Revision as of 13:25, 4 February 2021

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:

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

Index of Protocols

Lab Operations

DNA/Cloning

Microscopy

General Protocols

Protein work

Lipids

Phagocytosis Protocols

Cell Biology

Links to More Protocols

General Protocol Sites

BenchFly - Free Video Protocols
Protocols Online - large database of biology protocols
Open Wet Ware - large database of open protocols
Molecular Station - links to many lab-generated protocols
TheLabRat - various protocols & lab resourses.
Common Buffer Recipes @ TheLabRat
Chips & Tips - Microfluidics protocols

Free Science Ebooks

Analyzing fluorescence microscopy images with ImageJ
Bioimage Data Analysis - Free registration required

Useful Links

Molecular Biology Databases

Pubmed Gene - Find gene information
Pubmed RefSeq - Find reference sequences
Uniprot - Find protein sequence & structure
HapMap - Find human polymophisms
OMIM - Find human gene-assocations
PANTHER - Automated Protein Function Classification
BioGrid - Protein Interactions
Ensemble Genome - Browse multiple genomes
Human Protein Atlas - Info onn gene exrpession, antibody's, etc
Gene Cards - Condenced information on genes
iHOP - Information Hyperlinked Over Proteins
Human Protein Reference Database
PDB - Protein Structures
PolyPhen2 - SNP Phenotype Predictor
SIFT - SNP Phenotype Predictor/db
TimeTree - evolutionary divergence database

Molecular Biology Tools

NCBI Blast
ExPASy Tools
OligoCalc - PCR primer Tm calculator
NEB Cutter
NEB Isoschizomers
Reverse-Complement DNA Sequence
Ligation Calculator
AddGene - clone by e-mail!
PattenProt - search genomes for protein patterns
Biology Workbench
EMBL Sequence Tools
NCBI ORF Finder
BCM Search Launcher
SWISS Model protein modeling
Secondary Structure Prediction
PredictProtein - Protein structure prediction
STRAP - Protein aligments with structure

Microscopy Tools

Microscopy U - Everything you want to know about microscopes
Paper on Image Processing Standards - How not to loose your job
Fluorophore Spectra Viewer at Life Technology
Fluorescent Spectra Database - FRET and other
Yet More Spectra - from Arizona University
www.confocal-microscopy.org - Data on LSM methods and equipment
FIJI - FREE imageJ based image processing program
Free image processing textbook
Lectures on image processing
VAA3D FREE viewer for large 3/4/5D datasets

Journal Resources

Pubmed
Pubmed Central (USA)
Pubmed Central (Canada)
Google Scholar
Eigenfactor - free journal imapct scores

In Vivo Tools

EMAP - Virtual mouse anatomy
Mouse phenome database - mouse phenotypes

Protease Tools

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

Genomics Resources

GWAS Central

Chemical Tools

ChemSpider - General chemistry database
PubChem - Chemical structure database

Lipid Tools

Lipid Maps - Lipidomics gateway at Nature
Avanti Lipids - Buy lipids

@@ Line 122: / Line 122: @@
 = Useful Links =
+{|width="100%"
-{| width="100%" cellspacing="1" cellpadding="1" border="0"
+|- style="vertical-align:top;"
-|- valign="top"
+|
-|
+==== 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://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]
+|
+==== 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>

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