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