Heit Lab Wiki - User contributions [en]

Main Page

2021-02-04T13:25:15Z

Bheit:

[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]
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.  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 [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software. 

'''''Lab members:'''''

*To get a wiki account please contact Dr. Heit.
*Log in (upper-right side of screen) to add/edit pages.  
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols.
*To create a new page, [[Create new|follow these instructions]].

 

= Index of Protocols =
{|width="100%"
|- style="vertical-align:top;"
|
==== Lab Operations ====
*[[Entrance Protocol]]
*[[Exit Protocol]]
*[[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]]
|
==== DNA/Cloning ====

*[[Colony PCR]]
*[[PCR]]
*[[Digests]]
*[[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]]
|
==== Microscopy ====
*[[Competition of Charged Molecules with Lipophilic Cations]]
*[[Immunostaining|Fluorescent Immunostaining]]
*[[Inhibition of Focal Contact Signaling]]
*[[Single Particle Tracking]]
*[[Staining for GSD]]
*[[Reducing Photobleaching]]
*[[Acid Washing Coverslips]]
*[[Live Cell FRET]]
*[[3D Printed PDMS Chambers]]
|
|- style="vertical-align:top;"
|
==== General Protocols ====
*[[Common buffers|Common Buffers]]
*[[Cell Culture Guidelines]]
*[[Bacterial Growth Media]]
*[[Primary Macrophage Culture]]
*[[Freezing and Thawing Cells]]
*[[Raw Cell Transfection]]
*[[J774 Cell Transfection]]
*[[Antibiotics]]
*[[Antibiotic Plates]]
*[[Agarose Gels]]
*[[Water Bath Antibiotic Solution]]
|
==== Protein work ====
*[[Western Blotting]]
*[[Immunoprecipitation]]
*[[Fab preparation]]
*[[Fab Purification by FPLC|Fab purification using FPLC]]
*[[Updated FPLC Size Exclusion Procedure]]
*[[Coomassie Staining]]
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]
*[[Stripping & Reprobing Blots|Stripping & Reprobing Blots]]
|
==== Lipids ====
*[[Asymmetric liposomes]]
*[[Lipid Coated Bead Preparation]]
*[[Lipid Extraction from Cells]]
*[[Lipisome and Lipid-Coated Beads]]
|
|- style="vertical-align:top;"
|
==== Phagocytosis Protocols ====

*[[Opsonization]]
*[[Preparation of Silica-Magnetic Beads]]
*[[Synchronised Phagocytosis]]
*[[Phagosome Isolation]]
*[[Primary Human Macrophages]]
*[[Labelled E coli]]
*[[Inside-out Labelling of Bacteria]]
*[[Gentamicin Protection Assay]]
*[[Preparation of Digestion-Tracking Bacteria]]
|
==== Cell Biology ====
*[[Ablation of Recycling Endosomes]]
*[[Cell-Type Specific Transfection Protocols]]
*[[G418 & Puromycin Kill Curves|G418 & Puromycin Kill Curves]]
*[[Apoptosis Detection with AnnexinV and PI]]

|}

= Links to More Protocols =
{|width="100%"
|- style="vertical-align:top;"
|
==== 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 & 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 & Tips] - Microfluidics protocols
|
==== Free Science Ebooks ====
*[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

|}

= Useful Links =
{|width="100%"
|- style="vertical-align:top;"
|
==== 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.uniprot.org/ Uniprot] - Find protein sequence & structure
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins
*[http://www.hprd.org/index_html Human Protein Reference Database]
*[http://www.wwpdb.org/ PDB] - Protein Structures
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database
|
==== Molecular Biology Tools ====
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]
*[http://ca.expasy.org/ ExPASy Tools]
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]
*[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]
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]
*[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://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] - FREE 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 
|
==== 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]
|
==== Chemical Tools ====

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

Main Page

2021-02-04T13:17:50Z

Bheit:

[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]
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.  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 [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software. 

'''''Lab members:'''''

*To get a wiki account please contact Dr. Heit.
*Log in (upper-right side of screen) to add/edit pages.  
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols.
*To create a new page, [[Create new|follow these instructions]].

 

= Index of Protocols =
{|width="100%"
|- style="vertical-align:top;"
|
==== Lab Operations ====
*[[Entrance Protocol]]
*[[Exit Protocol]]
*[[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]]
|
==== DNA/Cloning ====

*[[Colony PCR]]
*[[PCR]]
*[[Digests]]
*[[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]]
|
==== Microscopy ====
*[[Competition of Charged Molecules with Lipophilic Cations]]
*[[Immunostaining|Fluorescent Immunostaining]]
*[[Inhibition of Focal Contact Signaling]]
*[[Single Particle Tracking]]
*[[Staining for GSD]]
*[[Reducing Photobleaching]]
*[[Acid Washing Coverslips]]
*[[Live Cell FRET]]
*[[3D Printed PDMS Chambers]]
|
|- style="vertical-align:top;"
|
==== General Protocols ====
*[[Common buffers|Common Buffers]]
*[[Cell Culture Guidelines]]
*[[Bacterial Growth Media]]
*[[Primary Macrophage Culture]]
*[[Freezing and Thawing Cells]]
*[[Raw Cell Transfection]]
*[[J774 Cell Transfection]]
*[[Antibiotics]]
*[[Antibiotic Plates]]
*[[Agarose Gels]]
*[[Water Bath Antibiotic Solution]]
|
==== Protein work ====
*[[Western Blotting]]
*[[Immunoprecipitation]]
*[[Fab preparation]]
*[[Fab Purification by FPLC|Fab purification using FPLC]]
*[[Updated FPLC Size Exclusion Procedure]]
*[[Coomassie Staining]]
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]
*[[Stripping & Reprobing Blots|Stripping & Reprobing Blots]]
|
==== Lipids ====
*[[Asymmetric liposomes]]
*[[Lipid Coated Bead Preparation]]
*[[Lipid Extraction from Cells]]
*[[Lipisome and Lipid-Coated Beads]]
|
|- style="vertical-align:top;"
|
==== Phagocytosis Protocols ====

*[[Opsonization]]
*[[Preparation of Silica-Magnetic Beads]]
*[[Synchronised Phagocytosis]]
*[[Phagosome Isolation]]
*[[Primary Human Macrophages]]
*[[Labelled E coli]]
*[[Inside-out Labelling of Bacteria]]
*[[Gentamicin Protection Assay]]
*[[Preparation of Digestion-Tracking Bacteria]]
|
==== Cell Biology ====
*[[Ablation of Recycling Endosomes]]
*[[Cell-Type Specific Transfection Protocols]]
*[[G418 & Puromycin Kill Curves|G418 & Puromycin Kill Curves]]
*[[Apoptosis Detection with AnnexinV and PI]]

|}

= Links to More Protocols =
{|width="100%"
|- style="vertical-align:top;"
|
==== 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 & 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 & Tips] - Microfluidics protocols
|
==== Free Science Ebooks ====
*[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

|}

= Useful Links =

{| width="100%" cellspacing="1" cellpadding="1" border="0"
|- valign="top"
|
===== 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.uniprot.org/ Uniprot] - Find protein sequence & structure 
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms 
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations 
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions 
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes 
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc 
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes 
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins 
*[http://www.hprd.org/index_html Human Protein Reference Database] 
*[http://www.wwpdb.org/ PDB] - Protein Structures 
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database 

 

===== 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

 

===== Genomics Resources =====
*[http://www.gwascentral.org GWAS Central]

|
===== Molecular Biology Tools =====

*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]
*[http://ca.expasy.org/ ExPASy Tools] 
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator 
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter] 
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers] 
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence] 
*[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] 
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools] 
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder] 
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher] 
*[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 

 

===== ''In Vivo'' Tools =====

*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy 
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes 

|
===== Microscopy Tools =====

*[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] - FREE 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

 

===== 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

 

===== Lipid Tools =====

*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids

 

===== Chemical Tools =====

*[http://www.chemspider.com/ ChemSpider] - General chemistry database
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database

 

 

|}

Main Page

2021-02-04T13:14:41Z

Bheit:

[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]
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.  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 [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software. 

'''''Lab members:'''''

*To get a wiki account please contact Dr. Heit.
*Log in (upper-right side of screen) to add/edit pages.  
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols.
*To create a new page, [[Create new|follow these instructions]].

 

= Index of Protocols =
{|width="100%"
|- style="vertical-align:top;"
|
==== Lab Operations ====
*[[Entrance Protocol]]
*[[Exit Protocol]]
*[[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]]
|
==== DNA/Cloning ====

*[[Colony PCR]]
*[[PCR]]
*[[Digests]]
*[[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]]
|
==== Microscopy ====
*[[Competition of Charged Molecules with Lipophilic Cations]]
*[[Immunostaining|Fluorescent Immunostaining]]
*[[Inhibition of Focal Contact Signaling]]
*[[Single Particle Tracking]]
*[[Staining for GSD]]
*[[Reducing Photobleaching]]
*[[Acid Washing Coverslips]]
*[[Live Cell FRET]]
*[[3D Printed PDMS Chambers]]
|
|- style="vertical-align:top;"
|
==== General Protocols ====
*[[Common buffers|Common Buffers]]
*[[Cell Culture Guidelines]]
*[[Bacterial Growth Media]]
*[[Primary Macrophage Culture]]
*[[Freezing and Thawing Cells]]
*[[Raw Cell Transfection]]
*[[J774 Cell Transfection]]
*[[Antibiotics]]
*[[Antibiotic Plates]]
*[[Agarose Gels]]
*[[Water Bath Antibiotic Solution]]
|
==== Protein work ====
*[[Western Blotting]]
*[[Immunoprecipitation]]
*[[Fab preparation]]
*[[Fab Purification by FPLC|Fab purification using FPLC]]
*[[Updated FPLC Size Exclusion Procedure]]
*[[Coomassie Staining]]
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]
*[[Stripping & Reprobing Blots|Stripping & Reprobing Blots]]
|
==== Lipids ====
*[[Asymmetric liposomes]]
*[[Lipid Coated Bead Preparation]]
*[[Lipid Extraction from Cells]]
*[[Lipisome and Lipid-Coated Beads]]
|
|- style="vertical-align:top;"
|
==== Phagocytosis Protocols ====

*[[Opsonization]]
*[[Preparation of Silica-Magnetic Beads]]
*[[Synchronised Phagocytosis]]
*[[Phagosome Isolation]]
*[[Primary Human Macrophages]]
*[[Labelled E coli]]
*[[Inside-out Labelling of Bacteria]]
*[[Gentamicin Protection Assay]]
*[[Preparation of Digestion-Tracking Bacteria]]
|
==== Cell Biology ====
*[[Ablation of Recycling Endosomes]]
*[[Cell-Type Specific Transfection Protocols]]
*[[G418 & Puromycin Kill Curves|G418 & Puromycin Kill Curves]]
*[[Apoptosis Detection with AnnexinV and PI]]

|}

= Links to More Protocols =
{| width="100%" cellspacing="1" cellpadding="1" border="0" align="left"
|- valign="top"
|
===== 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 & 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 & Tips] - Microfluidics protocols

|
===== Free Science Ebooks =====
*[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
|}

= Useful Links =

{| width="100%" cellspacing="1" cellpadding="1" border="0"
|- valign="top"
|
===== 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.uniprot.org/ Uniprot] - Find protein sequence & structure 
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms 
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations 
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions 
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes 
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc 
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes 
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins 
*[http://www.hprd.org/index_html Human Protein Reference Database] 
*[http://www.wwpdb.org/ PDB] - Protein Structures 
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database 

 

===== 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

 

===== Genomics Resources =====
*[http://www.gwascentral.org GWAS Central]

|
===== Molecular Biology Tools =====

*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]
*[http://ca.expasy.org/ ExPASy Tools] 
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator 
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter] 
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers] 
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence] 
*[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] 
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools] 
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder] 
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher] 
*[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 

 

===== ''In Vivo'' Tools =====

*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy 
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes 

|
===== Microscopy Tools =====

*[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] - FREE 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

 

===== 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

 

===== Lipid Tools =====

*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids

 

===== Chemical Tools =====

*[http://www.chemspider.com/ ChemSpider] - General chemistry database
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database

 

 

|}

Main Page

2021-02-04T13:05:34Z

Bheit:

[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]
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.  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 [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software. 

'''''Lab members:'''''

*To get a wiki account please contact Dr. Heit.
*Log in (upper-right side of screen) to add/edit pages.  
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols.
*To create a new page, [[Create new|follow these instructions]].

 

= Index of Protocols =
{|
|
==== Lab Operations ====
*[[Entrance Protocol]]
*[[Exit Protocol]]
*[[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]]
|
==== DNA/Cloning ====

*[[Colony PCR]]
*[[PCR]]
*[[Digests]]
*[[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]]
|
==== Microscopy ====
*[[Competition of Charged Molecules with Lipophilic Cations]]
*[[Immunostaining|Fluorescent Immunostaining]]
*[[Inhibition of Focal Contact Signaling]]
*[[Single Particle Tracking]]
*[[Staining for GSD]]
*[[Reducing Photobleaching]]
*[[Acid Washing Coverslips]]
*[[Live Cell FRET]]
*[[3D Printed PDMS Chambers]]
|
|-
|
==== General Protocols ====
*[[Common buffers|Common Buffers]]
*[[Cell Culture Guidelines]]
*[[Bacterial Growth Media]]
*[[Primary Macrophage Culture]]
*[[Freezing and Thawing Cells]]
*[[Raw Cell Transfection]]
*[[J774 Cell Transfection]]
*[[Antibiotics]]
*[[Antibiotic Plates]]
*[[Agarose Gels]]
*[[Water Bath Antibiotic Solution]]
|
==== Protein work ====
*[[Western Blotting]]
*[[Immunoprecipitation]]
*[[Fab preparation]]
*[[Fab Purification by FPLC|Fab purification using FPLC]]
*[[Updated FPLC Size Exclusion Procedure]]
*[[Coomassie Staining]]
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]
*[[Stripping & Reprobing Blots|Stripping & Reprobing Blots]]
|
==== Lipids ====
*[[Asymmetric liposomes]]
*[[Lipid Coated Bead Preparation]]
*[[Lipid Extraction from Cells]]
*[[Lipisome and Lipid-Coated Beads]]
|
|-
|
==== Phagocytosis Protocols ====

*[[Opsonization]]
*[[Preparation of Silica-Magnetic Beads]]
*[[Synchronised Phagocytosis]]
*[[Phagosome Isolation]]
*[[Primary Human Macrophages]]
*[[Labelled E coli]]
*[[Inside-out Labelling of Bacteria]]
*[[Gentamicin Protection Assay]]
*[[Preparation of Digestion-Tracking Bacteria]]
|
==== Cell Biology ====
*[[Ablation of Recycling Endosomes]]
*[[Cell-Type Specific Transfection Protocols]]
*[[G418 & Puromycin Kill Curves|G418 & Puromycin Kill Curves]]
*[[Apoptosis Detection with AnnexinV and PI]]
|
|
|-
|
|
|
|
|}
{| width="100%" cellspacing="1" cellpadding="1" border="0" align="left"
|- valign="top"
|
===== Lab Operations =====

*[[Entrance Protocol|Entrance Protocol]]
*[[Exit Protocol|Exit Protocol]]
*[[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]]

 

===== General Protocols =====

*[[Common buffers|Common Buffers]]
*[[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]]

 

===== Phagocytosis Protocols =====

*[[Opsonization|Opsonization]]
*[[Preparation of Silica-Magnetic Beads|Preparation of Silica-Magnetic Beads]]
*[[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]]
 
|

===== 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)]]
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 & ZYCY10P3S2T)]]
*[[E. coli Transduction|Transducing ''E. coli'']]
*[[Transformation|Transformation]]
*[[Neon® Transfection System|Neon® Transfection System]]
*[[Generating Minicircles|Generating Minicircles]]
 

===== Protein work =====

*[[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 & Reprobing Blots]]

 

===== Cell Biology =====

*[[Ablation of Recycling Endosomes|Ablation of Recycling Endosomes]]
*[[Cell-Type Specific Transfection Protocols|Cell-Type Specific Transfection Protocols]]
*[[G418 & Puromycin Kill Curves|G418 & Puromycin Kill Curves]]
*[[Apoptosis Detection with AnnexinV and PI|Apoptosis Detection with AnnexinV and PI]]
 
|

===== Microscopy =====

*[[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]] 
 

|}
 
----
 
= Links to More Protocols =
{| width="100%" cellspacing="1" cellpadding="1" border="0" align="left"
|- valign="top"
|
===== 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 & 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 & Tips] - Microfluidics protocols

|
===== Free Science Ebooks =====
*[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
|}

= Useful Links =

{| width="100%" cellspacing="1" cellpadding="1" border="0"
|- valign="top"
|
===== 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.uniprot.org/ Uniprot] - Find protein sequence & structure 
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms 
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations 
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions 
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes 
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc 
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes 
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins 
*[http://www.hprd.org/index_html Human Protein Reference Database] 
*[http://www.wwpdb.org/ PDB] - Protein Structures 
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database 

 

===== 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

 

===== Genomics Resources =====
*[http://www.gwascentral.org GWAS Central]

|
===== Molecular Biology Tools =====

*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]
*[http://ca.expasy.org/ ExPASy Tools] 
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator 
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter] 
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers] 
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence] 
*[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] 
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools] 
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder] 
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher] 
*[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 

 

===== ''In Vivo'' Tools =====

*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy 
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes 

|
===== Microscopy Tools =====

*[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] - FREE 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

 

===== 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

 

===== Lipid Tools =====

*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids

 

===== Chemical Tools =====

*[http://www.chemspider.com/ ChemSpider] - General chemistry database
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database

 

 

|}

Main Page

2021-02-04T12:54:58Z

Bheit:

[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]
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.  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 [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software. 

'''''Lab members:'''''

*To get a wiki account please contact Dr. Heit.
*Log in (upper-right side of screen) to add/edit pages.  
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols.
*To create a new page, [[Create new|follow these instructions]].

 

= Index of Protocols =

{| width="100%" cellspacing="1" cellpadding="1" border="0" align="left"
|- valign="top"
|
===== Lab Operations =====

*[[Entrance Protocol|Entrance Protocol]]
*[[Exit Protocol|Exit Protocol]]
*[[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]]

 

===== General Protocols =====

*[[Common buffers|Common Buffers]]
*[[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]]

 

===== Phagocytosis Protocols =====

*[[Opsonization|Opsonization]]
*[[Preparation of Silica-Magnetic Beads|Preparation of Silica-Magnetic Beads]]
*[[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]]
 
|

===== 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)]]
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 & ZYCY10P3S2T)]]
*[[E. coli Transduction|Transducing ''E. coli'']]
*[[Transformation|Transformation]]
*[[Neon® Transfection System|Neon® Transfection System]]
*[[Generating Minicircles|Generating Minicircles]]
 

===== Protein work =====

*[[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 & Reprobing Blots]]

 

===== Cell Biology =====

*[[Ablation of Recycling Endosomes|Ablation of Recycling Endosomes]]
*[[Cell-Type Specific Transfection Protocols|Cell-Type Specific Transfection Protocols]]
*[[G418 & Puromycin Kill Curves|G418 & Puromycin Kill Curves]]
*[[Apoptosis Detection with AnnexinV and PI|Apoptosis Detection with AnnexinV and PI]]
 
|

===== Microscopy =====

*[[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]] 
 

|}
 
----
 
= Links to More Protocols =
{| width="100%" cellspacing="1" cellpadding="1" border="0" align="left"
|- valign="top"
|
===== 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 & 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 & Tips] - Microfluidics protocols

|
===== Free Science Ebooks =====
*[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
|}

= Useful Links =

{| width="100%" cellspacing="1" cellpadding="1" border="0"
|- valign="top"
|
===== 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.uniprot.org/ Uniprot] - Find protein sequence & structure 
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms 
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations 
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions 
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes 
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc 
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes 
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins 
*[http://www.hprd.org/index_html Human Protein Reference Database] 
*[http://www.wwpdb.org/ PDB] - Protein Structures 
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database 

 

===== 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

 

===== Genomics Resources =====
*[http://www.gwascentral.org GWAS Central]

|
===== Molecular Biology Tools =====

*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]
*[http://ca.expasy.org/ ExPASy Tools] 
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator 
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter] 
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers] 
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence] 
*[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] 
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools] 
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder] 
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher] 
*[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 

 

===== ''In Vivo'' Tools =====

*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy 
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes 

|
===== Microscopy Tools =====

*[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] - FREE 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

 

===== 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

 

===== Lipid Tools =====

*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids

 

===== Chemical Tools =====

*[http://www.chemspider.com/ ChemSpider] - General chemistry database
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database

 

 

|}

Main Page

2021-02-04T12:52:29Z

Bheit:

[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]
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.  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 [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software. 

'''''Lab members:'''''

*To get a wiki account please contact Dr. Heit.
*Log in (upper-right side of screen) to add/edit pages.  
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols.
*To create a new page, [[Create new|follow these instructions]].

 

= Index of Protocols =

{| width="100%" cellspacing="1" cellpadding="1" border="0" align="left"
|- valign="top"
|
===== Lab Operations =====

*[[Entrance Protocol|Entrance Protocol]]
*[[Exit Protocol|Exit Protocol]]
*[[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]]

 

===== General Protocols =====

*[[Common buffers|Common Buffers]]
*[[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]]

 

===== Phagocytosis Protocols =====

*[[Opsonization|Opsonization]]
*[[Preparation of Silica-Magnetic Beads|Preparation of Silica-Magnetic Beads]]
*[[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]]

|

===== 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)]]
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 & ZYCY10P3S2T)]]
*[[E. coli Transduction|Transducing ''E. coli'']]
*[[Transformation|Transformation]]
*[[Neon® Transfection System|Neon® Transfection System]]
*[[Generating Minicircles|Generating Minicircles]]
 

===== Protein work =====

*[[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 & Reprobing Blots]]

 

===== Cell Biology =====

*[[Ablation of Recycling Endosomes|Ablation of Recycling Endosomes]]
*[[Cell-Type Specific Transfection Protocols|Cell-Type Specific Transfection Protocols]]
*[[G418 & Puromycin Kill Curves|G418 & Puromycin Kill Curves]]
*[[Apoptosis Detection with AnnexinV and PI|Apoptosis Detection with AnnexinV and PI]]

|

===== Microscopy =====

*[[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]] 

|}
<hr>
= Links to More Protocols =
{| width="100%" cellspacing="1" cellpadding="1" border="0" align="left"
|- valign="top"
|
===== 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 & 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 & Tips] - Microfluidics protocols

|
===== Free Science Ebooks =====
*[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
|}

= Useful Links =

{| width="100%" cellspacing="1" cellpadding="1" border="0"
|- valign="top"
|
===== 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.uniprot.org/ Uniprot] - Find protein sequence & structure 
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms 
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations 
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions 
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes 
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc 
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes 
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins 
*[http://www.hprd.org/index_html Human Protein Reference Database] 
*[http://www.wwpdb.org/ PDB] - Protein Structures 
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database 

 

===== 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

 

===== Genomics Resources =====
*[http://www.gwascentral.org GWAS Central]

|
===== Molecular Biology Tools =====

*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]
*[http://ca.expasy.org/ ExPASy Tools] 
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator 
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter] 
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers] 
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence] 
*[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] 
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools] 
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder] 
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher] 
*[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 

 

===== ''In Vivo'' Tools =====

*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy 
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes 

|
===== Microscopy Tools =====

*[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] - FREE 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

 

===== 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

 

===== Lipid Tools =====

*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids

 

===== Chemical Tools =====

*[http://www.chemspider.com/ ChemSpider] - General chemistry database
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database

 

 

|}

Main Page

2021-02-04T12:50:50Z

Bheit:

[[File:PnW.png|thumb|300x300px|Visit our Lab's Webpage at [http://www.phagocytes.ca www.phagocytes.ca]]]
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.  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 [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software. 

'''''Lab members:'''''

*To get a wiki account please contact Dr. Heit.
*Log in (upper-right side of screen) to add/edit pages.  
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols.
*To create a new page, [[Create new|follow these instructions]].

 

= Index of Protocols =

{| width="100%" cellspacing="1" cellpadding="1" border="0" align="left"
|- valign="top"
|
===== Lab Operations =====

*[[Entrance Protocol|Entrance Protocol]]
*[[Exit Protocol|Exit Protocol]]
*[[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]]

 

===== General Protocols =====

*[[Common buffers|Common Buffers]]
*[[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]]

 

===== Phagocytosis Protocols =====

*[[Opsonization|Opsonization]]
*[[Preparation of Silica-Magnetic Beads|Preparation of Silica-Magnetic Beads]]
*[[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]]

|

===== 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)]]
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 & ZYCY10P3S2T)]]
*[[E. coli Transduction|Transducing ''E. coli'']]
*[[Transformation|Transformation]]
*[[Neon® Transfection System|Neon® Transfection System]]
*[[Generating Minicircles|Generating Minicircles]]
 

===== Protein work =====

*[[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 & Reprobing Blots]]

 

===== Cell Biology =====

*[[Ablation of Recycling Endosomes|Ablation of Recycling Endosomes]]
*[[Cell-Type Specific Transfection Protocols|Cell-Type Specific Transfection Protocols]]
*[[G418 & Puromycin Kill Curves|G418 & Puromycin Kill Curves]]
*[[Apoptosis Detection with AnnexinV and PI|Apoptosis Detection with AnnexinV and PI]]

|

===== Microscopy =====

*[[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]] 

 

 

|}

= Links to More Protocols =
{| width="100%" cellspacing="1" cellpadding="1" border="0" align="left"
|- valign="top"
|
===== 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 & 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 & Tips] - Microfluidics protocols

|
===== Free Science Ebooks =====
*[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
|}

= Useful Links =

{| width="100%" cellspacing="1" cellpadding="1" border="0"
|- valign="top"
|
===== 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.uniprot.org/ Uniprot] - Find protein sequence & structure 
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms 
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations 
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions 
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes 
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc 
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes 
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins 
*[http://www.hprd.org/index_html Human Protein Reference Database] 
*[http://www.wwpdb.org/ PDB] - Protein Structures 
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database 

 

===== 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

 

===== Genomics Resources =====
*[http://www.gwascentral.org GWAS Central]

|
===== Molecular Biology Tools =====

*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]
*[http://ca.expasy.org/ ExPASy Tools] 
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator 
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter] 
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers] 
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence] 
*[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] 
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools] 
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder] 
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher] 
*[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 

 

===== ''In Vivo'' Tools =====

*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy 
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes 

|
===== Microscopy Tools =====

*[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] - FREE 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

 

===== 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

 

===== Lipid Tools =====

*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids

 

===== Chemical Tools =====

*[http://www.chemspider.com/ ChemSpider] - General chemistry database
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database

 

 

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