<!-- Preferences start here * Set PAGETITLE = Barrick Lab :: Protocols Preferences end here --> ---+ Protocols and Laboratory Reference ---++ Stock Solutions * [[ProtocolsReagentRecipes][Reagent and Buffer Recipes]] * [[ProtocolsMediaRecipes][Media Recipes]] * [[ProtocolsAntibioticStockSolutions][Antibiotic Stock Solutions and Working Concentrations]] ---++ PCR * [[ProceduresPrimerDesign][Primer Design]] * [[http://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?ORGANISM=413997&INPUT_SEQUENCE=NC_012967.1&log$=seqview_list_primer][Design Primers for REL606 (NCBI)]] * [[ProtocolsOrderingPrimers][Ordering Primers]] * [[ProceduresStandardPCR][Standard PCR]] * [[Protocols16SSequencing][16S rRNA PCR and Sequencing to Identify Unknown Microbes]] ---++ Sequence Analysis * REL606 Resources: [[http://www.ncbi.nlm.nih.gov//genomes/geblast.cgi?gi=24777][Blast]] [[http://www.ncbi.nlm.nih.gov/nuccore/254160123][Genbank]] * [[http://www.ncbi.nlm.nih.gov/BLAST/bl2seq/wblast2.cgi][Blast2Seq (NCBI)]] * [[http://www.ncbi.nlm.nih.gov/gorf/gorf.html][ORF Finder (NCBI)]] * [[http://www.ebi.ac.uk/Tools/emboss/transeq/index.html][EMBOSS Transeq]] - DNA to protein translation. ---++ Microbiology * [[ProtocolsFluctuationTests][Fluctuation Tests]]<br>Measure bacterial mutation rates to antibiotic resistance, phage resistance, or reversion of auxotrophy. * [[ProceduresFluctuationTest][Phage T5 Fluctuation Test]] * [[ProceduresPhageFarming][Phage Lysate Preparation (T4,T5,T6) and Determining Phage Titer]] * [[ProtocolsElectrocompetentCells][Making Electrocompetent Cells]] * [[ProceduresUVMutagenesis][UV Mutagenesis]] * [[ProceduresEColiMicroarray][E. coli Microarray Experiments]] * [[ReferencePlasmids][Commonly used plasmids]] * [[ProjectsCloningStrainConstruction][Cloning and Strain Construction Projects]] ---++ Genetic Modification * [[ProtocolsGeneGorgingMarker][Gene Gorging Neutral Markers]] * [[ProceduresGeneGorgingEvolvedAlleles][Gene Gorging Evolved Alleles]] * [[ProcedureGeneKnockout][Gene Knockouts (Datsenko and Wanner Method)]] (Keio Strain Background) ---++ Genome Re-sequencing and Mutation Validation * [[ProceduresGenomicDNAResequencing][Genomic DNA Isolation]]<br>Isolate gDNA for genome re-sequencing. * [[ProceduresTargetedSequencing][Targeted Sequencing of a Specific Gene]]<br>To validate point mutations and small indels predicted from whole-genome re-sequencing. * [[ProceduresPulsedFieldGelElectrophoresisMapping][Pulsed-Field Gel Electrophoresis (PFGE) Mapping]]<br>To validate large-scale chromosomal rearrangements, deletions, and duplications. * [[ProceduresVeracodeGoldenGateGenotyping][Veracode Golden Gate Genotyping]] ---++ Experimental Evolution of Bacteria * [[ProtocolsAraMarker][Selecting Arabinose Marker Revertants]] * [[ProceduresLongTermCompetitions][Long Term Line Competitions]] * [[ProceduresEvolvabilityCompetitions][96-Well Microplate Competitions]] * [[ProcedureMixingandPlatingChecklist][Plating Checklist]] * [[ProceduresChangingEnvironmentLongTerm][Changing Environment Long Terms]] * [[ProceduresMarkerDivergenceLongTerm][Marker Divergence Long Terms]] * [[ProcedurePinTool][Using the Deep 96-Well Pin Tool]] * [[ProceduresPopulationMetagenomicsLongTerm][Population Metagenomics Long Term]] * [[ProceduresGenomeMinimizationGrowthDeathAssays][Genome Minimization Growth/Death Assays]] * [[ProceduresASKAEvolutionExperiment][ASKA Strain Evolution Experiment]] * [[ProceduresEvolvabilityRiboseSubpopulations][Identifying Ribose Operon Deletions]] * [[ProcedureEvolvabilityMutationAccumulation][Mutation Accumulation for Microsatellite Strains]] ---++ Bioinformatics / Source Code Management * [[ProtocolsSettingUpAutotools][Setting up compilation using Autotools]] * [[ProtocolsUploadingDataToSRA][Uploading sequencing data to the NCBI Short-Read Archive]] * [[ProtocolsRunningBreseqOnTACC][Running <i>breseq</i> on TACC]] * [[ProtocolsBreseqResults][How to interpret and check <i>breseq</i> results]] ---++ See Also * [[http://openwetware.org/wiki/Electrocompetent_cells][OpenWetWare]] a Wiki of biological protocols
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Topic revision: r54 - 2011-05-18 - LindseyWolf