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This is a Wiki web, a readable/editable resource. This Wiki focuses on molecular biology, protocols, reagents etc. This web is administrated by AndyPierce

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protocols

• nucleic acids
  
  • GenomicDnaIsolation fragments about 50 kbp
    
  • HighMwGenomicDna megabase size fragments
    
  • SouthernBlotting
    
  • EthanolPrecipitation for concentration of nucleic acids
    
  • PlasmidMiniprep
    
  • QiagenPlasmidMaxiprep
    
  • Making a radioactive DNA probe:
    
    • RadiolabelingDna (by random priming)
      
    • PcrRadiolabeling (for maximal probe specific activity)
      
      • ProbeCleanup to calculate probe specific activity and remove unincorporated nucleotides
        
  • HoechstFluorimetry for measuring DNA concentrations too low for an A₂₆₀ reading
    
  • electrophoresis
    
    • NativeLoadingDye for nucleic acids on non-denaturing agarose gels
      
    • AgaroseGelBuffers
      
    • OwlElectrophoresisSystem
      
    • EthidiumBromide
      
• proteins
  
  • AffinityTag
    
  • electrophoresis
    
    • SDS-PAGE for denaturing protein separation
      
      • MiniProteanThreeRecipes
        
      • MiniProteanThreeInstructions
        
    • MultiphasicBufferSystems for non-denaturing protein separation
      
    • staining methods
      
      • CoomassieBlue staining
        
      • ZincNegativeStain
        
  • WesternBlotting
    
  • SdsLysis for really quick-and-dirty whole cell protein extracts
    
  • RipaBuffer for slightly less quick-and-dirty whole cell protein extracts
    
• bacteria
  
  • GlycerolStock preparation for long-term bacterial storage
    
  • LB growth medium
    
    • BacterialAntibiotics for selective growth of resistant plasmids
      
  • StreakForIsolation of colonies arising from a single bacterium
    
  • ElectrocompetentCellPreparation of E. coli
    
  • BacterialElectroporation in order to transform plasmids
    
  • BlueJuice for seeing LacZ alpha-complementation in bacterial colonies
    
• cell biology
  
  • FreezingTissueCultureCells
    
  • ThawingTissueCultureCells
    
  • ElectroporatingTissueCultureCells
    
  • ColonyStaining for easy counting of adherent tissue culture cell colonies
    
  • CultureMedium for generic mammalian tissue culture cells
    
  • FlowCytometry
    
  • AcridineOrange -- very useful metachromatic vital stain
    
  • PropidiumIodide -- for distinguishing live cells from dead cells
    
  • NusseNuclearPreparation for cell cycle analysis of nuclei by flow cytometry
    
  • IsolatingNuclei from solid tissues
    
  • ChromosomeSpreads including R-banding and G-banding
    
  • CulturingMouseEmbryonicStemCells
    
  • FluorescencePlusGiemsa (FPG) staining of sister chromatid exchanges
    
    • GiemsaStain
      
  • QuickLeukocyteAnalysis using AcridineOrange with whole blood.
    
  • DnaVsRnaAnalysis using AcridineOrange
    
  • LeukocyteIsolation for removal of erythrocytes from whole blood
    
  • PhosphateBufferedSaline (PBS)
    
• safety
  
  • BiologicalSafety
    
    • NIH recombinant DNA: http://www4.od.nih.gov/oba/rac/guidelines_02/NIH_Guidelines_Apr_02.htm
      
  • ChemicalSafety
    
    • online MSDS: http://msds.ehs.cornell.edu/msdssrch.asp
      
  • CompressedGasSafety
    
  • ElectricalSafety??
    
  • RadiationSafety
    
  • HeatedLiquidsSafety
    
  • SharpsSafety
    
  • UltravioletlightSafety
    

DnaRepairGenes lists gene names across species with some indication of function
SpliceSite

formulae:

• RateOfTranscription calculates the rate of transcription given some reporter with a known half-life
  
• DoublingTime calculates the doubling time of an exponential culture given an initial count, a final count, and the time interval between the two observations
  

useful web-links:

human and mouse provisional genome sequences	http://genome.ucsc.edu
data on genomic DNA digestion frequencies	http://tools.neb.com
human cDNA database	http://fldb.hri.co.jp/cgi-bin/cDNA3/public/publication/index.cgi
DNA repair genes	http://www.cgal.icnet.uk/DNA_Repair_Genes.html
human codon preference	http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=Homo+sapiens+%5Bgbpri%5D&aa=1&style=N
PCR primer design	http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi
oligo properties calculator	http://www.basic.northwestern.edu/biotools/oligocalc.html
oligo Tm and dimer prediction	http://www.biocenter.helsinki.fi/bi/Programs/TmJava.htm
human siRNA database	http://www.human-siRNA-database.net
validated siRNA database	http://sirecords.umn.edu/siRecords
wistar siRNA predictor	http://hydra1.wistar.upenn.edu/Projects/siRNA/siRNAindex.htm
power analysis	http://www.math.uiowa.edu/~rlenth/Power/