Protocols

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Protocols in Development Please Contribute! Pulse-chase protein production Fixing cells β-galactosidase assay RNA Half-life Denaturing acrylamide gel purification of nucleic acids Quantification of nucleic acids	In vivo <showhide> Escherichia coli__HIDER__ <hide> • Bacterial Cell culture • Bacterial Transformation   • Preparing chemically competent cells (TSS)   • Transforming chemically competent cells (TSS)   • Preparing electrocompetent cells   • Transforming electrocompetent cells • β-Galactosidase Assay (A better Miller) • Colony PCR • Making long-term stock bacteria • Miniprep • P1vir phage transduction • Pour LB plates • Protein expression resource • S N Chemostat Protocol </hide> </showhide> <showhide> Mesoplasma florum__HIDER__ <hide> • Preparing culture media </hide> </showhide> <showhide> T7__HIDER__ <hide> • Purification T7: Cesium Chloride • Simple lysate protocol from plaque/lysate </hide> </showhide> <showhide> Yeast__HIDER__ <hide> • Assaying mating • Cell Cycle Arrest • Dropout plates • High Efficiency Transformation • Layering plates • Pour YPD plates • Simple Yeast Lysate (for Western etc.) • Time-Lapse Microscopy • Yeast Colony PCR • Yeast DNA Prep </hide> </showhide>		In vitro <showhide> Nucleic acids__HIDER__ <hide> • Nucleic acid precipitation • Phenol/chloroform extraction </hide> </showhide> <showhide> DNA__HIDER__ <hide> • Agarose gel electrophoresis • Annealing Primers • Designing Primers • DNA Ligation • Double stranding oligo libraries • Library Generating • Miniprep • PCR • Phosphate treatment linearized vector • Polony Protocols(Church/Mitra Lab) • PNK Treatment of DNA ends • Purification of DNA • Reconstituting Primers • Restriction Digest • 'Round-the-horn site-directed mutagenesis • Sequencing DNA • Site-directed Mutagenesis • Templiphi </hide> </showhide> <showhide> RNA__HIDER__ <hide> • In vitro transcription w/ T7 RNA polymerase • Northern Blot, 32P End-Labeled Probes • Probe Prep, 32P End-Labeled Probes • RNA Extraction • RNAse Protection Assay </hide> </showhide> <showhide> Protein__HIDER__ <hide> • Acrylamide gels and SDS-PAGE • Coomassie Destain • Coomassie Stain • HPLC • Silver staining • Western Blot • Purification His-tagged proteins • Free Sulfhydryl Determination </hide> </showhide>
	In silico <showhide> Sequence Analysis__HIDER__ <hide> • BLAST • CLUSTALW </hide> </showhide> <showhide> Structure__HIDER__ <hide> • THREADER • Homology Modeling </hide> </showhide> <showhide> Pathway Modelling__HIDER__ <hide> • Flux Balance Analysis • Minimisation of Metabolic Adjustment </hide> </showhide>		Other <showhide> Flow Cytometry__HIDER__ <hide> • Flow Calibration </hide> </showhide> <showhide> Microfluidics__HIDER__ <hide> • Design Microfluidic Chip • Order Microfluidic Chip from Foundry • Operate Microfluidic Chemostat </hide> </showhide> <showhide> Microscopy__HIDER__ <hide> • Agarose Pads • Quantitative Microscopy • Time-Lapse Microscopy </hide> </showhide> <showhide> Plate reader__HIDER__ <hide> • Perkin Elmer Victor3 Plate reader usage protocols </hide> </showhide> General resources • Protocol-online Contains a lot of useful protocols and a popular discussion section.

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