Retired Protocols

• Designing a new part
  Designing a new part for use in the BTK
• Bee Microbiome Toolkit (BTK)
  Golden Gate part kit for work in non-model bacterial species

Retired on May 23, 2014

• Crush-Soak Elution
  Recover DNA or RNA samples from polyacrylamide gels.
• Ethanol Precipitation
  Precipitate DNA or RNA samples to remove salts and concentrate.
• Primer Extension
• Total Alkaline Digest of Embedded RNA linkages
• Setting up compilation using Autotools
• Interpreting breseq output.
  How to interpret, check, and manually correct breseq results.
• Pulsed-Field Gel Electrophoresis (PFGE) Mapping
  To validate large-scale chromosomal rearrangements, deletions, and duplications.
• Using APE
• Measuring the Rate of Attrition in frozen or cooled samples
• Extracting Clean Metagenomic DNA From Soil

Previously Retired

• E. coli Microarray
• Veracode Golden Gate Genotyping

• 96-Well Microplate Competitions
  • Plating Checklist
• Changing Environment Long Terms
• Marker Divergence Long Terms
  • Using the Deep 96-Well Pin Tool
• Population Metagenomics Long Term
• Genome Minimization Growth/Death Assays
• ASKA Strain Evolution Experiment

Retired Protocols

• Designing a new part
  Designing a new part for use in the BTK

Retired on May 23, 2014

• Crush-Soak Elution
  Recover DNA or RNA samples from polyacrylamide gels.
• Ethanol Precipitation
  Precipitate DNA or RNA samples to remove salts and concentrate.
• Primer Extension
• Total Alkaline Digest of Embedded RNA linkages
• Setting up compilation using Autotools
• Interpreting breseq output.
  How to interpret, check, and manually correct breseq results.
• Pulsed-Field Gel Electrophoresis (PFGE) Mapping
  To validate large-scale chromosomal rearrangements, deletions, and duplications.
• Using APE
• Measuring the Rate of Attrition in frozen or cooled samples
• Extracting Clean Metagenomic DNA From Soil

Previously Retired

• E. coli Microarray
• Veracode Golden Gate Genotyping
• Phage T5 Fluctuation Test
• 96-Well Microplate Competitions
  • Plating Checklist
• Changing Environment Long Terms
• Marker Divergence Long Terms
  • Using the Deep 96-Well Pin Tool
• Population Metagenomics Long Term
• Genome Minimization Growth/Death Assays
• ASKA Strain Evolution Experiment

Retired Protocols

Retired on May 23, 2014

• Crush-Soak Elution
  Recover DNA or RNA samples from polyacrylamide gels.
• Ethanol Precipitation
  Precipitate DNA or RNA samples to remove salts and concentrate.
• Primer Extension
• Total Alkaline Digest of Embedded RNA linkages
• Setting up compilation using Autotools
• Interpreting breseq output.
  How to interpret, check, and manually correct breseq results.
• Pulsed-Field Gel Electrophoresis (PFGE) Mapping
  To validate large-scale chromosomal rearrangements, deletions, and duplications.
• Using APE
• Measuring the Rate of Attrition in frozen or cooled samples
• Extracting Clean Metagenomic DNA From Soil

Previously Retired

• E. coli Microarray
• Veracode Golden Gate Genotyping
• Phage T5 Fluctuation Test
• 96-Well Microplate Competitions
  • Plating Checklist
• Changing Environment Long Terms
• Marker Divergence Long Terms
  • Using the Deep 96-Well Pin Tool
• Population Metagenomics Long Term
• Genome Minimization Growth/Death Assays
• ASKA Strain Evolution Experiment

Retired Protocols

Retired on May 23, 2014

• Crush-Soak Elution
  Recover DNA or RNA samples from polyacrylamide gels.
• Ethanol Precipitation
  Precipitate DNA or RNA samples to remove salts and concentrate.
• Primer Extension
• Total Alkaline Digest of Embedded RNA linkages
• Setting up compilation using Autotools
• Interpreting breseq output.
  How to interpret, check, and manually correct breseq results.
• Pulsed-Field Gel Electrophoresis (PFGE) Mapping
  To validate large-scale chromosomal rearrangements, deletions, and duplications.
• Using APE
• Measuring the Rate of Attrition in frozen or cooled samples
• Extracting Clean Metagenomic DNA From Soil

Previously Retired

• E. coli Microarray
• Veracode Golden Gate Genotyping
• Phage T5 Fluctuation Test
• 96-Well Microplate Competitions
  • Plating Checklist
• Changing Environment Long Terms
• Marker Divergence Long Terms
  • Using the Deep 96-Well Pin Tool
• Population Metagenomics Long Term
• Genome Minimization Growth/Death Assays
• ASKA Strain Evolution Experiment

Retired Protocols

Retired on May 23, 2014

• Crush-Soak Elution
  Recover DNA or RNA samples from polyacrylamide gels.
• Ethanol Precipitation
  Precipitate DNA or RNA samples to remove salts and concentrate.
• Primer Extension
• Total Alkaline Digest of Embedded RNA linkages
• Setting up compilation using Autotools
• Interpreting breseq output.
  How to interpret, check, and manually correct breseq results.
• Pulsed-Field Gel Electrophoresis (PFGE) Mapping
  To validate large-scale chromosomal rearrangements, deletions, and duplications.
• Using APE
• Measuring the Rate of Attrition in frozen or cooled samples
• Extracting Clean Metagenomic DNA From Soil

Previously Retired

• E. coli Microarray
• Veracode Golden Gate Genotyping
• Phage T5 Fluctuation Test
• 96-Well Microplate Competitions
  • Plating Checklist
• Changing Environment Long Terms
• Marker Divergence Long Terms
  • Using the Deep 96-Well Pin Tool
• Population Metagenomics Long Term
• Genome Minimization Growth/Death Assays
• ASKA Strain Evolution Experiment

Retired Protocols

Retired on May 23, 2014

• Measuring the Rate of Attrition in frozen or cooled samples

Previously Retired

• E. coli Microarray
• Veracode Golden Gate Genotyping
• Phage T5 Fluctuation Test
• 96-Well Microplate Competitions
  • Plating Checklist
• Changing Environment Long Terms
• Marker Divergence Long Terms
  • Using the Deep 96-Well Pin Tool
• Population Metagenomics Long Term
• Genome Minimization Growth/Death Assays
• ASKA Strain Evolution Experiment

Retired Protocols

Retired on May 23, 2014

Previously Retired

• E. coli Microarray
• Veracode Golden Gate Genotyping
• Phage T5 Fluctuation Test
• 96-Well Microplate Competitions
  • Plating Checklist
• Changing Environment Long Terms
• Marker Divergence Long Terms
  • Using the Deep 96-Well Pin Tool
• Population Metagenomics Long Term
• Genome Minimization Growth/Death Assays
• ASKA Strain Evolution Experiment

Retired Protocols

• E. coli Microarray
• Veracode Golden Gate Genotyping
• Phage T5 Fluctuation Test
• 96-Well Microplate Competitions
  • Plating Checklist
• Changing Environment Long Terms
• Marker Divergence Long Terms
  • Using the Deep 96-Well Pin Tool
• Population Metagenomics Long Term
• Genome Minimization Growth/Death Assays
• ASKA Strain Evolution Experiment

Retired Protocols

• E. coli Microarray
• Veracode Golden Gate Genotyping
• Phage T5 Fluctuation Test

Retired Protocols

• E. coli Microarray
• Veracode Golden Gate Genotyping
• Phage T5 Fluctuation Test