Protocols

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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! Cloning - quick transformant screen Pulse-chase protein production Fixing cells Real-time RT-PCR β-galactosidase assay Denaturing acrylamide gel purification of nucleic acids Quantification of 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 Gel shift Making construction plasmid Isolation of murine splenocytes Intracellular cytokine staining for flow cytometry (mouse)	In vivo <showhide> Escherichia coli__HIDER__ <hide> Bacterial cell culture Bacterial Transformation Preparing chemically competent cells Transforming chemically competent cells Electrocompetent cells Electroporation Preparing chemically competent cells (Inoue) Transforming chemically competent cells (Inoue) TOP10 chemically competent cells beta-Galactosidase Assay (A better Miller) Colony PCR Making a long term stock of bacteria Miniprep P1vir phage transduction Recombineering Endy:Pouring plates Protein expression resource S_N Chemostat Protocol </hide> </showhide> <showhide> Mesoplasma florum__HIDER__ <hide> Culture media Mesoplasma florum:Microarray design </hide> </showhide> <showhide> Mouse__HIDER__ <hide> Mouse keratinocyte cultures </hide> </showhide> <showhide> Mycobacterium smegmatis__HIDER__ <hide> Transformation by electroporation </hide> </showhide> <showhide> T7__HIDER__ <hide> Cesium Chloride Purification of T7 Studier Lysate Prep </hide> </showhide> <showhide> Yeast__HIDER__ <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 </hide> </showhide>	In vitro <showhide> Nucleic acids__HIDER__ <hide> Nucleic acid precipitation Phenol/chloroform extraction Quantitating nucleic acids </hide> </showhide> <showhide> DNA__HIDER__ <hide> Agarose gel electrophoresis Annealing Primers Centrifugal filtration/Nucleic acids DNA Ligation DNA Synthesis from Oligos Designing primers Double stranding oligo libraries Library Generation Miniprep PCR PCR Overlap Extension PNK Treatment of DNA Ends Phosphatase treatment of linearized vector Polony Protocols Purification of DNA Reconstituting primers Restriction digest 'Round-the-horn site-directed mutagenesis Sequencing DNA Site-directed mutagenesis TempliPhi Affymetrix DNA Labeling </hide> </showhide> <showhide> RNA__HIDER__ <hide> RNA Quality Control In vitro transcription with T7 RNA polymerase Northern Blot, 32P End-Labeled Probes Probe Prep, 32P End-Labeled Probes RNA extraction Sauer:RNA Purification from E. coli RNA electrophoresis RNA half-life RNase Protection Assay Affymetrix One cycle labeling Affymetrix Small sample labeling Affymetrix Prokaryotic Labeling </hide> </showhide> <showhide> Protein__HIDER__ <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 </hide> </showhide> <showhide> Plant specific protocols__HIDER__ <hide> Banana DNA Isolation </hide> </showhide>
	In silico <showhide> Sequence Analysis__HIDER__ <hide> BLAST CLUSTALW Protein motifs Plasmapper </hide> </showhide> <showhide> Structure__HIDER__ <hide> THREADER Homology Modelling </hide> </showhide> <showhide> Pathway Modelling__HIDER__ <hide> FBA MoMA </hide> </showhide> <showhide> X-Ray Crystallography__HIDER__ <hide> Coot for Model Building </hide> </showhide>	Other <showhide> Flow Cytometry__HIDER__ <hide> Flow Calibration Endy:FACS protocols </hide> </showhide> <showhide> Microfluidics__HIDER__ <hide> Design a Microfluidic Chip Order a Microfluidic Chip from the Foundry Operate Microfluidic Chemostat </hide> </showhide> <showhide> Microscopy__HIDER__ <hide> Agarose Pads for Microscopy Quantitative Microscopy Silver: Time-Lapse Microscopy </hide> </showhide> <showhide> Plate reader__HIDER__ <hide> Endy:Victor3 plate readerPlate reader usage protocols </hide> </showhide> <showhide> General resources__HIDER__ <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. </hide> </showhide> <showhide> Need help with protocols?__HIDER__ <hide> Questions and Answers on OWW </hide> </showhide>

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