Protocols

Protocols in development

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• 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)

Adding new protocols

• Adding a new lab- or person-specific protocol
• Adding a new consensus protocol
• What is a consensus protocol?
• Nature Methods article on OWW protocols

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

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<showhide> Mesoplasma florum__HIDER__ <hide>

• Culture media
• Mesoplasma florum:Microarray design

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<showhide> Mouse__HIDER__ <hide>

• Mouse keratinocyte cultures

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<showhide> Mycobacterium smegmatis__HIDER__ <hide>

• Transformation by electroporation

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<showhide> T7__HIDER__ <hide>

• Cesium Chloride Purification of T7
• Studier Lysate Prep

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<showhide> Yeast__HIDER__ <hide>

• Yeast culture media
• Preserving yeast cultures
• Assaying mating
• Cell Cycle Arrest
• Dropout plates for yeast
• High Efficiency Transformation
• Layered plates
• Silver: Lysate for Western (for Western etc.)
• Silver: Time-Lapse Microscopy
• Yeast Colony PCR
• Yeast DNA Prep

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In vitro

<showhide> Nucleic acids__HIDER__ <hide>

• Nucleic acid precipitation
• Phenol/chloroform extraction

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<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

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<showhide> RNA__HIDER__ <hide>

• In vitro transcription with T7 RNA polymerase
• Northern Blot, 32P End-Labeled Probes
• Probe Prep, 32P End-Labeled Probes
• RNA Extraction
• RNA Half-life
• RNase Protection Assay
• Affymetrix One cycle labeling
• Affymetrix Small sample labeling
• Affymetrix Prokaryotic Labeling

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<showhide> Protein__HIDER__ <hide>

• Acrylamide gels
• Chromatin Immunoprecipitation
• Keating:Experimental Protocols:HPLC
• Silver staining
• Protein Preps: Yeast
  • Denaturing Protein Extraction
  • Native Protein Extraction
• Purification of His-tagged proteins
• Free Sulfhydryl Determination
• Expression and purification of ³⁵S-labeled proteins
• Western blot

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In silico

<showhide> Sequence Analysis__HIDER__ <hide>

• BLAST
• CLUSTALW
• Protein motifs
• Plasmapper

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<showhide> Structure__HIDER__ <hide>

• THREADER
• Homology Modelling

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<showhide> Pathway Modelling__HIDER__ <hide>

• FBA
• MoMA

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<showhide> X-Ray Crystallography__HIDER__ <hide>

• Coot for Model Building

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Other

<showhide> Flow Cytometry__HIDER__ <hide>

• Flow Calibration
• Endy:FACS protocols

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<showhide> Microfluidics__HIDER__ <hide>

• Design a Microfluidic Chip
• Order a Microfluidic Chip from the Foundry
• Operate Microfluidic Chemostat

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<showhide> Microscopy__HIDER__ <hide>

• Agarose Pads for Microscopy
• Quantitative Microscopy
• Silver: Time-Lapse Microscopy

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<showhide> Plate reader__HIDER__ <hide>

• Endy:Victor3 plate readerPlate reader usage protocols

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<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.

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<showhide> Need help with protocols?__HIDER__ <hide>

• Questions and Answers on OWW

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