Main Page

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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 Entrance Protocol Exit Protocol Guidelines for Proper Use of Laboratory Notebooks Proper Saving of Experimental Files Setting up Access to Network Drives & Wiki	DNA/Cloning Agarose Gels Colony PCR Digests Gibson Assembly Ligation PCR		Transfections and Transductions J774 Cell Transfection Raw Cell Transfection THP1 Culture and Differentiation Neon® Transfection System Titering Pseudo-typed Lentiviruses Transduction of THP-1s Nucleofector
General Protocols Antibiotics Antibiotic Plates Bacterial Growth Media Cell Culture Guidelines Common Buffers Freezing and Thawing Cells Water Bath Antibiotic Solution	Cell Biology Ablation of Recycling Endosomes Apoptosis Detection with AnnexinV and PI Cell-Type Specific Transfection Protocols G418 & Puromycin Kill Curves Primary Human Macrophages Primary Murine Macrophages		Lipids Asymmetric liposomes Lipid Extraction from Cells Bead Preparation Lipisome and Lipid-Coated Beads Lipid Coated Bead Preparation Opsonization Preparation of Silica-Magnetic Beads
Bacteria Work Generating Competent E. coli (TFB, BL21 & ZYCY10P3S2T) Generating Minicircles Inside-out Labelling of Bacteria Labelled E coli Preparation of Digestion-Tracking Bacteria Quick 'n' Easy Competent E. coli (Dh5a) Transducing E. coli Transformation Phagocytosis Protocols Gentamicin Protection Assay Phagosome Isolation Synchronised Phagocytosis	Protein Work Bradford Assay Coomassie Staining Fab preparation Fab purification using FPLC Immunoprecipitation Nitrogen Cavitation Receptor activation by Cross-Linking Stripping & Reprobing Blots Updated FPLC Size Exclusion Procedure Western Blotting		Microscopy 3D Printed PDMS Chambers Acid Washing Coverslips Competition of Charged Molecules with Lipophilic Cations Fluorescent Immunostaining FRET in FIJI Inhibition of Focal Contact Signaling Immuno-FISH Live Cell FRET (depreciated) Reducing Photobleaching Single Particle Tracking Staining for GSD Traction Force Microscopy 3D Printed Microscopy Chambers Micropatterning Proteins Frustrated Phagocytosis

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 London Regional Microscopy Facility Bookings 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