]&lt;br /&gt;
* [[Neon® Transfection System]]&lt;br /&gt;
* [[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
*[[Transduction of THP-1s]]&lt;br /&gt;
*[[Nucleofector]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Primary Macrophage Culture|Primary Murine Macrophages]]&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
&lt;br /&gt;
'''Bead Preparation'''&lt;br /&gt;
&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
*[[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|'''Bacteria Work'''&lt;br /&gt;
&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
==== Protein Work ====&lt;br /&gt;
*[[Bradford Assay]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
|&lt;br /&gt;
|'''Microscopy'''&lt;br /&gt;
*[[Nucleofector|3D Printed PDMS Chambers]]&lt;br /&gt;
*[[Nucleofector|Acid Washing Coverslips]]&lt;br /&gt;
*[[Nucleofector|Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Nucleofector|Fluorescent Immunostaining]]&lt;br /&gt;
*[[Nucleofector|FRET in FIJI]]&lt;br /&gt;
*[[Nucleofector|Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Nucleofector|Immuno-FISH]]&lt;br /&gt;
*[[Nucleofector|Live Cell FRET]] [[Nucleofector|(depreciated)]]&lt;br /&gt;
*[[Nucleofector|Reducing Photobleaching]]&lt;br /&gt;
*[[Nucleofector|Single Particle Tracking]]&lt;br /&gt;
*[[Nucleofector|Staining for GSD]]&lt;br /&gt;
*[[Nucleofector|Traction Force Microscopy]]&lt;br /&gt;
&lt;br /&gt;
*&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====General Protocol Sites====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols&lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols&lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols&lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols&lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses.&lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat&lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols&lt;br /&gt;
|&lt;br /&gt;
====Free Science Ebooks====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
=Useful Links=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Molecular Biology Databases====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
=====Microscopy Tools===== &lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Journal Resources====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
====''In Vivo'' Tools====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
====Protease Tools====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Genomics Resources====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
====Chemical Tools====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
====Lipid Tools====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=155</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=155"/>
		<updated>2022-02-23T20:14:18Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: /* Index of Protocols */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[Digests]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
|'''Transfections and Transductions'''&lt;br /&gt;
* [[J774 Cell Transfection]]&lt;br /&gt;
* [[Raw Cell Transfection]]&lt;br /&gt;
* [[Neon® Transfection System]]&lt;br /&gt;
* [[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
*[[Transduction of THP-1s]]&lt;br /&gt;
*[[Nucleofector]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Primary Macrophage Culture|Primary Murine Macrophages]]&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
&lt;br /&gt;
'''Bead Preparation'''&lt;br /&gt;
&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
*[[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|'''Bacteria Work'''&lt;br /&gt;
&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
|&lt;br /&gt;
==== Protein Work ====&lt;br /&gt;
*[[Bradford Assay]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
|'''Microscopy'''&lt;br /&gt;
*[[Nucleofector|3D Printed PDMS Chambers]]&lt;br /&gt;
*[[Nucleofector|Acid Washing Coverslips]]&lt;br /&gt;
*[[Nucleofector|Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Nucleofector|Fluorescent Immunostaining]]&lt;br /&gt;
*[[Nucleofector|FRET in FIJI]]&lt;br /&gt;
*[[Nucleofector|Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Nucleofector|Immuno-FISH]]&lt;br /&gt;
*[[Nucleofector|Live Cell FRET]] [[Nucleofector|(depreciated)]]&lt;br /&gt;
*[[Nucleofector|Reducing Photobleaching]]&lt;br /&gt;
*[[Nucleofector|Single Particle Tracking]]&lt;br /&gt;
*[[Nucleofector|Staining for GSD]]&lt;br /&gt;
*[[Nucleofector|Traction Force Microscopy]]&lt;br /&gt;
&lt;br /&gt;
*&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====General Protocol Sites====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols&lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols&lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols&lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols&lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses.&lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat&lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols&lt;br /&gt;
|&lt;br /&gt;
====Free Science Ebooks====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
=Useful Links=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Molecular Biology Databases====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
=====Microscopy Tools===== &lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Journal Resources====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
====''In Vivo'' Tools====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
====Protease Tools====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Genomics Resources====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
====Chemical Tools====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
====Lipid Tools====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=154</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=154"/>
		<updated>2022-02-23T20:12:06Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: /* Index of Protocols */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[Digests]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
|'''Transfections and Transductions'''&lt;br /&gt;
* [[J774 Cell Transfection]]&lt;br /&gt;
* [[Raw Cell Transfection]]&lt;br /&gt;
* [[Neon® Transfection System]]&lt;br /&gt;
* [[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
*[[Transduction of THP-1s]]&lt;br /&gt;
*[[Nucleofector]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
|&lt;br /&gt;
==== Protein work ====&lt;br /&gt;
*[[Bradford Assay]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Bead Preparation'''&lt;br /&gt;
&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
*[[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|'''Bacteria Work'''&lt;br /&gt;
&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Primary Macrophage Culture|Primary Murine Macrophages]]&lt;br /&gt;
|'''Microscopy'''&lt;br /&gt;
*[[Nucleofector|3D Printed PDMS Chambers]]&lt;br /&gt;
*[[Nucleofector|Acid Washing Coverslips]]&lt;br /&gt;
*[[Nucleofector|Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Nucleofector|Fluorescent Immunostaining]]&lt;br /&gt;
*[[Nucleofector|FRET in FIJI]]&lt;br /&gt;
*[[Nucleofector|Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Nucleofector|Immuno-FISH]]&lt;br /&gt;
*[[Nucleofector|Live Cell FRET]] [[Nucleofector|(depreciated)]]&lt;br /&gt;
*[[Nucleofector|Reducing Photobleaching]]&lt;br /&gt;
*[[Nucleofector|Single Particle Tracking]]&lt;br /&gt;
*[[Nucleofector|Staining for GSD]]&lt;br /&gt;
*[[Nucleofector|Traction Force Microscopy]]&lt;br /&gt;
&lt;br /&gt;
*&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====General Protocol Sites====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols&lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols&lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols&lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols&lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses.&lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat&lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols&lt;br /&gt;
|&lt;br /&gt;
====Free Science Ebooks====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
=Useful Links=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Molecular Biology Databases====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
=====Microscopy Tools===== &lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Journal Resources====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
====''In Vivo'' Tools====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
====Protease Tools====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Genomics Resources====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
====Chemical Tools====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
====Lipid Tools====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=153</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=153"/>
		<updated>2022-02-23T20:10:41Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[Digests]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
|'''Transfections and Transductions'''&lt;br /&gt;
* [[J774 Cell Transfection]]&lt;br /&gt;
* [[Raw Cell Transfection]]&lt;br /&gt;
* [[Neon® Transfection System]]&lt;br /&gt;
* [[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
*[[Transduction of THP-1s]]&lt;br /&gt;
*[[Nucleofector]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
|&lt;br /&gt;
==== Protein work ====&lt;br /&gt;
*[[Bradford Assay]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Bead Preparation'''&lt;br /&gt;
&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
*[[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|'''Bacteria Work'''&lt;br /&gt;
&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Primary Macrophage Culture|Primary Murine Macrophages]]&lt;br /&gt;
|[[Nucleofector|Microscopy]]&lt;br /&gt;
*[[Nucleofector|3D Printed PDMS Chambers]]&lt;br /&gt;
*[[Nucleofector|Acid Washing Coverslips]]&lt;br /&gt;
*[[Nucleofector|Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Nucleofector|Fluorescent Immunostaining]]&lt;br /&gt;
*[[Nucleofector|FRET in FIJI]]&lt;br /&gt;
*[[Nucleofector|Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Nucleofector|Immuno-FISH]]&lt;br /&gt;
*[[Nucleofector|Live Cell FRET]] [[Nucleofector|(depreciated)]]&lt;br /&gt;
*[[Nucleofector|Reducing Photobleaching]]&lt;br /&gt;
*[[Nucleofector|Single Particle Tracking]]&lt;br /&gt;
*[[Nucleofector|Staining for GSD]]&lt;br /&gt;
*[[Nucleofector|Traction Force Microscopy]]&lt;br /&gt;
&lt;br /&gt;
*&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====General Protocol Sites====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols&lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols&lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols&lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols&lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses.&lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat&lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols&lt;br /&gt;
|&lt;br /&gt;
====Free Science Ebooks====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
=Useful Links=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Molecular Biology Databases====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
=====Microscopy Tools===== &lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Journal Resources====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
====''In Vivo'' Tools====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
====Protease Tools====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Genomics Resources====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
====Chemical Tools====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
====Lipid Tools====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Bradford_Assay&amp;diff=149</id>
		<title>Bradford Assay</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Bradford_Assay&amp;diff=149"/>
		<updated>2022-01-18T19:29:04Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''Introduction'''&lt;br /&gt;
&lt;br /&gt;
The Bradford assay should be used to quantify total protein within a sample relative to a standard curve. This is important when running proteins on SDS-PAGE/Western blot, where each lane must contain an identical amount of total protein. This way, the intensity of the bands can be compared between different lanes, as standardizing the amount of protein loaded per lane will account for any variation in cell count from which the proteins were derived. &lt;br /&gt;
'''Protocol'''&lt;br /&gt;
&lt;br /&gt;
'''Protocol'''&lt;br /&gt;
&lt;br /&gt;
''Some things to know'':&lt;br /&gt;
&lt;br /&gt;
* This protocol assumes the use of bovine serum albumin (BSA) for the standard curve, which has a linear range of 200 μg/mL to 1000 μg/mL within Bio-Rad's protein assay dye. &lt;br /&gt;
* If your protein is within a supernatant containing an acid indicator, such as phenol red, this may interfere with the assay. If your protein is within a solution containing phenol red, then ensure that all samples, standards, and blanks are diluted with that media (e.g. Serum free DMEM).&lt;br /&gt;
* Each tube will have extra volume to ensure you have enough for the last replicate and to avoid air bubbles.&lt;br /&gt;
* Reverse pipetting technique is highly recommended to avoid air bubbles and to ensure accuracy. &lt;br /&gt;
''For a 96 well plate''&lt;br /&gt;
&lt;br /&gt;
# Using a 0.2 μm filter and 15 mL syringe, filter approximately 4 mL of Bio-Rad Protein Assay Dye Reagent Concentrate (Bradford Dye) into a 5 mL Eppendorf tube or 15 mL falcon tube. Let it warm to room temperature. &lt;br /&gt;
# Collect lysate or supernatant from the cells. Keep on ice.&lt;br /&gt;
# In separate 1.5 mL tubes, dilute the sample using ddH2O (or whatever buffer/media is appropriate) into 1:2 and 1:10 dilutions into a total of 600 μL. ('''NOTE:''' Do not use the 1:2 diluted sample to prepare the 1:10 tube. Use the original, undiluted sample to prepare the 1:10 dilution)&lt;br /&gt;
# Prepare a 1 mg/mL stock solution of BSA by dissolving BSA in ddH2O. Prepare a dilution series using ddH2O (or whatever buffer/media is appropriate) in 1.5 mL tubes: 1 mg/mL, 0.8 mg/mL, 0.6 mg/mL, 0.4 mg/mL, and 0.2 mg/mL.&lt;br /&gt;
# See '''Figure 1''' for a general plate setup. Using the reverse pipetting technique, pipet 160 μL of blank, standard, and samples into each appropriate well. Avoid creating air bubbles.&lt;br /&gt;
# Spin down the plate at 300 rpm for 1 min to remove bubbles and any liquid on the side of the well.&lt;br /&gt;
# Pour 4 mL of filtered Bradford Dye into a multichannel pipette reservoir. Using a multichannel pipette, pipet 40 μL of dye into each well. If a multichannel pipette is not available, '''''quickly''''' pipet 40 μL of dye into each well using a P200 pipette. &lt;br /&gt;
# Incubate for at least 5 minutes at room temperature. Do not exceed 1 hr. &lt;br /&gt;
# Take off the lid of the plate, and place it into a plate reader/spectrometer.&lt;br /&gt;
# Measure absorbance at 595 nm.&lt;br /&gt;
[[File:Bradford plate layout.png|thumb|'''Figure 1.''' General plate layout |border|center]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
''Analysis using the standard curve''&lt;br /&gt;
&lt;br /&gt;
# Export results from spectrometer to Excel.&lt;br /&gt;
# Subtract the average absorbance of each well by the average absorbance of the blank.&lt;br /&gt;
# Plot the known standard concentrations (X-axis; 0.2, 0.4, 0.6, 0.8, and 1.0 mg/mL) with the average absorbance at each concentration (Y-axis). '''Add a line of best fit and display the equation with R&amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt; value.''' Ideally, the R&amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt; value should be ≥ 0.99. R&amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt; &amp;lt; 0.94 curves should not be used. &lt;br /&gt;
# Calculate the average absorbance for the samples of interest by using the equation of the line graph y = mx+b (Absorbance = Slope*Concentration + b) and solve for x.&lt;br /&gt;
# If the calculated concentration falls within the linear range of the standard curve (0.2 - 1.0 mg/mL), then it is accurate. If necessary, determine the concentration of the undiluted sample by multiplying by the dilution factor. &lt;br /&gt;
&lt;br /&gt;
# &lt;br /&gt;
&lt;br /&gt;
#&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=146</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=146"/>
		<updated>2022-01-18T14:32:43Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[Digests]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
|&lt;br /&gt;
==== Microscopy ====&lt;br /&gt;
*[[3D Printed PDMS Chambers]]&lt;br /&gt;
*[[Acid Washing Coverslips]]&lt;br /&gt;
*[[Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Immunostaining|Fluorescent Immunostaining]]&lt;br /&gt;
*[[FRET in FIJI]]&lt;br /&gt;
*[[Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Immuno-FISH]]&lt;br /&gt;
*[[Live Cell FRET]] (depreciated)&lt;br /&gt;
*[[Reducing Photobleaching]]&lt;br /&gt;
*[[Single Particle Tracking]]&lt;br /&gt;
*[[Staining for GSD]]&lt;br /&gt;
*[[Traction Force Microscopy]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
|&lt;br /&gt;
==== Protein work ====&lt;br /&gt;
*[[Bradford Assay]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Bead Preparation'''&lt;br /&gt;
&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
*[[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|'''Bacteria Work'''&lt;br /&gt;
&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Primary Macrophage Culture|Primary Murine Macrophages]]&lt;br /&gt;
|'''Transfections and Transductions'''&lt;br /&gt;
* [[J774 Cell Transfection]]&lt;br /&gt;
* [[Raw Cell Transfection]]&lt;br /&gt;
* [[Neon® Transfection System]]&lt;br /&gt;
* [[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
*[[Transduction of THP-1s]]&lt;br /&gt;
&lt;br /&gt;
*&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====General Protocol Sites====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols&lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols&lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols&lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols&lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses.&lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat&lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols&lt;br /&gt;
|&lt;br /&gt;
====Free Science Ebooks====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
=Useful Links=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Molecular Biology Databases====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
=====Microscopy Tools===== &lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Journal Resources====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
====''In Vivo'' Tools====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
====Protease Tools====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Genomics Resources====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
====Chemical Tools====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
====Lipid Tools====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=145</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=145"/>
		<updated>2022-01-18T14:30:37Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[Digests]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
|&lt;br /&gt;
==== Microscopy ====&lt;br /&gt;
*[[3D Printed PDMS Chambers]]&lt;br /&gt;
*[[Acid Washing Coverslips]]&lt;br /&gt;
*[[Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Immunostaining|Fluorescent Immunostaining]]&lt;br /&gt;
*[[FRET in FIJI]]&lt;br /&gt;
*[[Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Immuno-FISH]]&lt;br /&gt;
*[[Live Cell FRET]] (depreciated)&lt;br /&gt;
*[[Reducing Photobleaching]]&lt;br /&gt;
*[[Single Particle Tracking]]&lt;br /&gt;
*[[Staining for GSD]]&lt;br /&gt;
*[[Traction Force Microscopy]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
|&lt;br /&gt;
==== Protein work ====&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
*[[Bradford Assay]]&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Bead Preparation'''&lt;br /&gt;
&lt;br /&gt;
* [[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|'''Bacteria Work'''&lt;br /&gt;
&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Primary Macrophage Culture|Primary Murine Macrophages]]&lt;br /&gt;
|'''Transfections and Transductions'''&lt;br /&gt;
* [[J774 Cell Transfection]]&lt;br /&gt;
* [[Raw Cell Transfection]]&lt;br /&gt;
* [[Neon® Transfection System]]&lt;br /&gt;
* [[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
*[[Transduction of THP-1s]]&lt;br /&gt;
&lt;br /&gt;
*&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====General Protocol Sites====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols&lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols&lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols&lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols&lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses.&lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat&lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols&lt;br /&gt;
|&lt;br /&gt;
====Free Science Ebooks====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
=Useful Links=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Molecular Biology Databases====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
=====Microscopy Tools===== &lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Journal Resources====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
====''In Vivo'' Tools====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
====Protease Tools====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Genomics Resources====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
====Chemical Tools====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
====Lipid Tools====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Entrance_Protocol&amp;diff=144</id>
		<title>Entrance Protocol</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Entrance_Protocol&amp;diff=144"/>
		<updated>2022-01-17T17:37:26Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Beginning in a new lab can be an overwhelming experience.&amp;amp;nbsp; This guide is intended to aid new members in starting up as quickly as possible.&lt;br /&gt;
&lt;br /&gt;
= Accounts &amp;amp;amp; Certification =&lt;br /&gt;
&lt;br /&gt;
#Incoming personnel must be registered with UWO as either staff or students.&amp;amp;nbsp; Ensure that you are registered, and have received a UWO ID card. &lt;br /&gt;
#Keys are only available for technicians, graduate students and postdocs.&amp;amp;nbsp; Please see Dr. Heit about receiving keys. &lt;br /&gt;
#You will have (at least) two computer accounts at UWO: &lt;br /&gt;
#*Your UWO/Schulich IT account.&amp;amp;nbsp; This gives you access to UWO e-mail and other network services.&amp;amp;nbsp; This account should have been setup for you as part of your registration process.&amp;amp;nbsp; If not, contact [http://www.uwo.ca/its/ UWO ITS]. &lt;br /&gt;
#*Your in-lab account.&amp;amp;nbsp; This will give you access to the servers and workstations within the Heit lab.&amp;amp;nbsp; See Dr. Heit for setting up this account   &lt;br /&gt;
#All staff using any laboratory on campus must complete the required safety courses.&amp;amp;nbsp; The exact courses which an individual must complete will depend partially on their project.&amp;amp;nbsp; Detailed requirements can be found at [http://www.uwo.ca/humanresources/facultystaff/h_and_s/h_and_s_index.htm UWO health and Safety].&amp;amp;nbsp; At a &amp;lt;u&amp;gt;minimum&amp;lt;/u&amp;gt;, all Heit lab members will need: &lt;br /&gt;
#*WHIMIS &lt;br /&gt;
#*Biosafety &lt;br /&gt;
#*Chemical Safety &lt;br /&gt;
#*Most will need laser safety as well   &lt;br /&gt;
#International students/postdocs coming from non-English speaking nations may want to consider taking an English as a Second Language course.&amp;amp;nbsp; The Student Development Centre has [http://www.sdc.uwo.ca/int/index.html?link_esl information on these programs].&amp;lt;br&amp;gt; &lt;br /&gt;
#All members of the lab must keep a laboratory notebook.&amp;amp;nbsp; Please read and follow the [[Labbook|lab notebook guidelines]]. &lt;br /&gt;
&lt;br /&gt;
= Laboratory Policies =&lt;br /&gt;
&lt;br /&gt;
===== Ethics =====&lt;br /&gt;
&lt;br /&gt;
Our laboratory follows several ethical guidelines.&amp;amp;nbsp; Laboratory members should be familiar with, and follow, these guidelines:&lt;br /&gt;
&lt;br /&gt;
*UWO's research ethics policies, as outlined at UWO's Office for [http://www.uwo.ca/research/ethics/index.html Research Ethics webpage] &lt;br /&gt;
*UWO's policies on [http://www.uwo.ca/univsec/handbook/appeals/scholastic_discipline_grad.pdf scholastic discpline] (PDF) &lt;br /&gt;
*The ethics standards set by the [http://www.hc-sc.gc.ca/sr-sr/advice-avis/reb-cer/index-eng.php Canadian Institutes of Health Research]&amp;lt;br&amp;gt; &lt;br /&gt;
&lt;br /&gt;
===== Attendance &amp;amp;amp; Vacation&amp;lt;br&amp;gt; =====&lt;br /&gt;
&lt;br /&gt;
''Attendance:''&lt;br /&gt;
&lt;br /&gt;
*No formal system of timecards is currently implemented.&amp;amp;nbsp; &lt;br /&gt;
*It is expected that graduate students and post-doctoral fellows work full-time (40 hours/week).&amp;amp;nbsp; To be successful, most graduate and post-graduate projects may require a greater time investment than this. &lt;br /&gt;
**No specific work-hours are assigned, so long as sufficient hours are being worked. However, students and post-docs must ensure that they are attending all mandatory meetings, journal clubs, seminars and training sessions. &lt;br /&gt;
**If necessary, mandated work-hours will be assigned on a case-by-case basis.   &lt;br /&gt;
*Employees (technicians, research associates) and term employees (work-study, paid summer students) are expected to work the hours assigned in their contract, and to work during regular business hours (unless other arrangements have been made) &lt;br /&gt;
**Undergraduates must work during regular business hours, or at the time outlined by their supervisor, as they do not have access to the lab when others are not present. &lt;br /&gt;
**Undergraduate students in honours programs are expected to attend the lab for at least 6 hours per week during the fall and winter semester&amp;lt;br&amp;gt;   &lt;br /&gt;
&lt;br /&gt;
''Vacation''&lt;br /&gt;
&lt;br /&gt;
*Dr. Heit must be made aware of planned vacations at least one week in advance&lt;br /&gt;
*For most employees, graduate students and post-doctoral fellows, vacation time is set in the employment contract &lt;br /&gt;
*Additional time may be awarded based on merit or need&lt;br /&gt;
*Unless previous arrangements have been made, undergraduates are not awarded vacation aside from statutory holidays, reading week, and the inter-semester break&amp;lt;br&amp;gt; &lt;br /&gt;
&lt;br /&gt;
===== Laboratory Jobs&amp;lt;br&amp;gt; =====&lt;br /&gt;
&lt;br /&gt;
A variety of lab equipment needs frequent maintenance and consumables need restocking to ensure proper functioning of the lab.&amp;amp;nbsp; All laboratory members are required to aid in this process.&amp;amp;nbsp; Lab jobs will be assigned on an ad-hoc basis.&amp;amp;nbsp; These jobs include, but are not limited to:&lt;br /&gt;
&lt;br /&gt;
*Refilling &amp;amp;amp; autoclaving tip boxes &lt;br /&gt;
*Refilling tissue culture supplies &lt;br /&gt;
*Preparation of heat-inactivated FBS &lt;br /&gt;
*Cleaning of vacuum traps &lt;br /&gt;
*Dishes &lt;br /&gt;
*Autoclave bags &lt;br /&gt;
*Chemical disposal &lt;br /&gt;
*Cleaning/organisation of lab benches and bays &lt;br /&gt;
&lt;br /&gt;
===== Lab Meetings =====&lt;br /&gt;
&lt;br /&gt;
Lab meetings are critical to the proper and successful operation of any lab.&amp;amp;nbsp; These allow for issues to be addressed, progress to be monitored, and offer a formalised opportunity for others to provide input to help advance your project.&amp;amp;nbsp; With the exception of undergraduate students, all lab members are required to attend:&lt;br /&gt;
&lt;br /&gt;
*A weekly one-on-one meeting with Dr. Heit.&amp;amp;nbsp; To this meeting bring: &lt;br /&gt;
&lt;br /&gt;
#&lt;br /&gt;
#*Your lab notebook &lt;br /&gt;
#*Results from the past week &lt;br /&gt;
#*Any issues or difficulties you wish to discuss   &lt;br /&gt;
&lt;br /&gt;
*Lab meetings as they are scheduled &lt;br /&gt;
&lt;br /&gt;
#&lt;br /&gt;
#*One or two individuals will present their project at each lab meeting &lt;br /&gt;
#*Time will be allocated at the beginning of the meeting to discuss expenses, conferences, lab issues, etc.   &lt;br /&gt;
&lt;br /&gt;
===== Common Area (office space) =====&lt;br /&gt;
&lt;br /&gt;
Office space is available in the office attached to the lab.&amp;amp;nbsp; Whenever possible, individuals will have an assigned space in this office.&amp;amp;nbsp; Because this space is shared it is important that the following guidelines be followed:&lt;br /&gt;
&lt;br /&gt;
*Please keep it quiet if people are working in the office &lt;br /&gt;
*Remove all food scraps &lt;br /&gt;
*Empty the trash &amp;amp;amp; recycling when full &lt;br /&gt;
*Keep the door closed when unoccupied &lt;br /&gt;
*Never take any laboratory supplies, chemicals or biohazards into the office &lt;br /&gt;
*Personal protective equipment like lab coats must never be worn in the office &lt;br /&gt;
*'''The server rack must never be moved, altered or disconnected.&amp;amp;nbsp; DO NOT&amp;amp;nbsp;STORE''' '''ITEMS ON&amp;amp;nbsp;THE RACK''' &lt;br /&gt;
&lt;br /&gt;
===== Evaluations =====&lt;br /&gt;
&lt;br /&gt;
Graduate and undergraduate students may have department or university mandated evaluations as part of their training program.&amp;amp;nbsp; Aside from these formalized evaluations, the following evaluations should be expected:&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
''Undergraduate students (honours, volunteers and work-study):''&lt;br /&gt;
&lt;br /&gt;
*A weekly or monthly meeting where you progress is reviewed.&amp;amp;nbsp; Note: this meeting may be held jointy with your supervising graduate student/post-doc. &lt;br /&gt;
*If class schedules permit, attendance at lab meetings is required &lt;br /&gt;
&lt;br /&gt;
''Graduate Students, Post-Doctoral Fellows and Staff'':&lt;br /&gt;
&lt;br /&gt;
*Weekly one-on-one meeting with Dr. Heit to review progress &lt;br /&gt;
*Attendance at all lab meetings is required &lt;br /&gt;
*Annual formal review (this can be held more often, if required)&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Exit_Protocol&amp;diff=143</id>
		<title>Exit Protocol</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Exit_Protocol&amp;diff=143"/>
		<updated>2022-01-17T17:32:48Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;It is critical that members leaving the lab properly archive all materials so that they can be found and used by others.&amp;amp;nbsp; This is critical to the success of both yourself and the lab - misplaced data, constructs and cell lines can both slow research in the lab and lead to a loss of authorship.&amp;amp;nbsp; To ensure a smooth transition please follow these guidelines:&lt;br /&gt;
&lt;br /&gt;
#Ensure all data, manuscripts, figures, analysis files and any other computer documents that may be of use to the lab are copied into your folder on the lab server.&amp;amp;nbsp; All of these files should be stored here already (as per the [[ExpFile|File Storage]] standards), but make sure that all files on the server are present and up-to-date.&lt;br /&gt;
#Move all relevant contents of 4, -20 and -80° boxes and move any samples into centralized lab boxes. Inform Dr. Heit or the Research Technician of the location of these items. If you are unsure of where to store items for long term, ask the Research Technician. Do not leave any personal storage boxes in these locations.&lt;br /&gt;
#Ensure all [[Labbook|laboratory notebook]] entries are up-to-date and dated, the contents filled out properly, and all attached documents secured with archival-quality tape or staples.&lt;br /&gt;
#Deposit laboratory notebook with Dr. Heit.&amp;amp;nbsp; Feel free to make a copy for yourself.&amp;amp;nbsp; ORIGINAL COPIES OF THE LABORATORY NOTEBOOKS ARE LAB PROPERTY AND MUST NEVER BE REMOVED FROM THE LAB.&lt;br /&gt;
#Return any personal protective equipment (PPE) or other laboratory equipment purchased by the lab to the lab's central store&lt;br /&gt;
#Contact the necessary UWO offices to terminate your ID card, any grants/fellowships/studentships, and other university accounts.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Important note:''' not uncommon for data to be published years after the lab member who generated the data has left the lab.&amp;amp;nbsp; Please update your contact information with Dr. Heit for at least 5 years after leaving the lab to ensure you receive credit (i.e. authorship) for any articles produced from your data.&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=142</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=142"/>
		<updated>2022-01-17T16:26:55Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[Digests]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
|&lt;br /&gt;
==== Microscopy ====&lt;br /&gt;
*[[Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Immunostaining|Fluorescent Immunostaining]]&lt;br /&gt;
*[[Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Immuno-FISH]]&lt;br /&gt;
*[[Single Particle Tracking]]&lt;br /&gt;
*[[Staining for GSD]]&lt;br /&gt;
*[[Reducing Photobleaching]]&lt;br /&gt;
*[[Acid Washing Coverslips]]&lt;br /&gt;
*[[Live Cell FRET]] (depreciated)&lt;br /&gt;
*[[3D Printed PDMS Chambers]]&lt;br /&gt;
*[[FRET in FIJI]]&lt;br /&gt;
*[[Traction Force Microscopy]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
|&lt;br /&gt;
==== Protein work ====&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
*[[Bradford Assay]]&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Bead Preparation'''&lt;br /&gt;
&lt;br /&gt;
* [[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|'''Bacteria Work'''&lt;br /&gt;
&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Primary Macrophage Culture|Primary Murine Macrophages]]&lt;br /&gt;
|'''Transfections and Transductions'''&lt;br /&gt;
* [[J774 Cell Transfection]]&lt;br /&gt;
* [[Raw Cell Transfection]]&lt;br /&gt;
* [[Neon® Transfection System]]&lt;br /&gt;
* [[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
*[[Transduction of THP-1s]]&lt;br /&gt;
&lt;br /&gt;
*&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====General Protocol Sites====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols&lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols&lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols&lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols&lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses.&lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat&lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols&lt;br /&gt;
|&lt;br /&gt;
====Free Science Ebooks====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
=Useful Links=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Molecular Biology Databases====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
=====Microscopy Tools===== &lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Journal Resources====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
====''In Vivo'' Tools====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
====Protease Tools====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Genomics Resources====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
====Chemical Tools====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
====Lipid Tools====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=141</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=141"/>
		<updated>2022-01-17T16:20:27Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
*[[Digests]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
|&lt;br /&gt;
==== Microscopy ====&lt;br /&gt;
*[[Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Immunostaining|Fluorescent Immunostaining]]&lt;br /&gt;
*[[Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Single Particle Tracking]]&lt;br /&gt;
*[[Staining for GSD]]&lt;br /&gt;
*[[Reducing Photobleaching]]&lt;br /&gt;
*[[Acid Washing Coverslips]]&lt;br /&gt;
*[[Live Cell FRET]] (depreciated)&lt;br /&gt;
*[[3D Printed PDMS Chambers]]&lt;br /&gt;
*[[FRET in FIJI]]&lt;br /&gt;
*[[Traction Force Microscopy]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Primary Macrophage Culture]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
|&lt;br /&gt;
==== Protein work ====&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
*[[Bradford Assay]]&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Bead Preparation'''&lt;br /&gt;
&lt;br /&gt;
* [[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|'''Bacteria Work'''&lt;br /&gt;
&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Immuno-FISH]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
|'''Transfections and Transductions'''&lt;br /&gt;
* [[J774 Cell Transfection]]&lt;br /&gt;
* [[Raw Cell Transfection]]&lt;br /&gt;
* [[Neon® Transfection System]]&lt;br /&gt;
* [[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
*[[Transduction of THP-1s]]&lt;br /&gt;
&lt;br /&gt;
*&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====General Protocol Sites====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols&lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols&lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols&lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols&lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses.&lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat&lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols&lt;br /&gt;
|&lt;br /&gt;
====Free Science Ebooks====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
=Useful Links=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Molecular Biology Databases====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
=====Microscopy Tools===== &lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Journal Resources====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
====''In Vivo'' Tools====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
====Protease Tools====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Genomics Resources====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
====Chemical Tools====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
====Lipid Tools====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=127</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=127"/>
		<updated>2022-01-11T17:17:24Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
*[[Digests]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
|&lt;br /&gt;
==== Microscopy ====&lt;br /&gt;
*[[Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Immunostaining|Fluorescent Immunostaining]]&lt;br /&gt;
*[[Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Single Particle Tracking]]&lt;br /&gt;
*[[Staining for GSD]]&lt;br /&gt;
*[[Reducing Photobleaching]]&lt;br /&gt;
*[[Acid Washing Coverslips]]&lt;br /&gt;
*[[Live Cell FRET]] (depreciated)&lt;br /&gt;
*[[3D Printed PDMS Chambers]]&lt;br /&gt;
*[[FRET in FIJI]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Primary Macrophage Culture]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
|&lt;br /&gt;
==== Protein work ====&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Immuno-FISH]]&lt;br /&gt;
|'''Transfections and Transductions'''&lt;br /&gt;
* [[J774 Cell Transfection]]&lt;br /&gt;
* [[Raw Cell Transfection]]&lt;br /&gt;
* [[Neon® Transfection System]]&lt;br /&gt;
* [[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
*[[Transduction of THP-1s]]&lt;br /&gt;
&lt;br /&gt;
*&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====General Protocol Sites====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols&lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols&lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols&lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols&lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses.&lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat&lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols&lt;br /&gt;
|&lt;br /&gt;
====Free Science Ebooks====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
=Useful Links=&lt;br /&gt;
{| width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Molecular Biology Databases====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
=====Microscopy Tools===== &lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Journal Resources====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
====''In Vivo'' Tools====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
====Protease Tools====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
====Genomics Resources====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
====Chemical Tools====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
====Lipid Tools====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Transduction_of_THP-1s&amp;diff=126</id>
		<title>Transduction of THP-1s</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Transduction_of_THP-1s&amp;diff=126"/>
		<updated>2022-01-11T17:16:43Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: Created page with &amp;quot;'''Transduction Reaction'''  * The volume of the reaction is based on the amount of virus available, the number of cells and the MOI being used     *   Prepare the mixture as follows: **  X uL of concentrated virus **  X uL of SF Macrophage Media (chose this volume based on the vessel the cells will be grown in ** 1000X polybrene   '''Protocol'''  # Count cells, add cells to appropriate size tube, spin down at 400 x G for 5 minutes # Re-suspend cells in the transduct...&amp;quot;&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''Transduction Reaction'''&lt;br /&gt;
&lt;br /&gt;
* The volume of the reaction is based on the amount of virus available, the number of cells and the MOI being used   &lt;br /&gt;
&lt;br /&gt;
*   Prepare the mixture as follows:&lt;br /&gt;
**  X uL of concentrated virus&lt;br /&gt;
**  X uL of SF Macrophage Media (chose this volume based on the vessel the cells will be grown in&lt;br /&gt;
** 1000X polybrene&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Protocol'''&lt;br /&gt;
&lt;br /&gt;
# Count cells, add cells to appropriate size tube, spin down at 400 x G for 5 minutes&lt;br /&gt;
# Re-suspend cells in the transduction reaction mixture&lt;br /&gt;
# Spin at 400 X G, 10 degrees for 1 hour 30 minutes&lt;br /&gt;
# Re-suspend the cells in the virus containing media and transfer to an appropriate size flask or plate, incubate overnight at 37 degrees overnight&lt;br /&gt;
# Transfer the contents of the flask to a new tube, spin down and replace the media with 500 uL of fresh complete RPMI&lt;br /&gt;
# Incubate plate for 48-72 hours at 37 °C&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Notes'''&lt;br /&gt;
&lt;br /&gt;
* Number of cells: Select number of cells that allows for an MOI of 300, some literature suggests MOI up to 500&lt;br /&gt;
* If making a cell line add selection media at the incubation period in step 6. I would also suggest comparing live/dead cell counts for both the control and the transduced cells before every media change to determine if the selection process is working&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=125</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=125"/>
		<updated>2022-01-11T17:09:33Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{|width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
*[[Digests]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
|&lt;br /&gt;
==== Microscopy ====&lt;br /&gt;
*[[Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Immunostaining|Fluorescent Immunostaining]]&lt;br /&gt;
*[[Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Single Particle Tracking]]&lt;br /&gt;
*[[Staining for GSD]]&lt;br /&gt;
*[[Reducing Photobleaching]]&lt;br /&gt;
*[[Acid Washing Coverslips]]&lt;br /&gt;
*[[Live Cell FRET]] (depreciated)&lt;br /&gt;
*[[3D Printed PDMS Chambers]]&lt;br /&gt;
*[[FRET in FIJI]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Primary Macrophage Culture]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
|&lt;br /&gt;
==== Protein work ====&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Immuno-FISH]]&lt;br /&gt;
|'''Transfections and Transductions'''&lt;br /&gt;
* [[J774 Cell Transfection]]&lt;br /&gt;
* [[Raw Cell Transfection]]&lt;br /&gt;
* [[Neon® Transfection System]]&lt;br /&gt;
* [[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
&lt;br /&gt;
* &lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols =&lt;br /&gt;
{|width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== General Protocol Sites ====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols &lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols &lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols &lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols &lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses. &lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat &lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols &lt;br /&gt;
|&lt;br /&gt;
==== Free Science Ebooks ====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Useful Links =&lt;br /&gt;
{|width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Databases ====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools ====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
===== Microscopy Tools =====&lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Journal Resources ====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
==== ''In Vivo'' Tools ====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
==== Protease Tools ====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Genomics Resources ====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
==== Chemical Tools ====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
==== Lipid Tools ====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=124</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=124"/>
		<updated>2022-01-11T17:01:26Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: /* Index of Protocols */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{|width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
*[[Digests]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
*[[Neon® Transfection System]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
|&lt;br /&gt;
==== Microscopy ====&lt;br /&gt;
*[[Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Immunostaining|Fluorescent Immunostaining]]&lt;br /&gt;
*[[Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Single Particle Tracking]]&lt;br /&gt;
*[[Staining for GSD]]&lt;br /&gt;
*[[Reducing Photobleaching]]&lt;br /&gt;
*[[Acid Washing Coverslips]]&lt;br /&gt;
*[[Live Cell FRET]] (depreciated)&lt;br /&gt;
*[[3D Printed PDMS Chambers]]&lt;br /&gt;
*[[FRET in FIJI]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Primary Macrophage Culture]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Raw Cell Transfection]]&lt;br /&gt;
*[[J774 Cell Transfection]]&lt;br /&gt;
*[[Mammalian Cell Transfection]]&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
*[[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
|&lt;br /&gt;
==== Protein work ====&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Immuno-FISH]]&lt;br /&gt;
|'''Transfections and Transductions'''&lt;br /&gt;
* &lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols =&lt;br /&gt;
{|width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== General Protocol Sites ====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols &lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols &lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols &lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols &lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses. &lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat &lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols &lt;br /&gt;
|&lt;br /&gt;
==== Free Science Ebooks ====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Useful Links =&lt;br /&gt;
{|width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Databases ====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools ====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
===== Microscopy Tools =====&lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Journal Resources ====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
==== ''In Vivo'' Tools ====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
==== Protease Tools ====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Genomics Resources ====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
==== Chemical Tools ====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
==== Lipid Tools ====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Titering_Pseudo-typed_Lentiviruses&amp;diff=122</id>
		<title>Titering Pseudo-typed Lentiviruses</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Titering_Pseudo-typed_Lentiviruses&amp;diff=122"/>
		<updated>2021-12-06T14:54:27Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;-       for titering one “batch” of collected virus&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Cell Seeding'''&lt;br /&gt;
&lt;br /&gt;
1.     Seed 6 wells of a 12 well plate with 30 000 – 50 000 HeLas per well on coverslips&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Transduction'''&lt;br /&gt;
&lt;br /&gt;
1.     Prepare “transduction media” by mixing 6 µL of polybrene (1000X) in 6 mL of DMEM+10% FBS&lt;br /&gt;
&lt;br /&gt;
2.     Remove media from the plate and replace with 900 µL of transduction media in each well&lt;br /&gt;
&lt;br /&gt;
3.     Begin the serial dilution by adding 100 µL of virus to the first well. There is often a vial set aside labelled as 10X diluted (the starting dilution will be a 100X dilution). Mix the    &lt;br /&gt;
&lt;br /&gt;
contents of  the well by pipetting up and down, discard the pipette tip.&lt;br /&gt;
&lt;br /&gt;
4.     Using a new pipette tip take 100 µL out of the first well and add it to the second well, mix the contents of the well the same as before, discarding the pipette tip.&lt;br /&gt;
&lt;br /&gt;
5.     Continue the dilution series by adding 100 µL from the second well into the third well and mixing, followed by 100 µL from the third well into the fourth well and 100 µL from       &lt;br /&gt;
&lt;br /&gt;
the fourth well to the fifth well. Mixing well and discarding the tips in between each well.&lt;br /&gt;
&lt;br /&gt;
6.     The last well is reserved for an untransduced control.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Preparing the cells for imaging'''&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
1.     After 24-48 hours (48 hours is preferred) remove the media and wash the cells with PBS. This should be done in the biosafety cabinet.&lt;br /&gt;
&lt;br /&gt;
2.     Add 1 mL of 4% PFA to each well, incubate at RT for 20 min. After this step the plate may be removed from the biosafety cab&lt;br /&gt;
&lt;br /&gt;
3.      If the vector that is packaged does not have a fluorescent tag, immunostain for the target gene.&lt;br /&gt;
&lt;br /&gt;
4.     Rinse wells with PBS and add 1 mL of 1:10 000 Hoechst in PBS to each well, incubate at RT for 10 minutes&lt;br /&gt;
&lt;br /&gt;
5.     Rinse 1-2 times with PBS&lt;br /&gt;
&lt;br /&gt;
6.     Mount on slides or image on the same day using a spaceship&lt;br /&gt;
&lt;br /&gt;
'''Imaging'''&lt;br /&gt;
&lt;br /&gt;
1.     Image each dilution on 40X magnification, using the blue channel for Hoechst, and the green for ZsGreen featuring viruses, take 5 images per dilution.&lt;br /&gt;
&lt;br /&gt;
2.     It is common to have very few positive cells on the 10 000X dilution and no positive cells on the 100 000X and 1 000 000X dilution. Stop imaging after you image a dilution     &lt;br /&gt;
&lt;br /&gt;
that has 0 cells  transduced.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Calculating the viral titer'''&lt;br /&gt;
&lt;br /&gt;
-       There is an ImageJ script for counting the cells, however the thresholding it uses isn’t always appropriate&lt;br /&gt;
&lt;br /&gt;
-       Add the total number of cells counted and number of positive cells need to the appropriate columns in the &amp;quot;Lentivirus Titrations&amp;quot; spreadsheet, it will calculate the titer for you   &lt;br /&gt;
&lt;br /&gt;
For each dilution&lt;br /&gt;
&lt;br /&gt;
1.     Count all the nuclei on all five images (you can also stop at ~ 100 nuclei)&lt;br /&gt;
&lt;br /&gt;
2.     Count all the ZsGreen positive cells in all five images&lt;br /&gt;
&lt;br /&gt;
3.     Calculate the % positive  (# of green cells/# of nuclei X 100)&lt;br /&gt;
&lt;br /&gt;
4.     Calculate the titer of each dilution&lt;br /&gt;
&lt;br /&gt;
   Titer (TU/L) = (number of cells X percent of positive cells)/(volume in well X dilution factor)&lt;br /&gt;
&lt;br /&gt;
5.     Average the titers for each dilution where:  the percent positive is &amp;lt;30% and &amp;gt;0%. &lt;br /&gt;
&lt;br /&gt;
* The average titer is the one you will use for future MOI calculations&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Titering_Pseudo-typed_Lentiviruses&amp;diff=121</id>
		<title>Titering Pseudo-typed Lentiviruses</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Titering_Pseudo-typed_Lentiviruses&amp;diff=121"/>
		<updated>2021-12-06T14:54:01Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;-       for titering one “batch” of collected virus&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Cell Seeding'''&lt;br /&gt;
&lt;br /&gt;
1.     Seed 6 wells of a 12 well plate with 30 000 – 50 000 HeLas per well on coverslips&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Transduction'''&lt;br /&gt;
&lt;br /&gt;
1.     Prepare “transduction media” by mixing 6 µL of polybrene (1000X) in 6 mL of DMEM+10% FBS&lt;br /&gt;
&lt;br /&gt;
2.     Remove media from the plate and replace with 900 µL of transduction media in each well&lt;br /&gt;
&lt;br /&gt;
3.     Begin the serial dilution by adding 100 µL of virus to the first well. There is often a vial set aside labelled as 10X diluted (the starting dilution will be a 100X dilution). Mix the    &lt;br /&gt;
&lt;br /&gt;
contents of  the well by pipetting up and down, discard the pipette tip.&lt;br /&gt;
&lt;br /&gt;
4.     Using a new pipette tip take 100 µL out of the first well and add it to the second well, mix the contents of the well the same as before, discarding the pipette tip.&lt;br /&gt;
&lt;br /&gt;
5.     Continue the dilution series by adding 100 µL from the second well into the third well and mixing, followed by 100 µL from the third well into the fourth well and 100 µL from the fourth well to the fifth well. Mixing well and discarding the tips in between each well.&lt;br /&gt;
&lt;br /&gt;
6.     The last well is reserved for an untransduced control.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Preparing the cells for imaging'''&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
1.     After 24-48 hours (48 hours is preferred) remove the media and wash the cells with PBS. This should be done in the biosafety cabinet.&lt;br /&gt;
&lt;br /&gt;
2.     Add 1 mL of 4% PFA to each well, incubate at RT for 20 min. After this step the plate may be removed from the biosafety cab&lt;br /&gt;
&lt;br /&gt;
3.      If the vector that is packaged does not have a fluorescent tag, immunostain for the target gene.&lt;br /&gt;
&lt;br /&gt;
4.     Rinse wells with PBS and add 1 mL of 1:10 000 Hoechst in PBS to each well, incubate at RT for 10 minutes&lt;br /&gt;
&lt;br /&gt;
5.     Rinse 1-2 times with PBS&lt;br /&gt;
&lt;br /&gt;
6.     Mount on slides or image on the same day using a spaceship&lt;br /&gt;
&lt;br /&gt;
'''Imaging'''&lt;br /&gt;
&lt;br /&gt;
1.     Image each dilution on 40X magnification, using the blue channel for Hoechst, and the green for ZsGreen featuring viruses, take 5 images per dilution.&lt;br /&gt;
&lt;br /&gt;
2.     It is common to have very few positive cells on the 10 000X dilution and no positive cells on the 100 000X and 1 000 000X dilution. Stop imaging after you image a dilution     &lt;br /&gt;
&lt;br /&gt;
that has 0 cells  transduced.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Calculating the viral titer'''&lt;br /&gt;
&lt;br /&gt;
-       There is an ImageJ script for counting the cells, however the thresholding it uses isn’t always appropriate&lt;br /&gt;
&lt;br /&gt;
-       Add the total number of cells counted and number of positive cells need to the appropriate columns in the &amp;quot;Lentivirus Titrations&amp;quot; spreadsheet, it will calculate the titer for you   &lt;br /&gt;
&lt;br /&gt;
For each dilution&lt;br /&gt;
&lt;br /&gt;
1.     Count all the nuclei on all five images (you can also stop at ~ 100 nuclei)&lt;br /&gt;
&lt;br /&gt;
2.     Count all the ZsGreen positive cells in all five images&lt;br /&gt;
&lt;br /&gt;
3.     Calculate the % positive  (# of green cells/# of nuclei X 100)&lt;br /&gt;
&lt;br /&gt;
4.     Calculate the titer of each dilution&lt;br /&gt;
&lt;br /&gt;
   Titer (TU/L) = (number of cells X percent of positive cells)/(volume in well X dilution factor)&lt;br /&gt;
&lt;br /&gt;
5.     Average the titers for each dilution where:  the percent positive is &amp;lt;30% and &amp;gt;0%. &lt;br /&gt;
&lt;br /&gt;
* The average titer is the one you will use for future MOI calculations&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Titering_Pseudo-typed_Lentiviruses&amp;diff=120</id>
		<title>Titering Pseudo-typed Lentiviruses</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Titering_Pseudo-typed_Lentiviruses&amp;diff=120"/>
		<updated>2021-12-06T14:51:17Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;-       for titering one “batch” of collected virus&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Cell Seeding'''&lt;br /&gt;
&lt;br /&gt;
1.     Seed 6 wells of a 12 well plate with 30 000 – 50 000 HeLas per well on coverslips&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Transduction'''&lt;br /&gt;
&lt;br /&gt;
1.     Prepare “transduction media” by mixing 6 µL of polybrene (1000X) in 6 mL of DMEM+10% FBS&lt;br /&gt;
&lt;br /&gt;
2.     Remove media from the plate and replace with 900 µL of transduction media in each well&lt;br /&gt;
&lt;br /&gt;
3.     Begin the serial dilution by adding 100 µL of virus to the first well. There is often a vial set aside labelled as 10X diluted (the starting dilution will be a 100X dilution). Mix the contents of        the well by pipetting up and down, discard the pipette tip.&lt;br /&gt;
&lt;br /&gt;
4.     Using a new pipette tip take 100 µL out of the first well and add it to the second well, mix the contents of the well the same as before, discarding the pipette tip.&lt;br /&gt;
&lt;br /&gt;
5.     Continue the dilution series by adding 100 µL from the second well into the third well and mixing, followed by 100 µL from the third well into the fourth well and 100 µL from the fourth well to the fifth well. Mixing well and discarding the tips in between each well.&lt;br /&gt;
&lt;br /&gt;
6.     The last well is reserved for an untransduced control.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Preparing the cells for imaging'''&lt;br /&gt;
&lt;br /&gt;
1.     After 24-48 hours (48 hours is preferred) remove the media and wash the cells with PBS. This should be done in the biosafety cabinet.&lt;br /&gt;
&lt;br /&gt;
2.     Add 1 mL of 4% PFA to each well, incubate at RT for 20 min. After this step the plate may be removed from the biosafety cab&lt;br /&gt;
&lt;br /&gt;
3.     If the vector that is packaged does not have a fluorescent tag, immunostain for the target gene.&lt;br /&gt;
&lt;br /&gt;
4.     Rinse wells with PBS and add 1 mL of 1:10 000 Hoechst in PBS to each well, incubate at RT for 10 minutes&lt;br /&gt;
&lt;br /&gt;
5.     Rinse 1-2 times with PBS&lt;br /&gt;
&lt;br /&gt;
6.     Mount on slides or image on the same day using a spaceship&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Imaging'''&lt;br /&gt;
&lt;br /&gt;
1.     Image each dilution on 40X magnification, using the blue channel for Hoechst, and the green for ZsGreen featuring viruses, take 5 images per dilution.&lt;br /&gt;
&lt;br /&gt;
2.     It is common to have very few positive cells on the 10 000X dilution and no positive cells on the 100 000X and 1 000 000X dilution. Stop imaging after you image a dilution     &lt;br /&gt;
&lt;br /&gt;
that has 0 cells  transduced.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Calculating the viral titer'''&lt;br /&gt;
&lt;br /&gt;
-       There is an ImageJ script for counting the cells, however the thresholding it uses isn’t always appropriate&lt;br /&gt;
&lt;br /&gt;
-       Add the total number of cells counted and number of positive cells need to the appropriate columns in the &amp;quot;Lentivirus Titrations&amp;quot; spreadsheet, it will calculate the titer for you   &lt;br /&gt;
&lt;br /&gt;
For each dilution&lt;br /&gt;
&lt;br /&gt;
1.     Count all the nuclei on all five images (you can also stop at ~ 100 nuclei)&lt;br /&gt;
&lt;br /&gt;
2.     Count all the ZsGreen positive cells in all five images&lt;br /&gt;
&lt;br /&gt;
3.     Calculate the % positive  (# of green cells/# of nuclei X 100)&lt;br /&gt;
&lt;br /&gt;
4.     Calculate the titer of each dilution&lt;br /&gt;
&lt;br /&gt;
   Titer (TU/L) = (number of cells X percent of positive cells)/(volume in well X dilution factor)&lt;br /&gt;
&lt;br /&gt;
5.     Average the titers for each dilution where:  the percent positive is &amp;lt;30% and &amp;gt;0%. &lt;br /&gt;
&lt;br /&gt;
* The average titer is the one you will use for future MOI calculations&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Titering_Pseudo-typed_Lentiviruses&amp;diff=119</id>
		<title>Titering Pseudo-typed Lentiviruses</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Titering_Pseudo-typed_Lentiviruses&amp;diff=119"/>
		<updated>2021-12-06T14:25:35Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;-       for titering one “batch” of collected virus&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Cell Seeding'''&lt;br /&gt;
&lt;br /&gt;
1.     Seed 6 wells of a 12 well plate with 30 000 – 50 000 HeLas per well on coverslips&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Transduction'''&lt;br /&gt;
&lt;br /&gt;
1.     Prepare “transduction media” by mixing 6 µL of polybrene (1000X) in 6 mL of DMEM+10% FBS&lt;br /&gt;
&lt;br /&gt;
2.     Remove media from the plate and replace with 900 µL of transduction media in each well&lt;br /&gt;
&lt;br /&gt;
3.     Begin the serial dilution by adding 100 µL of virus to the first well. There is often a vial set aside labelled as 10X diluted (the starting dilution will be a 100X dilution). Mix the contents of        the well by pipetting up and down, discard the pipette tip.&lt;br /&gt;
&lt;br /&gt;
4.     Using a new pipette tip take 100 µL out of the first well and add it to the second well, mix the contents of the well the same as before, discarding the pipette tip.&lt;br /&gt;
&lt;br /&gt;
5.     Continue the dilution series by adding 100 µL from the second well into the third well and mixing, followed by 100 µL from the third well into the fourth well and 100 µL from the fourth well to the fifth well. Mixing well and discarding the tips in between each well.&lt;br /&gt;
&lt;br /&gt;
6.     The last well is reserved for an untransduced control.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Preparing the cells for imaging'''&lt;br /&gt;
&lt;br /&gt;
1.     After 24-48 hours (48 hours is preferred) remove the media and wash the cells with PBS. This should be done in the biosafety cabinet.&lt;br /&gt;
&lt;br /&gt;
2.     Add 1 mL of 4% PFA to each well, incubate at RT for 20 min. After this step the plate may be removed from the biosafety cabinet.&lt;br /&gt;
&lt;br /&gt;
3.      If the vector that is packaged does not have a fluorescent tag, immunostain for the target gene. &lt;br /&gt;
&lt;br /&gt;
4.     Rinse wells with PBS and add 1 mL of 1:10 000 Hoechst in PBS to each well, incubate at RT for 10 minutes&lt;br /&gt;
&lt;br /&gt;
5.     Rinse 1-2 times with PBS&lt;br /&gt;
&lt;br /&gt;
6.     Mount on slides or image on the same day using a spaceship&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Imaging'''&lt;br /&gt;
&lt;br /&gt;
1.     Image each dilution on 40X magnification, using the blue channel for Hoechst, and the green for ZsGreen featuring viruses, take 5 images per dilution.&lt;br /&gt;
&lt;br /&gt;
2.     It is common to have very few positive cells on the 10 000X dilution and no positive cells on the 100 000X and 1 000 000X dilution. Stop imaging after you image a dilution that has 0 cells  transduced.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Calculating the viral titer'''&lt;br /&gt;
&lt;br /&gt;
-       There is an ImageJ script for counting the cells, however the thresholding it uses isn’t always appropriate&lt;br /&gt;
&lt;br /&gt;
-       Add the total number of cells counted and number of positive cells need to the appropriate columns in the &amp;quot;Lentivirus Titrations&amp;quot; spreadsheet, it will calculate the titer for you   &lt;br /&gt;
&lt;br /&gt;
For each dilution&lt;br /&gt;
&lt;br /&gt;
1.     Count all the nuclei on all five images (you can also stop at ~ 100 nuclei)&lt;br /&gt;
&lt;br /&gt;
2.     Count all the ZsGreen positive cells in all five images&lt;br /&gt;
&lt;br /&gt;
3.     Calculate the % positive  (# of green cells/# of nuclei X 100)&lt;br /&gt;
&lt;br /&gt;
4.     Calculate the titer of each dilution&lt;br /&gt;
&lt;br /&gt;
   Titer (TU/L) = (number of cells X percent of positive cells)/(volume in well X dilution factor)&lt;br /&gt;
&lt;br /&gt;
5.     Average the titers for each dilution where:  the percent positive is &amp;lt;30% and &amp;gt;0%. &lt;br /&gt;
&lt;br /&gt;
* The average titer is the one you will use for future MOI calculations&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Titering_Pseudo-typed_Lentiviruses&amp;diff=118</id>
		<title>Titering Pseudo-typed Lentiviruses</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Titering_Pseudo-typed_Lentiviruses&amp;diff=118"/>
		<updated>2021-12-06T14:25:13Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;-       for titering one “batch” of collected virus&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Cell Seeding'''&lt;br /&gt;
&lt;br /&gt;
1.     Seed 6 wells of a 12 well plate with 30 000 – 50 000 HeLas per well on coverslips&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Transduction'''&lt;br /&gt;
&lt;br /&gt;
1.     Prepare “transduction media” by mixing 6 µL of polybrene (1000X) in 6 mL of DMEM+10% FBS&lt;br /&gt;
&lt;br /&gt;
2.     Remove media from the plate and replace with 900 µL of transduction media in each well&lt;br /&gt;
&lt;br /&gt;
3.     Begin the serial dilution by adding 100 µL of virus to the first well. There is often a vial set aside labelled as 10X diluted (the starting dilution will be a 100X dilution). Mix the contents of        the well by pipetting up and down, discard the pipette tip.&lt;br /&gt;
&lt;br /&gt;
4.     Using a new pipette tip take 100 µL out of the first well and add it to the second well, mix the contents of the well the same as before, discarding the pipette tip.&lt;br /&gt;
&lt;br /&gt;
5.     Continue the dilution series by adding 100 µL from the second well into the third well and mixing, followed by 100 µL from the third well into the fourth well and 100 µL from the fourth well to the fifth well. Mixing well and discarding the tips in between each well.&lt;br /&gt;
&lt;br /&gt;
6.     The last well is reserved for an untransduced control.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Preparing the cells for imaging'''&lt;br /&gt;
&lt;br /&gt;
1.     After 24-48 hours (48 hours is preferred) remove the media and wash the cells with PBS. This should be done in the biosafety cabinet.&lt;br /&gt;
&lt;br /&gt;
2.     Add 1 mL of 4% PFA to each well, incubate at RT for 20 min. After this step the plate may be removed from the biosafety cabinet.&lt;br /&gt;
&lt;br /&gt;
3.     If the vector that is packaged does not have a fluorescent tag, immunostain for the target gene. &lt;br /&gt;
&lt;br /&gt;
4.     Rinse wells with PBS and add 1 mL of 1:10 000 Hoechst in PBS to each well, incubate at RT for 10 minutes&lt;br /&gt;
&lt;br /&gt;
5.     Rinse 1-2 times with PBS&lt;br /&gt;
&lt;br /&gt;
6.     Mount on slides or image on the same day using a spaceship&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Imaging'''&lt;br /&gt;
&lt;br /&gt;
1.     Image each dilution on 40X magnification, using the blue channel for Hoechst, and the green for ZsGreen featuring viruses, take 5 images per dilution.&lt;br /&gt;
&lt;br /&gt;
2.     It is common to have very few positive cells on the 10 000X dilution and no positive cells on the 100 000X and 1 000 000X dilution. Stop imaging after you image a dilution that has 0 cells        transduced.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Calculating the viral titer'''&lt;br /&gt;
&lt;br /&gt;
-       There is an ImageJ script for counting the cells, however the thresholding it uses isn’t always appropriate&lt;br /&gt;
&lt;br /&gt;
-       Add the total number of cells counted and number of positive cells need to the appropriate columns in the &amp;quot;Lentivirus Titrations&amp;quot; spreadsheet, it will calculate the titer for you   &lt;br /&gt;
&lt;br /&gt;
For each dilution&lt;br /&gt;
&lt;br /&gt;
1.     Count all the nuclei on all five images (you can also stop at ~ 100 nuclei)&lt;br /&gt;
&lt;br /&gt;
2.     Count all the ZsGreen positive cells in all five images&lt;br /&gt;
&lt;br /&gt;
3.     Calculate the % positive  (# of green cells/# of nuclei X 100)&lt;br /&gt;
&lt;br /&gt;
4.     Calculate the titer of each dilution&lt;br /&gt;
&lt;br /&gt;
   Titer (TU/L) = (number of cells X percent of positive cells)/(volume in well X dilution factor)&lt;br /&gt;
&lt;br /&gt;
5.     Average the titers for each dilution where:  the percent positive is &amp;lt;30% and &amp;gt;0%. &lt;br /&gt;
&lt;br /&gt;
* The average titer is the one you will use for future MOI calculations&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Titering_Pseudo-typed_Lentiviruses&amp;diff=117</id>
		<title>Titering Pseudo-typed Lentiviruses</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Titering_Pseudo-typed_Lentiviruses&amp;diff=117"/>
		<updated>2021-11-29T19:22:51Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;-       for titering one “batch” of collected virus&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Cell Seeding'''&lt;br /&gt;
&lt;br /&gt;
1.     Seed 6 wells of a 12 well plate with 30 000 – 50 000 HeLas per well on coverslips&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Transduction'''&lt;br /&gt;
&lt;br /&gt;
1.     Prepare “transduction media” by mixing 6 µL of polybrene (1000X) in 6 mL of DMEM+10% FBS&lt;br /&gt;
&lt;br /&gt;
2.     Remove media from the plate and replace with 900 µL of transduction media in each well&lt;br /&gt;
&lt;br /&gt;
3.     Begin the serial dilution by adding 100 µL of virus to the first well. There is often a vial set aside labelled as 10X diluted (the starting dilution will be a 100X dilution). Mix the contents of        the well by pipetting up and down, discard the pipette tip.&lt;br /&gt;
&lt;br /&gt;
4.     Using a new pipette tip take 100 µL out of the first well and add it to the second well, mix the contents of the well the same as before, discarding the pipette tip.&lt;br /&gt;
&lt;br /&gt;
5.     Continue the dilution series by adding 100 µL from the second well into the third well and mixing, followed by 100 µL from the third well into the fourth well and 100 µL from the fourth well to the fifth well. Mixing well and discarding the tips in between each well.&lt;br /&gt;
&lt;br /&gt;
6.     The last well is reserved for an untransduced control.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Preparing the cells for imaging'''&lt;br /&gt;
&lt;br /&gt;
1.     After 24-48 hours (48 hours is preferred) remove the media and wash the cells with PBS. This should be done in the biosafety cabinet.&lt;br /&gt;
&lt;br /&gt;
2.     Add 1 mL of 4% PFA to each well, incubate at RT for 20 min. After this step the plate may be removed from the biosafety cabinet.&lt;br /&gt;
&lt;br /&gt;
3.     Rinse wells with PBS and add 1 mL of 1:10 000 Hoechst in PBS to each well, incubate at RT for 10 minutes&lt;br /&gt;
&lt;br /&gt;
4.     Rinse 1-2 times with PBS&lt;br /&gt;
&lt;br /&gt;
5.     Mount on slides or image on the same day using a spaceship&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Imaging'''&lt;br /&gt;
&lt;br /&gt;
1.     Image each dilution on 40X magnification, using the blue channel for Hoechst, and the green for ZsGreen featuring viruses, take 5 images per dilution.&lt;br /&gt;
&lt;br /&gt;
2.     It is common to have very few positive cells on the 10 000X dilution and no positive cells on the 100 000X and 1 000 000X dilution. Stop imaging after you image a dilution that has 0 cells        transduced.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Calculating the viral titer'''&lt;br /&gt;
&lt;br /&gt;
-       There is an ImageJ script for counting the cells, however the thresholding it uses isn’t always appropriate&lt;br /&gt;
&lt;br /&gt;
-       Add the total number of cells counted and number of positive cells need to the appropriate columns in the &amp;quot;Lentivirus Titrations&amp;quot; spreadsheet, it will calculate the titer for you   &lt;br /&gt;
&lt;br /&gt;
For each dilution&lt;br /&gt;
&lt;br /&gt;
1.     Count all the nuclei on all five images (you can also stop at ~ 100 nuclei)&lt;br /&gt;
&lt;br /&gt;
2.     Count all the ZsGreen positive cells in all five images&lt;br /&gt;
&lt;br /&gt;
3.     Calculate the % positive  (# of green cells/# of nuclei X 100)&lt;br /&gt;
&lt;br /&gt;
4.     Calculate the titer of each dilution&lt;br /&gt;
&lt;br /&gt;
   Titer (TU/L) = (number of cells X percent of positive cells)/(volume in well X dilution factor)&lt;br /&gt;
&lt;br /&gt;
5.     Average the titers for each dilution where:  the percent positive is &amp;lt;30% and &amp;gt;0%. &lt;br /&gt;
&lt;br /&gt;
* The average titer is the one you will use for future MOI calculations&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Antibiotics&amp;diff=116</id>
		<title>Antibiotics</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Antibiotics&amp;diff=116"/>
		<updated>2021-11-29T18:25:53Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Protocol ==&lt;br /&gt;
&lt;br /&gt;
==== Ampicillin&amp;lt;br&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Preparation of 5 mL of 100 mg/mL:&lt;br /&gt;
&lt;br /&gt;
#Add 0.5 g of ampicilin into a 12 mL tube.&lt;br /&gt;
#Add 2.5 mL of ddH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O into the tube and mix gently by tapping the side of the tube.&lt;br /&gt;
#Add 2.5 mL of 100% ethanol and mix the tube again.&lt;br /&gt;
#Filter with a 0.22 μm syringe filter&lt;br /&gt;
#Aliquot out 1 mL into each of 5 microcentrifuge tubes.&lt;br /&gt;
#Label the tubes as 1000x ampicillin and write the date.&lt;br /&gt;
#Place tubes in the antibiotics box in the -20 °C freezer.&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Note: Ampicillin stock will only be good for approximately 6 months.&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Kanamycin&amp;lt;br&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Preparation of 5 mL of 50 mg/mL&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
#Add 0.25 g of kanamycin into a 12 mL tube.&amp;lt;br&amp;gt;&lt;br /&gt;
#Add 5 mL ddH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O into the tube and mix by shaking tube.&amp;lt;br&amp;gt;&lt;br /&gt;
#Aliquot out 1 mL into each of 5 microcentrifuge tubes.&amp;lt;br&amp;gt;&lt;br /&gt;
#Label the tubes as 1000x kanamycin and write the date.&amp;lt;br&amp;gt;&lt;br /&gt;
#Place the tubes in the antibiotics box in the -20 °C freezer.&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Note: Kanamycin tubes must be kept in the fridge after being removed from the freezer. &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=115</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Main_Page&amp;diff=115"/>
		<updated>2021-11-25T15:19:49Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]&lt;br /&gt;
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.&amp;amp;nbsp; Only laboratory members may edit pages, but anyone is welcome to use these protocols.&amp;amp;nbsp; If you use these protocol, please cite us.&amp;amp;nbsp; A link for generating citations can be found on the left side of the page.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt; Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.&amp;lt;br&amp;gt; &amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''''Lab members:'''''&lt;br /&gt;
&lt;br /&gt;
*To get a wiki account please contact Dr. Heit. &lt;br /&gt;
*Log in&amp;amp;nbsp;(upper-right side of screen) to add/edit pages. &amp;amp;nbsp; &lt;br /&gt;
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols. &lt;br /&gt;
*To create a new page, [[Create new|follow these instructions]]. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Index of Protocols =&lt;br /&gt;
{|width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Lab Operations ====&lt;br /&gt;
*[[Entrance Protocol]]&lt;br /&gt;
*[[Exit Protocol]]&lt;br /&gt;
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]&lt;br /&gt;
*[[Saving Experimental Files|Proper Saving of Experimental Files]]&lt;br /&gt;
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp;amp;amp; Wiki]]&lt;br /&gt;
|&lt;br /&gt;
==== DNA/Cloning ====&lt;br /&gt;
&lt;br /&gt;
*[[Colony PCR]]&lt;br /&gt;
*[[PCR]]&lt;br /&gt;
*[[Digests]]&lt;br /&gt;
*[[Ligation]]&lt;br /&gt;
*[[Gibson Assembly]]&lt;br /&gt;
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]&lt;br /&gt;
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 &amp;amp; ZYCY10P3S2T)]]&lt;br /&gt;
*[[E. coli Transduction|Transducing ''E. coli'']]&lt;br /&gt;
*[[Transformation]]&lt;br /&gt;
*[[Neon® Transfection System]]&lt;br /&gt;
*[[Generating Minicircles]]&lt;br /&gt;
|&lt;br /&gt;
==== Microscopy ====&lt;br /&gt;
*[[Competition of Charged Molecules with Lipophilic Cations]]&lt;br /&gt;
*[[Immunostaining|Fluorescent Immunostaining]]&lt;br /&gt;
*[[Inhibition of Focal Contact Signaling]]&lt;br /&gt;
*[[Single Particle Tracking]]&lt;br /&gt;
*[[Staining for GSD]]&lt;br /&gt;
*[[Reducing Photobleaching]]&lt;br /&gt;
*[[Acid Washing Coverslips]]&lt;br /&gt;
*[[Live Cell FRET]] (depreciated)&lt;br /&gt;
*[[3D Printed PDMS Chambers]]&lt;br /&gt;
*[[FRET in FIJI]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== General Protocols ====&lt;br /&gt;
*[[Common buffers|Common Buffers]]&lt;br /&gt;
*[[Cell Culture Guidelines]]&lt;br /&gt;
*[[Bacterial Growth Media]]&lt;br /&gt;
*[[Primary Macrophage Culture]]&lt;br /&gt;
*[[Freezing and Thawing Cells]]&lt;br /&gt;
*[[Raw Cell Transfection]]&lt;br /&gt;
*[[J774 Cell Transfection]]&lt;br /&gt;
*[[Mammalian Cell Transfection]]&lt;br /&gt;
*[[Antibiotics]]&lt;br /&gt;
*[[Antibiotic Plates]]&lt;br /&gt;
*[[Agarose Gels]]&lt;br /&gt;
*[[Water Bath Antibiotic Solution]]&lt;br /&gt;
*[[Titering Pseudo-typed Lentiviruses]]&lt;br /&gt;
|&lt;br /&gt;
==== Protein work ====&lt;br /&gt;
*[[Western Blotting]]&lt;br /&gt;
*[[Immunoprecipitation]]&lt;br /&gt;
*[[Fab preparation]]&lt;br /&gt;
*[[Fab Purification by FPLC|Fab purification using FPLC]]&lt;br /&gt;
*[[Updated FPLC Size Exclusion Procedure]]&lt;br /&gt;
*[[Coomassie Staining]]&lt;br /&gt;
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]&lt;br /&gt;
*[[Stripping &amp;amp; Reprobing Blots|Stripping &amp;amp;amp; Reprobing Blots]]&lt;br /&gt;
*[[Nitrogen Cavitation]]&lt;br /&gt;
|&lt;br /&gt;
==== Lipids ====&lt;br /&gt;
*[[Asymmetric liposomes]]&lt;br /&gt;
*[[Lipid Coated Bead Preparation]]&lt;br /&gt;
*[[Lipid Extraction from Cells]]&lt;br /&gt;
*[[Lipisome and Lipid-Coated Beads]]&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Phagocytosis Protocols ====&lt;br /&gt;
&lt;br /&gt;
*[[Opsonization]]&lt;br /&gt;
*[[Preparation of Silica-Magnetic Beads]]&lt;br /&gt;
*[[Synchronised Phagocytosis]]&lt;br /&gt;
*[[Phagosome Isolation]]&lt;br /&gt;
*[[Primary Human Macrophages]]&lt;br /&gt;
*[[Labelled E coli]]&lt;br /&gt;
*[[Inside-out Labelling of Bacteria]]&lt;br /&gt;
*[[Gentamicin Protection Assay]]&lt;br /&gt;
*[[Preparation of Digestion-Tracking Bacteria]]&lt;br /&gt;
|&lt;br /&gt;
==== Cell Biology ====&lt;br /&gt;
*[[Ablation of Recycling Endosomes]]&lt;br /&gt;
*[[Cell-Type Specific Transfection Protocols]]&lt;br /&gt;
*[[G418 &amp;amp; Puromycin Kill Curves|G418 &amp;amp;amp; Puromycin Kill Curves]]&lt;br /&gt;
*[[Apoptosis Detection with AnnexinV and PI]]&lt;br /&gt;
*[[Immuno-FISH]]&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Links to More Protocols =&lt;br /&gt;
{|width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== General Protocol Sites ====&lt;br /&gt;
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols &lt;br /&gt;
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols &lt;br /&gt;
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols &lt;br /&gt;
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols &lt;br /&gt;
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp;amp;amp; lab resourses. &lt;br /&gt;
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat &lt;br /&gt;
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp;amp;amp; Tips] - Microfluidics protocols &lt;br /&gt;
|&lt;br /&gt;
==== Free Science Ebooks ====&lt;br /&gt;
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]&lt;br /&gt;
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
= Useful Links =&lt;br /&gt;
{|width=&amp;quot;100%&amp;quot;&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Databases ====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences&lt;br /&gt;
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp;amp;amp; structure&lt;br /&gt;
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations&lt;br /&gt;
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification&lt;br /&gt;
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions&lt;br /&gt;
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes&lt;br /&gt;
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc&lt;br /&gt;
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes&lt;br /&gt;
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins&lt;br /&gt;
*[http://www.hprd.org/index_html Human Protein Reference Database]&lt;br /&gt;
*[http://www.wwpdb.org/ PDB] - Protein Structures&lt;br /&gt;
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor&lt;br /&gt;
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db&lt;br /&gt;
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database&lt;br /&gt;
|&lt;br /&gt;
==== Molecular Biology Tools ====&lt;br /&gt;
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]&lt;br /&gt;
*[http://ca.expasy.org/ ExPASy Tools]&lt;br /&gt;
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator&lt;br /&gt;
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]&lt;br /&gt;
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]&lt;br /&gt;
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]&lt;br /&gt;
*[http://www.addgene.org/ AddGene] - clone by e-mail!&lt;br /&gt;
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns&lt;br /&gt;
*[http://workbench.sdsc.edu/ Biology Workbench]&lt;br /&gt;
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]&lt;br /&gt;
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]&lt;br /&gt;
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]&lt;br /&gt;
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction&lt;br /&gt;
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure&lt;br /&gt;
|&lt;br /&gt;
===== Microscopy Tools =====&lt;br /&gt;
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]&lt;br /&gt;
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes&lt;br /&gt;
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job&lt;br /&gt;
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology&lt;br /&gt;
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other&lt;br /&gt;
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University&lt;br /&gt;
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment&lt;br /&gt;
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - &amp;lt;u&amp;gt;FREE&amp;lt;/u&amp;gt; imageJ based image processing program&lt;br /&gt;
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook&lt;br /&gt;
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]&lt;br /&gt;
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Journal Resources ====&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]&lt;br /&gt;
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]&lt;br /&gt;
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]&lt;br /&gt;
*[http://scholar.google.com Google Scholar]&lt;br /&gt;
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores&lt;br /&gt;
|&lt;br /&gt;
==== ''In Vivo'' Tools ====&lt;br /&gt;
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy&lt;br /&gt;
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes&amp;lt;br&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
==== Protease Tools ====&lt;br /&gt;
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database&lt;br /&gt;
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map&lt;br /&gt;
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction&lt;br /&gt;
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database&lt;br /&gt;
|&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
==== Genomics Resources ====&lt;br /&gt;
*[http://www.gwascentral.org GWAS Central]&lt;br /&gt;
|&lt;br /&gt;
==== Chemical Tools ====&lt;br /&gt;
&lt;br /&gt;
*[http://www.chemspider.com/ ChemSpider] - General chemistry database&lt;br /&gt;
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database&lt;br /&gt;
|&lt;br /&gt;
==== Lipid Tools ====&lt;br /&gt;
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''&lt;br /&gt;
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Titering_Pseudo-typed_Lentiviruses&amp;diff=114</id>
		<title>Titering Pseudo-typed Lentiviruses</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Titering_Pseudo-typed_Lentiviruses&amp;diff=114"/>
		<updated>2021-11-25T15:17:34Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: Created page with &amp;quot;-       for titering one “batch” of collected virus   '''Cell Seeding'''  1.     Seed 6 wells of a 12 well plate with 30 000 – 50 000 HeLas per well on coverslips   '''Transduction'''  1.     Prepare “transduction media” by mixing 6 µL of polybrene (1000X) in 6 mL of DMEM+10% FBS  2.     Remove media from the plate and replace with 900 µL of transduction media in each well  3.     Begin the serial dilution by adding 100 µL of virus to the first we...&amp;quot;&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;-       for titering one “batch” of collected virus&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Cell Seeding'''&lt;br /&gt;
&lt;br /&gt;
1.     Seed 6 wells of a 12 well plate with 30 000 – 50 000 HeLas per well on coverslips&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Transduction'''&lt;br /&gt;
&lt;br /&gt;
1.     Prepare “transduction media” by mixing 6 µL of polybrene (1000X) in 6 mL of DMEM+10% FBS&lt;br /&gt;
&lt;br /&gt;
2.     Remove media from the plate and replace with 900 µL of transduction media in each well&lt;br /&gt;
&lt;br /&gt;
3.     Begin the serial dilution by adding 100 µL of virus to the first well. There is often a vial set aside labelled as 10X diluted (the starting dilution will be a 100X dilution). Mix the contents of        the well by pipetting up and down, discard the pipette tip.&lt;br /&gt;
&lt;br /&gt;
4.     Using a new pipette tip take 100 µL out of the first well and add it to the second well, mix the contents of the well the same as before, discarding the pipette tip.&lt;br /&gt;
&lt;br /&gt;
5.     Continue the dilution series by adding 100 µL from the second well into the third well and mixing, followed by 100 µL from the third well into the fourth well and 100 µL from the fourth well to the fifth well. Mixing well and discarding the tips in between each well.&lt;br /&gt;
&lt;br /&gt;
6.     The last well is reserved for an untransduced control.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Preparing the cells for imaging'''&lt;br /&gt;
&lt;br /&gt;
1.     After 24-48 hours (48 hours is preferred) remove the media and wash the cells with PBS. This should be done in the biosafety cabinet.&lt;br /&gt;
&lt;br /&gt;
2.     Add 1 mL of 4% PFA to each well, incubate at RT for 20 min. After this step the plate may be removed from the biosafety cabinet.&lt;br /&gt;
&lt;br /&gt;
3.     Rinse wells with PBS and add 1 mL of 1:10 000 Hoechst in PBS to each well, incubate at RT for 10 minutes&lt;br /&gt;
&lt;br /&gt;
4.     Rinse 1-2 times with PBS&lt;br /&gt;
&lt;br /&gt;
5.     Mount on slides or image on the same day using a spaceship&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Imaging'''&lt;br /&gt;
&lt;br /&gt;
1.     Image each dilution on 40X magnification, using the blue channel for Hoechst, and the green for ZsGreen featuring viruses, take 5 images per dilution.&lt;br /&gt;
&lt;br /&gt;
2.     It is common to have very few positive cells on the 10 000X dilution and no positive cells on the 100 000X and 1 000 000X dilution. Stop imaging after you image a dilution that has 0 cells        transduced.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Calculating the viral titer'''&lt;br /&gt;
&lt;br /&gt;
-       there is an ImageJ script for counting the cells, however the thresholding it uses isn’t always appropriate&lt;br /&gt;
&lt;br /&gt;
-       Add the total number of cells counted and number of positive cells need to the appropriate columns in the &amp;quot;Lentivirus Titrations&amp;quot; spreadsheet, it will calculate the titer for you   &lt;br /&gt;
&lt;br /&gt;
For each dilution&lt;br /&gt;
&lt;br /&gt;
1.     Count all the nuclei on all five images (you can also stop at ~ 100 nuclei)&lt;br /&gt;
&lt;br /&gt;
2.     Count all the ZsGreen positive cells in all five images&lt;br /&gt;
&lt;br /&gt;
3.     Calculate the % positive  (# of green cells/# of nuclei X 100)&lt;br /&gt;
&lt;br /&gt;
4.     Calculate the titer of each dilution&lt;br /&gt;
&lt;br /&gt;
   Titer (TU/L) = (number of cells X percent of positive cells)/(volume in well X dilution factor)&lt;br /&gt;
&lt;br /&gt;
5.     Average the titers for each dilution where:  the percent positive is &amp;lt;30% and &amp;gt;0%. &lt;br /&gt;
&lt;br /&gt;
* The average titer is the one you will use for future MOI calculations&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
	<entry>
		<id>https://wiki.phagocytes.ca/index.php?title=Exit_Protocol&amp;diff=92</id>
		<title>Exit Protocol</title>
		<link rel="alternate" type="text/html" href="https://wiki.phagocytes.ca/index.php?title=Exit_Protocol&amp;diff=92"/>
		<updated>2021-09-13T13:42:45Z</updated>

		<summary type="html">&lt;p&gt;Akipp4: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;It is critical that members leaving the lab properly archive all materials so that they can be found and used by others.&amp;amp;nbsp; This is critical to the success of both yourself and the lab - misplaced data, constructs and cell lines can both slow research in the lab and lead to a loss of authorship.&amp;amp;nbsp; To ensure a smooth transition please follow these guidelines:&lt;br /&gt;
&lt;br /&gt;
#Ensure all data, manuscripts, figures, analysis files and any other computer documents that may be of use to the lab are copied into your folder on the lab server.&amp;amp;nbsp; All of these files should be stored here already (as per the [[ExpFile|File Storage]] standards), but make sure that all files on the server are present and up-to-date.&lt;br /&gt;
#Catalog all contents of 4, -20 and -80° boxes and move any samples into centralized lab boxes. Inform Dr. Heit or the Research Technician of the location of these items. If you are unsure of where to store items for long term, ask the Research Technician. Do not leave any personal storage boxes in these locations.   &lt;br /&gt;
#Ensure all [[Labbook|laboratory notebook]] entries are up-to-date and dated, the contents filled out properly, and all attached documents secured with archival-quality tape or staples.&lt;br /&gt;
#Deposit laboratory notebook with Dr. Heit.&amp;amp;nbsp; Feel free to make a copy for yourself.&amp;amp;nbsp; ORIGINAL COPIES OF THE LABORATORY NOTEBOOKS ARE LAB PROPERTY AND MUST NEVER BE REMOVED FROM THE LAB.&lt;br /&gt;
#Return any personal protective equipment (PPE) or other laboratory equipment purchased by the lab to the lab's central store&lt;br /&gt;
#Contact the necessary UWO offices to terminate your ID card, any grants/fellowships/studentships, and other university accounts.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Important note:''' not uncommon for data to be published years after the lab member who generated the data has left the lab.&amp;amp;nbsp; Please update your contact information with Dr. Heit for at least 5 years after leaving the lab to ensure you receive credit (i.e. authorship) for any articles produced from your data.&lt;/div&gt;</summary>
		<author><name>Akipp4</name></author>
	</entry>
</feed>