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= Index of Protocols =
= Index of Protocols =
 
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==== Lab Operations ====
===== Lab Operations =====
*[[Entrance Protocol]]
 
*[[Exit Protocol]]
*[[Entrance Protocol|Entrance Protocol]]  
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]
*[[Exit Protocol|Exit Protocol]]  
*[[Saving Experimental Files|Proper Saving of Experimental Files]]
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]  
*[[Saving Experimental Files|Proper Saving of Experimental Files]]  
*[[Setting Up Network Drives|Setting up Access to Network Drives & Wiki]]
*[[Setting Up Network Drives|Setting up Access to Network Drives & Wiki]]
|
==== DNA/Cloning ====


<br>
*[[Agarose Gels]]
*[[Colony PCR]]
*[[Gibson Assembly]]
*[[Ligation]]
*[[PCR]]
*[[Restriction Digest]]
|
|'''Transfections and Transductions'''
* [[J774 Cell Transfection]]
* [[Raw Cell Transfection]]
* [[THP1 Culture and Differentiation]]
* [[Neon® Transfection System]]
* [[Titering Pseudo-typed Lentiviruses]]
*[[Transduction of THP-1s]]
*[[Nucleofector]]
|
|- style="vertical-align:top;"
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===== General Protocols =====
==== General Protocols ====
*[[Antibiotics]]
*[[Antibiotic Plates]]
*[[Bacterial Growth Media]]
*[[Cell Culture Guidelines]]
*[[Common buffers|Common Buffers]]
*[[Freezing and Thawing Cells]]
*[[Water Bath Antibiotic Solution]]
|
==== Cell Biology ====
*[[Ablation of Recycling Endosomes]]
*[[Apoptosis Detection with AnnexinV and PI]]
*[[Cell-Type Specific Transfection Protocols]]
*[[G418 & Puromycin Kill Curves|G418 &amp; Puromycin Kill Curves]]
*[[Primary Human Macrophages]]
*[[Primary Macrophage Culture|Primary Murine Macrophages]]
|
|
==== Lipids ====
*[[Asymmetric liposomes]]
*[[Lipid Extraction from Cells]]


*[[Common buffers|Common Buffers]]
'''Bead Preparation'''
*[[Cell Culture Guidelines|Cell Culture Guidelines]]
*[[Bacterial Growth Media|Bacterial Growth Media]]
*[[Primary Macrophage Culture|Primary Macrophage Culture]]
*[[Freezing and Thawing Cells|Freezing and Thawing Cells]]
*[[Raw Cell Transfection|Raw Cell Transfection]]
*[[J774 Cell Transfection|J774 Cell Transfection]]
*[[Antibiotics|Antibiotics]]
*[[Antibiotic Plates|Antibiotic Plates]]
*[[Agarose Gels|Agarose Gels]]
*[[Water Bath Antibiotic Solution|Water Bath Antibiotic Solution]]


<br>
*[[Lipisome and Lipid-Coated Beads]]
*[[Lipid Coated Bead Preparation]]
*[[Opsonization]]
*[[Preparation of Silica-Magnetic Beads]]
|
|- style="vertical-align:top;"
|'''Bacteria Work'''


===== Phagocytosis Protocols =====
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 & ZYCY10P3S2T)]]
 
*[[Generating Minicircles]]
*[[Opsonization|Opsonization]]
*[[Inside-out Labelling of Bacteria]]
*[[Preparation of Silica-Magnetic Beads|Preparation of Silica-Magnetic Beads]]
*[[Labelled E coli]]
*[[Synchronised Phagocytosis|Synchronised Phagocytosis]]  
*[[Phagosome Isolation|Phagosome Isolation]]
*[[Primary Human Macrophages|Primary Human Macrophages]]
*[[Labelled E coli|Labelled E coli]]  
*[[Inside-out Labelling of Bacteria|Inside-out Labelling of Bacteria]]  
*[[Gentamicin Protection Assay|Gentamicin Protection Assay]]  
*[[Preparation of Digestion-Tracking Bacteria]]
*[[Preparation of Digestion-Tracking Bacteria]]
|
===== DNA/Cloning =====
*[[Colony PCR|Colony PCR]]
*[[PCR|PCR]]
*[[Digests|Digests]]
*[[Ligation|Ligation]]
*[[Gibson Assembly|Gibson Assembly]]
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 & ZYCY10P3S2T)]]
*[[E. coli Transduction|Transducing ''E. coli'']]
*[[E. coli Transduction|Transducing ''E. coli'']]
*[[Transformation|Transformation]]
*[[Transformation]]
*[[Neon® Transfection System|Neon® Transfection System]]
*[[Generating Minicircles|Generating Minicircles]]
<br>


===== Protein work =====
==== Phagocytosis Protocols ====
 
*[[Western Blotting|Western Blotting]]
*[[Immunoprecipitation|Immunoprecipitation]]
*[[Fab preparation|Fab preparation]]
*[[Fab Purification by FPLC|Fab purification using FPLC]]
*[[Updated FPLC Size Exclusion Procedure|Updated FPLC Size Exclusion Procedure]]
*[[Coomassie Staining|Coomassie Staining]]
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]
*[[Stripping & Reprobing Blots|Stripping &amp; Reprobing Blots]]
 
<br>
 
===== Cell Biology<br> =====
 
*[[Ablation of Recycling Endosomes|Ablation of Recycling Endosomes]]
*[[Cell-Type Specific Transfection Protocols|Cell-Type Specific Transfection Protocols]]
*[[G418 & Puromycin Kill Curves|G418 &amp; Puromycin Kill Curves]]
*[[Apoptosis Detection with AnnexinV and PI|Apoptosis Detection with AnnexinV and PI]]


*[[Gentamicin Protection Assay]]
*[[Phagosome Isolation]]
*[[Synchronised Phagocytosis]]
|
==== Protein Work ====
*[[Bradford Assay]]
*[[Coomassie Staining]]
*[[Fab preparation]]
*[[Fab Purification by FPLC|Fab purification using FPLC]]
*[[Immunoprecipitation]]
*[[Nitrogen Cavitation]]
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]
*[[Stripping & Reprobing Blots|Stripping &amp; Reprobing Blots]]
*[[Updated FPLC Size Exclusion Procedure]]
*[[Western Blotting]]
|
|
|'''Microscopy'''
*[[3D Printed PDMS Chambers]]
*[[Acid Washing Coverslips]]
*[[Competition of Charged Molecules with Lipophilic Cations]]
*[[Immunostaining|Fluorescent Immunostaining]]
*[[FRET in FIJI]]
*[[Inhibition of Focal Contact Signaling]]
*[[Immuno-FISH]]
*[[Live Cell FRET]] [[Nucleofector|(depreciated)]]
*[[Reducing Photobleaching]]
*[[Single Particle Tracking]]
*[[Staining for GSD]]
*[[Traction Force Microscopy]]
*[[3D Printed Microscopy Chambers]]


===== Microscopy =====
*[[Micropatterning Proteins]]
 
*[[Frustrated Phagocytosis]]
*[[Competition of Charged Molecules with Lipophilic Cations|Competition of Charged Molecules with Lipophilic Cations]]
*[[Immunostaining|Fluorescent Immunostaining]]  
*[[Inhibition of Focal Contact Signaling|Inhibition of Focal Contact Signaling]]
*[[Single Particle Tracking|Single Particle Tracking]]
*[[Staining for GSD|Staining for GSD]]
*[[Reducing Photobleaching|Reducing Photobleaching]]
*[[Acid Washing Coverslips|Acid Washing Coverslips]]
*[[Live Cell FRET|Live Cell FRET]]
*[[3D Printed PDMS Chambers|3D Printed PDMS Chambers]]
 
===== Lipids =====
 
*[[Asymmetric liposomes|Asymmetric liposomes]]
*[[Lipid Coated Bead Preparation]]
*[[Lipid Extraction from Cells|Lipid Extraction from Cells]]
*[[Lipisome and Lipid-Coated Beads|Lipisome and Lipid-Coated Beads]]<br>
 
 
|}
|}
<hr>
= Links to More Protocols =
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===== General Protocol Sites =====
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp; lab resourses.
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp; Tips] - Microfluidics protocols


= Links to More Protocols=
{| width="100%"
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===== Free Science Ebooks =====
====General Protocol Sites====
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp; lab resourses.
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp; Tips] - Microfluidics protocols
|
====Free Science Ebooks====
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required
|}
|}


= Useful Links =
=Useful Links=
 
{| width="100%"
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====Molecular Biology Databases====
===== Molecular Biology Databases =====
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information
 
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information<br>
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp; structure
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences<br>
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp; structure<br>
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms<br>
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations<br>
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification  
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions<br>
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes<br>
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc<br>
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes<br>
*[http://www.hprd.org/index_html Human Protein Reference Database]
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins<br>
*[http://www.wwpdb.org/ PDB] - Protein Structures
*[http://www.hprd.org/index_html Human Protein Reference Database]<br>
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor
*[http://www.wwpdb.org/ PDB] - Protein Structures<br>
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor  
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db  
|
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database<br>  
==== Molecular Biology Tools====
 
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]
<br>
*[http://ca.expasy.org/ ExPASy Tools]
 
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator
===== Journal Resources<br> =====
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]
 
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]  
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]  
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]  
*[http://www.addgene.org/ AddGene] - clone by e-mail!
*[http://scholar.google.com Google Scholar]  
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores  
*[http://workbench.sdsc.edu/ Biology Workbench]
 
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]
<br>
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]
 
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]
===== Genomics Resources<br> =====
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure
|
=====Microscopy Tools=====
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - <u>FREE</u> imageJ based image processing program
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets
|
|- style="vertical-align:top;"
|
====Journal Resources====
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]
*[http://scholar.google.com Google Scholar]
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores
|
====''In Vivo'' Tools====
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes<br>
|
====Protease Tools====
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database
|
|- style="vertical-align:top;"
|
====Genomics Resources====
*[http://www.gwascentral.org GWAS Central]
*[http://www.gwascentral.org GWAS Central]
|
====Chemical Tools====


|
*[http://www.chemspider.com/ ChemSpider] - General chemistry database
===== Molecular Biology Tools =====
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database
 
|
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]
====Lipid Tools====
*[http://ca.expasy.org/ ExPASy Tools]<br>
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator<br>
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]<br>
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]<br>
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]<br>
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]
*[http://www.addgene.org/ AddGene] - clone by e-mail!
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns
*[http://workbench.sdsc.edu/ Biology Workbench]<br>
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]<br>
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]<br>
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]<br>
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]<br>
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]<br>
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction<br>
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure<br>
 
<br>
 
===== ''In Vivo'' Tools<br> =====
 
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy<br>
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes<br>
 
|  
===== Microscopy Tools =====
 
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes<br>
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology<br>
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment<br>
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - <u>FREE</u> imageJ based image processing program
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]<br>
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets
 
<br>
 
===== Protease Tools =====
 
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database
 
<br>
 
===== Lipid Tools =====
 
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''  
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids  
 
<br>
 
===== Chemical Tools =====
 
*[http://www.chemspider.com/ ChemSpider] - General chemistry database
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database
 
<br>
 
<br>
 
|}
|}
<br>

Latest revision as of 18:50, 17 January 2025

Visit our Lab's Webpage at www.phagocytes.ca

Welcome to the protocol wiki for the lab of Dr. Bryan Heit, at the University of Western Ontario. This site contains the protocols, and other information, we frequently use in our lab.  Only laboratory members may edit pages, but anyone is welcome to use these protocols.  If you use these protocol, please cite us.  A link for generating citations can be found on the left side of the page.


Consult the User's Guide for information on using the wiki software.

Lab members:


Index of Protocols

Lab Operations

DNA/Cloning

 Transfections and Transductions

General Protocols

Cell Biology

Lipids

Bead Preparation

Bacteria Work

Phagocytosis Protocols

Protein Work

 Microscopy

Links to More Protocols

General Protocol Sites

Free Science Ebooks

Useful Links

Molecular Biology Databases

Molecular Biology Tools
Microscopy Tools

Journal Resources

In Vivo Tools

Protease Tools

  • MEROPS - Peptidase database
  • PMAP - Proteolysis Map
  • CASVM - Caspace substrate prediction
  • CASBAH - Caspase cleaveage site database

Genomics Resources

Chemical Tools

Lipid Tools

Retrieved from "https://wiki.phagocytes.ca/index.php?title=Main_Page&oldid=251"