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= Index of Protocols =
= Index of Protocols =
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==== DNA/Cloning ====
==== DNA/Cloning ====


*[[Agarose Gels]]
*[[Colony PCR]]
*[[Colony PCR]]
*[[Gibson Assembly]]
*[[Ligation]]
*[[PCR]]
*[[PCR]]
*[[Digests]]
*[[Restriction Digest]]
*[[Ligation]]
*[[Gibson Assembly]]
*[[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'']]
*[[Transformation]]
*[[Neon® Transfection System]]
*[[Generating Minicircles]]
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==== Microscopy ====
|'''Transfections and Transductions'''
*[[Competition of Charged Molecules with Lipophilic Cations]]
* [[J774 Cell Transfection]]
*[[Immunostaining|Fluorescent Immunostaining]]
* [[Raw Cell Transfection]]
*[[Inhibition of Focal Contact Signaling]]
* [[THP1 Culture and Differentiation]]
*[[Single Particle Tracking]]
* [[Neon® Transfection System]]
*[[Staining for GSD]]
* [[Titering Pseudo-typed Lentiviruses]]
*[[Reducing Photobleaching]]
*[[Transduction of THP-1s]]
*[[Acid Washing Coverslips]]
*[[Nucleofector]]
*[[Live Cell FRET]]
*[[3D Printed PDMS Chambers]]
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==== General Protocols ====
==== General Protocols ====
*[[Antibiotics]]
*[[Antibiotic Plates]]
*[[Bacterial Growth Media]]
*[[Cell Culture Guidelines]]
*[[Common buffers|Common Buffers]]
*[[Common buffers|Common Buffers]]
*[[Cell Culture Guidelines]]
*[[Bacterial Growth Media]]
*[[Primary Macrophage Culture]]
*[[Freezing and Thawing Cells]]
*[[Freezing and Thawing Cells]]
*[[Raw Cell Transfection]]
*[[J774 Cell Transfection]]
*[[Antibiotics]]
*[[Antibiotic Plates]]
*[[Agarose Gels]]
*[[Water Bath Antibiotic Solution]]
*[[Water Bath Antibiotic Solution]]
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==== Protein work ====
==== Cell Biology ====
*[[Western Blotting]]
*[[Ablation of Recycling Endosomes]]
*[[Immunoprecipitation]]
*[[Apoptosis Detection with AnnexinV and PI]]
*[[Fab preparation]]
*[[Cell-Type Specific Transfection Protocols]]
*[[Fab Purification by FPLC|Fab purification using FPLC]]
*[[G418 & Puromycin Kill Curves|G418 & Puromycin Kill Curves]]
*[[Updated FPLC Size Exclusion Procedure]]
*[[Primary Human Macrophages]]
*[[Coomassie Staining]]
*[[Primary Macrophage Culture|Primary Murine Macrophages]]
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]
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*[[Stripping & Reprobing Blots|Stripping & Reprobing Blots]]
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==== Lipids ====
==== Lipids ====
*[[Asymmetric liposomes]]
*[[Asymmetric liposomes]]
*[[Lipid Coated Bead Preparation]]
*[[Lipid Extraction from Cells]]
*[[Lipid Extraction from Cells]]
'''Bead Preparation'''
*[[Lipisome and Lipid-Coated Beads]]
*[[Lipisome and Lipid-Coated Beads]]
*[[Lipid Coated Bead Preparation]]
*[[Opsonization]]
*[[Preparation of Silica-Magnetic Beads]]
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|'''Bacteria Work'''
 
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 & ZYCY10P3S2T)]]
*[[Generating Minicircles]]
*[[Inside-out Labelling of Bacteria]]
*[[Labelled E coli]]
*[[Preparation of Digestion-Tracking Bacteria]]
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]
*[[E. coli Transduction|Transducing ''E. coli'']]
*[[Transformation]]
 
==== Phagocytosis Protocols ====
==== Phagocytosis Protocols ====


*[[Opsonization]]
*[[Gentamicin Protection Assay]]
*[[Preparation of Silica-Magnetic Beads]]
*[[Phagosome Isolation]]
*[[Synchronised Phagocytosis]]
*[[Synchronised Phagocytosis]]
*[[Phagosome Isolation]]
*[[Primary Human Macrophages]]
*[[Labelled E coli]]
*[[Inside-out Labelling of Bacteria]]
*[[Gentamicin Protection Assay]]
*[[Preparation of Digestion-Tracking Bacteria]]
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==== Cell Biology ====
==== Protein Work ====
*[[Ablation of Recycling Endosomes]]
*[[Bradford Assay]]
*[[Cell-Type Specific Transfection Protocols]]
*[[Coomassie Staining]]
*[[G418 & Puromycin Kill Curves|G418 & Puromycin Kill Curves]]
*[[Fab preparation]]
*[[Apoptosis Detection with AnnexinV and PI]]
*[[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 & Reprobing Blots]]
*[[Updated FPLC Size Exclusion Procedure]]
*[[Western Blotting]]
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|'''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]]


*[[Micropatterning Proteins]]
*[[Frustrated Phagocytosis]]
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= Links to More Protocols =
= Links to More Protocols=
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==== General Protocol Sites ====
====General Protocol Sites====
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols  
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols
*[http://www.protocol-online.org/ Protocols Online] - large database of biology 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://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.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols & lab resourses.  
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols & lab resourses.
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat  
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips & Tips] - Microfluidics protocols  
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips & Tips] - Microfluidics protocols
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==== Free Science Ebooks ====
====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
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= Useful Links =
=Useful Links=
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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/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/refseq/rsg/ Pubmed RefSeq] - Find reference sequences
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*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database
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==== Molecular Biology Tools ====
==== Molecular Biology Tools====
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]
*[http://ca.expasy.org/ ExPASy Tools]
*[http://ca.expasy.org/ ExPASy Tools]
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*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure
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===== Microscopy Tools =====
=====Microscopy Tools=====  
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]
*[http://fbs.robarts.ca/ London Regional Microscopy Facility Bookings]
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes
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==== Journal Resources ====
====Journal Resources====
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]
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*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores
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==== ''In Vivo'' Tools ====
====''In Vivo'' Tools====
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes<br>
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes<br>
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==== Protease Tools ====
====Protease Tools====
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map
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==== Genomics Resources ====
====Genomics Resources====
*[http://www.gwascentral.org GWAS Central]
*[http://www.gwascentral.org GWAS Central]
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==== Chemical Tools ====
====Chemical Tools====


*[http://www.chemspider.com/ ChemSpider] - General chemistry database
*[http://www.chemspider.com/ ChemSpider] - General chemistry database
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database
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==== Lipid Tools ====
====Lipid Tools====
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids
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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"