Protocols

---

Labs/Groups     Courses     Protocols     Blogs     Notebooks

---

Contributing protocols Add new protocols Add a new lab- or person-specific protocol Add a consensus protocol (?) Nature Methods article on OWW protocols Improve protocols in development Please Contribute! Pulse-chase protein production DNase Protocol Etchevers:ChIP francais DNA Precipitation Addition of 3' A overhangs to PCR products Baby cell column Chromosomal DNA isolation from E. coli Protocols isolate cancer microparticles	In vivo Escherichia coli [show][hide] Preparing chemically competent cells Electrocompetent cells Miniprep Electroporation Colony PCR Knight:Colony PCR Endy:Colony PCR Bacterial cell culture Endy:E. coli Western Blot Endy:STN Chemostat Protocol Beta-Galactosidase Assay (A better Miller) Knight:Preparing electrocompetent cells Miniprep/Qiagen kit Miniprep/Kit-free high-throughput protocol Transforming chemically competent cells Bacterial transformation Making a long term stock of bacteria P1vir phage transduction Preparing chemically competent cells (Inoue) Transforming chemically competent cells (Inoue) One step 'miniprep' method for the isolation of plasmid DNA TOP10 chemically competent cells Miniprep/GET buffer Knight:Electroporation Belcher/Knight: Electrocompetent Cells Lory:Quick transformant screen Seth:Quick Transformant Screen Sauer:Lysing E. coli with Lysozymes Maxiprep of plasmid DNA from E. coli Recombineering/Lambda red-mediated gene replacement Knight:DNA Spots Knight:Miniprep low copy plasmids Knight:Beta-galactosidase assay Knight:Beta-galactosidase assay/96 well format ChIP-Chip E. coli Engineering BioBrick vectors from BioBrick parts/Colony PCR Knight:Beta-galactosidase assay/Fluorescence Cell counting/plating Cell and tissue lysis hub Knight:Preparing stabs Duffy:LIC Cloning Cell cycle analysis Huang: Agarose Slides for Imaging In-fusion biobrick assembly Richard Lab:Electroporation of E. coli Richard Lab:Preparing electrocompetent cells Erman's Lab:DNA Miniprep with Alkaline Lysis Miniprep/TENS miniprep McClean:Competent Cells Gill:Rapid bacterial DNA prep Mesoplasma florum [show][hide] Culture media Mesoplasma florum:Microarray design Mesoplasma florum:Codon usage Mesoplasma florum:Physiology Mesoplasma florum:Genome Mouse [show][hide] Mouse keratinocyte cultures Isolation of murine splenocytes Intracellular cytokine staining for flow cytometry (mouse) Mouse tissue lysis for genotyping Tamoxifen administration to mice DNA extraction from tissue Cell and tissue lysis hub Sex genotyping of mice Mycobacterium smegmatis [show][hide] McKinney:TransformByElectroporation T7 [show][hide] Studier Lysate Prep Cesium Chloride Purification of T7 Gill:Making plate lysates Gill:Phage genomic DNA extraction Gill:Plating out phage Yeast [show][hide] High Efficiency Transformation Yeast DNA Prep Yeast Colony PCR Cell Cycle Arrest Layered plates Silver: Lysate for Western Silver: Colony PCR Silver: Time-Lapse Microscopy Assaying mating Dropout plates for yeast Endy:Yeast Colony PCR Preserving yeast cultures Freimoser:Protocols:FastYeastTransformation Spheroplast Transformation Cell and tissue lysis hub Smolke:Protocols/Western Smolke:Protocols/Library transformation McClean: Sporulation McClean: Colony PCR (Yeast) McClean: Alpha Factor Stock McClean: Cycloheximide Stock Solution McClean:Magic Marker Medias McClean:SC Media McClean: Genomic DNA Prep (Bust 'n' Grab Protocol) McClean: Glycerol stocks (yeast) McClean: Sequencing Colony PCR Product SDS-PAGE sample buffer (Morris formulation) McClean: Plasmid Loss Assay McClean: Fixation of Yeast (Bisaria Protocol) McClean: Fixation of Yeast (P. Xu Protocol) McClean:Making and Using Frozen Yeast Competant Cells McClean:SC Canavanine McClean: Fixation of Yeast (McClean Protocol) McClean:Genomic DNA prep (LiAc SDS method)	In vitro Nucleic acids [show][hide] Agarose gel electrophoresis Phenol/chloroform extraction Ethanol precipitation of nucleic acids Quantitating nucleic acids PCR techniques Real-time PCR QRT-PCR Alm:Agarose gel electrophoresis Q-PCR Bioanalyzer DIYbio:Notebook/Keiki Gels DNA [show][hide] MIT:Sequencing BioBrick DNA Agarose gel electrophoresis DNA ligation Yeast DNA Prep Endy:Templiphi Ethanol precipitation of small DNA fragments Purification of DNA Knight:Micropure EZ and Microcon purification Annealing primers PNK Treatment of DNA Ends Miniprep Designing primers Phosphatase treatment of linearized vector Knight:Annealing and primer extension with Klenow polymerase Knight:DNA ligation using NEB Quick Ligation Kit Site-directed mutagenesis Restriction digest Phenol/chloroform extraction Knight:Restriction Digest Knight:Site-directed mutagenesis/Single site Sequencing DNA PCR Ethanol precipitation of nucleic acids 'Round-the-horn site-directed mutagenesis Silver: PCR Knight:Agarose gel electrophoresis Knight:TOPO TA cloning Library Generation Resuspension of primers Miniprep/Qiagen kit Miniprep/Kit-free high-throughput protocol Endy:Double stranding oligo libraries One step 'miniprep' method for the isolation of plasmid DNA Cloning Knight:Sequencing DNA Knight:Annealing and primer extension with Taq polymerase Knight:Reconstituting primers DNA Synthesis from Oligos PCR Overlap Extension Kafatos:Minipreps Miniprep/GET buffer "Core Sample" PCR: Amplifying DNA from agarose gels Electrophoretic mobility shift assay Knight:Electrophoretic mobility shift assay Centrifugal filtration/Nucleic acids Affymetrix DNA labelling for gene expression arrays Jamesh008:consensus DNA ligation protocol Annealing and primer extension Lory:Quick transformant screen TempliPhi Knight:Maxiprep Knight:PhoenIX Maxiprep Kit Seth:Quick Transformant Screen Knight:TempliPhi Quantitating nucleic acids Maxiprep of plasmid DNA from E. coli PCR techniques Real-time PCR QRT-PCR Anneal Extend PCR Protocol - for linking 2 pieces of DNA Sauer:Stitching Genes by PCR Streptavidin purification of DNA fragments Streptomyces:Protocols/DNA Digest Etchevers:ChIP francais DNA Precipitation Knight:Site-directed mutagenesis/Multi site Knight:Miniprep low copy plasmids Alm:Agarose gel electrophoresis Q-PCR Knight:DNA ligation using T4 DNA ligase Cloning and sequencing NanoBio: PCR Sacks:RAD-seq Engineering BioBrick vectors from BioBrick parts/DNA ligation Engineering BioBrick vectors from BioBrick parts/Dephosphorylation Engineering BioBrick vectors from BioBrick parts/Restriction digest Assembly pcr Cloning Checklist Duffy:LIC Cloning Bioanalyzer Size selective DNA precipitation Weiss Lab:DNA labeling DIYbio:Notebook/Keiki Gels SB DNA blot (Southern) Richard Lab:Agarose Gel Electrophoresis Restriction Digest: Partial Richard Lab:Restriction Digest Polyacrylamide gel electrophoresis DNA Seq Prep Cloning Protocol DNA Quantification Rapid plant gDNA extraction Richard Lab:Amplified insert assembly Amplified insert assembly Miniprep/TENS miniprep Corum:PCR Corum:digest Corum:T4 Ligation Corum:DNA Digestion Corum:DNA Hybridization Corum:Digestion Corum:Whole Plasmid PCR Brennan:Miniprep for vaccinia virus DNA isolation RNA [show][hide] Agarose gel electrophoresis Endy:Northern Blot, 32P End-Labeled Probes RNA extraction Probe Prep, 32P End-Labeled Probes In vitro transcription with T7 RNA polymerase Phenol/chloroform extraction Endy:RNA extraction Ethanol precipitation of nucleic acids RNase Protection Assay Northern Blot, 32P End-Labeled Probes RNA Half-life Affymetrix One Cycle Eukaryotic Gene Expression Sample Processing RNA Quality Control Affymetrix Target Hybridization Affymetrix Two Cycle Eukaryotic Gene Expression Sample Processing Knight:In vitro transcription RNA electrophoresis Knight:RNA electrophoresis/Denaturing Knight:RNA electrophoresis Knight:RNA electrophoresis/Native Etchevers:Extraction ARN francais Sauer:RNA Purification from E. coli Quantitating nucleic acids PCR techniques Real-time PCR QRT-PCR/Single tube QRT-PCR Alm:Agarose gel electrophoresis QRT-PCR/Two tubes Q-PCR RNA extraction using trizol/tri Endy:Northern blot, AlkPhos end-labeled probes Bioanalyzer RNA blot (Northern) Dahlquist:DNA Microarray Protocol Griffin:Nested RT-PCR DIYbio:Notebook/Keiki Gels Making RNA probes with T7 transcription Protein [show][hide] Beta-galactosidase assay Acrylamide gels Endy:E. coli Western Blot Sauer:Expression/purification of 35S-Met proteins Silver: Lysate for Western Silver: Coomassie Stain Silver: Destain Keating:Experimental Protocols:HPLC Silver staining Purification of His-tagged proteins Free Sulfhydryl Determination Antigen retrieval Knight:Purification of His-tagged proteins/Denaturing Knight:NuPAGE electrophoresis Electrophoretic mobility shift assay Protein blot (Western) hub Chromatin Immunoprecipitation Knight:Electrophoretic mobility shift assay Knight:Purification of His-tagged proteins Knight:Purification of His-tagged proteins/Native Knight:Protein solubility Knight:Purification of His-tagged proteins/Denaturing with refolding Knight:Centrifuge desalting Knight:Centrifuge desalting/Zeba columns Knight:NuPAGE electrophoresis/Fast staining Knight:NuPAGE electrophoresis/Slow staining Knight:NuPAGE electrophoresis/Hybrid staining Sauer:Lysing E. coli with Lysozymes Dot Blot Knight:NuPAGE electrophoresis/Gel drying Etchevers:ChIP francais Alm:Agarose gel electrophoresis User:Leprevost/Purification of His-tagged proteins/Denaturing ISISBio:Protocols/p11 resin preparation ISISBio:Protocols/Sortase mediated ligation ISISBio:Protocols/Sortase mediated ligation/Small molecule ligation ISISBio:Protocols/Sortase mediated ligation/Solid support ligation ISISBio:Protocols/Sortase mediated ligation/Protein DNA ligation Bioanalyzer Griffin: Ultimate Immunoprecipitation Guide Griffin:Nuclear Extract Preparation Griffin:Western Blot Optimization Griffin:Immunohistochemistry Paraffin Griffin:Membrane Stripping and Reprobing Griffin:Antibody Elution Buffers Isolate leydig cells from testes Griffin:In Vitro Kinase Assay Griffin:Antibody Related Solutions & Recipes Griffin:Isolate Leukocytes from whole blood Lactobacillus planarum miniprep Fong:Bradford protein assay Prbbbb:small scale expression v1 Prbbbb:Coomassi Ethanol stain Prbbbb:inclusion body solubilization v1 Protein Purification - Salting Out Prbbbb:in vitro FRET FRB FKBP v1 Feruloyl Esterase Protocols Beta-galactosidase Screen Beta-glucuronidase protocols User:Behzad Damadzadeh/Notebook/PcTF Subcloning in E-coli/2012/05/23 SDS-PAGE sample buffer (Morris formulation) Mammalian cell culture [show][hide] Marek: Freeze-down/Thaw Griffin:Dual Immunofluorescence Cell Staining Griffin:Puromycin Selection Griffin:shRNA Transfection TissueCulture:splitting cells TissueCulture:Thawing cells Plant specific protocols [show][hide] Hop DNA Isolation Transformation Protocol for Tobacco Transformation Protocol for Arabidopsis Rapid plant gDNA extraction
	In silico Modeller FBA MoMA BLAST Homology Modelling Coot and WinCoot for X-ray Crystallography Model Building Protein motifs Plasmapper Wikiomics:Bioinfo tutorial Wikiomics:BLAST Wikiomics:ChIP-chip Wikiomics:Cloning in silico Wikiomics:Crystallography toolbox Wikiomics:Docking toolbox Wikiomics:Exon microarrays Wikiomics:FASTA Wikiomics:Multiple sequence alignment Wikiomics:PDB Wikiomics:Percentage identity Wikiomics:Phylogenetic databases Wikiomics:Protein function prediction Wikiomics:Protein mass spectrometry Wikiomics:Protein volume Wikiomics:PSI-BLAST Wikiomics:RNA databases Wikiomics:RNA gene-finding Wikiomics:RNA homology search Wikiomics:RNA phylogenetics Wikiomics:RNA secondary structure prediction Wikiomics:Sequence motifs Wikiomics:Site Directed Mutagenesis Wikiomics:Staden Wikiomics:Viewing and sharing genome annotations Tregwiki:Collected regulatory elements Butlin:Unix for Bioinformatics - advanced tutorial Wikiomics:Pathway analysis Butlin:Unix for Bioinformatics - basic tutorial Wikiomics:Genome annotation Wikiomics:BLAST tutorial Wikiomics:DNA sequencing Wikiomics:RNA splicing Wikiomics:SAGE Wikiomics:Orthologues Wikiomics:Mutation/SNP detection Jasieniuk:Converting codominant to dominant data SynBioSS Bionumerics Jasieniuk:Implementation of a method to calculate microsatellite genotype distance in polyploids Wikiomics:Repeat finding DataONE:Protocols/Find GEO reuses DataONE:Protocols/Scopus citation counts from PMIDs Wwwblast	Other Flow Cytometry [show][hide] Endy:FACS calibration with beads Synthetic Biology:BioBricks/Standard FACS protocol Endy:FACS protocols Shreffler:CFSE Labeling Shreffler:Basophil Activation Shreffler:BioCSI Basophil Activation Shreffler:Milk Program Shreffler:Basophil tSyk Shreffler:JAX Basophil Activation Shreffler:JAX Tcell studies Shreffler:Cisplatin Allergen Shreffler:Basophil Sensitization Shreffler:Eosinophil Isolation Shreffler:SCIT Basophil Activation Shreffler:Cryopreservation Microfluidics [show][hide] SortoStat/Operation Design a Microfluidic Chip Order a Microfluidic Chip from the Foundry Micado Tutorial Mathies:Valves Mathies:Drilling a Glass Microfluidic Wafer Mathies:Mask Making Mathies:Wafers Cleaning and Deposition Mathies:Photolithography Mathies:RIE Mathies:Glass Etching Mathies:Metal Deposition Mathies:Metal Etching Mathies:Glass Bonding Mathies:Nitride Mathies:Polyacrylamide Derivitization Mathies:Dynamic Coating Mathies:Sieving Matrices Mathies:Separation Buffer Mathies:Simulations Mathies:Introduction to Cell Culture Mathies:Culture in Broth Mathies:Calibration Curves Mathies:E COLI PCR Mathies:Glass Etching in BNC Mathies:RIE in BNC Mathies:Photolithography in BNC Mathies:Drilling in BNC Mathies:Back Door DropBase DropBase:Contact DropBase:Devices DropBase:droplet generation 4 inlets DropBase:droplet generation 3 inlets DropBase:droplet generation 2 inlets DropBase:droplet generation 3 inlets short delay DropBase:droplet generation 3 inlets long delay DropBase:droplet electrosorting DropBase:droplet electrosorting 2 DropBase:AADS DropBase:DLDS DropBase:Droplet generation 2 inlets DropBase:Picoinjection DropBase:Droplet sorting DropBase:Droplet 3 inlets DropBase:FFD-70-75 DropBase:ECD2 DropBase:ECD DropBase:TCD Dropbase: Double FF device Dropbase: Triple FF device Dropbase: Devices for 20 µm double emulsions Dropbase: Double-emulsion-01 Dropbase: Droplet generator Dropbase: Picoinjector Dropbase: AADS sorter Dropbase: Double-emulsion-02 DropBase:droplet electrosorting 3 DropBase:droplet electrosorting 4 DropBase:droplet electrosorting 5 Dropbase: 3-pL-droplets-01 Dropbase: VASA generator Dropbase: VASA 1st picoinjecton Dropbase: VASA 2nd picoinjecton DropBase:Fluidic connector Dropbase: 35um bead generator Dropbase: agarose bead generator DropBase:agarose bead generator Dropbase: spinDrop sorter Dropbase: spinDrop picoinjector DropBase:Anchored droplet DropBase:Sorter and FF devices DropBase:Picoinjection chip DropBase:droplet electrosorting 6 Microscopy [show][hide] Agarose Pads for Microscopy Fixing cells Methods to determine the size of an object in microns Silver: Time-Lapse Microscopy Koch Lab:Protocols/Microsphere-DNA tethering File:Low tech flow cell and wicks.JPG File:Low tech flow cell.JPG File:Low tech flow cell changing buffer with wick.JPG Koch Lab:Protocols/Microsphere-DNA tethering/Glass, dig, biotin, microsphere, 4kb DNA/Cleaning glass Paraffin embedding and sectioning Immunofluorescence Microscopy (Pf, live) Immunofluorescence Microscopy (Pf, fixed) TE antigen retrieval and immunostaining Mounting medium Nissl staining Plate reader [show][hide] Plate reader usage protocols Miscellaneous [show][hide] Endy:Pouring plates Endy:Pouring LB plates from prepped media Knight:pH meter/Calibration Knight:pH meter/Measurement Alm:Protoplasting Cell counting Category:Chromatography Category:Synchronization Category:Mammalian cell culture Category:Agarose gel electrophoresis Category:Human Category:Buffers Category:Alm Anthrone cellulose quantification General resources [show][hide] Current Protocols in Molecular Biology Downloadable pdfs. Molecular Cloning Protocol-online Useful protocols and a popular discussion section. iProtocol Abridged Current Protocols Invitrogen protocols. Not amenable to printing. JoVE is an online research journal for publishing visualized (video-based) biological experiments. Need help with protocols? [show][hide] Questions and Answers on OWW

Search protocols

[show all] [hide all]