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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 Fixing cells Q-PCR β-galactosidase assay Denaturing acrylamide gel purification of nucleic acids Quantitating nucleic acids Bacterial species identification Yeast artificial chromosomes One step 'miniprep' method for the isolation of plasmid DNA Cleaning Glass Coverslips "Core Sample" PCR: Amplifying DNA from agarose gels Broncho-alveolar Lavage Artificial transcriptional terminators Codon usage optimization Making construction plasmid Isolation of murine splenocytes Intracellular cytokine staining for flow cytometry (mouse) Streptavidin purification of DNA fragments	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 Mouse tissue lysis for genotyping Tamoxifen administration to mice DNA extraction from tissue Mycobacterium smegmatis [show][hide] Transformation by electroporation 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] Yeast culture media Preserving yeast cultures Assaying mating Cell Cycle Arrest Dropout plates for yeast High Efficiency Transformation Spheroplast Transformation Layered plates Silver: Lysate for Western (for Western etc.) Silver: Time-Lapse Microscopy Yeast Colony PCR Yeast DNA Prep	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] Acrylamide gels Chromatin Immunoprecipitation Electrophoretic mobility shift assay Keating:Experimental Protocols:HPLC Protein Preps: Yeast Denaturing Protein Extraction Native Protein Extraction Purification of His-tagged proteins Free Sulfhydryl Determination Sauer:Lysing E. coli with Lysozymes Expression and purification of 35S-labeled proteins Silver staining Western blot Dot Blot Plant specific protocols [show][hide] Hop DNA Isolation Transformation Protocol for Tobacco Transformation Protocol for Arabidopsis
	In silico Sequence Analysis [show][hide] BLAST CLUSTALW Protein motifs Plasmapper Structure [show][hide] THREADER Homology Modelling Pathway Modelling [show][hide] FBA MoMA X-Ray Crystallography [show][hide] Coot for Model Building	Other Flow Cytometry [show][hide] Flow Calibration Endy:FACS protocols Microfluidics [show][hide] Design a Microfluidic Chip Order a Microfluidic Chip from the Foundry Operate Microfluidic Chemostat Microscopy [show][hide] Agarose Pads for Microscopy Quantitative Microscopy Silver: Time-Lapse Microscopy Plate reader [show][hide] Endy:Victor3 plate readerPlate reader usage protocols 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

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