Protocols and Laboratory Reference

Organization

Protocols and Laboratory Reference

• Genomic DNA Isolation
  Isolate gDNA for genome re-sequencing.
• Targeted Sequencing of a Specific Gene
  To validate point mutations and small indels predicted from whole-genome re-sequencing.
• Pulsed-Field Gel Electrophoresis (PFGE) Mapping
  To validate large-scale chromosomal rearrangements, deletions, and duplications.

Experimental Evolution

Protocols and Laboratory Reference

• Genomic DNA Isolation
  Isolate gDNA for genome re-sequencing.
• Targeted Sequencing of a Specific Gene
  To validate point mutations and small indels predicted from whole-genome re-sequencing.
• Pulsed-Field Gel Electrophoresis (PFGE) Mapping
  To validate large-scale chromosomal rearrangements, deletions, and duplications.

Experimental Evolution

Protocols and Laboratory Reference

Bacteria (E. coli)

• Long Term Line Competitions
• 96-Well Microplate Competitions
  • Plating Checklist

Protocols and Laboratory Reference

• Media Recipes
• Antibiotic Stock Solutions and Working Concentrations

• Phage T5 Fluctuation Test
• Phage Lysate Preparation (T4,T5,T6) and Determining Phage Titer
• Making Electrocompetent Cells

Protocols and Laboratory Reference

• Media Recipes
• Antibiotic Stock Solutions and Working Concentrations

• Phage T5 Fluctuation Test
• Phage Lysate Preparation (T4,T5,T6) and Determining Phage Titer
• Making Electrocompetent Cells

Protocols and Laboratory Reference

• Primer Design
• PCR

• Gene and Genomic Sequencing
• Bacterial Genetic Code
• Design Primers for REL606 (NCBI)

Protocols and Laboratory Reference

Microbiology

• Antibiotic Resistance Fluctuation Tests
• Phage T5 Fluctuation Test
• Phage Lysate Preparation (T4,T5,T6) and Determining Phage Titer

Protocols and Laboratory Reference

• Antibiotic Resistance Fluctuation Tests
• Phage T5 Fluctuation Test
• Phage Lysate Preparation (T4,T5,T6) and Determining Phage Titer

• UV Mutagenesis
• E. coli Microarray Experiments
• Commonly used plasmids

Genetic Modification

• Gene Gorging Evolved Alleles
• Gene Knockouts (Datsenko and Wanner Method) (Keio Strain Background)

Protocols and Laboratory Reference

Sequence Analysis

• Primer Design

Protocols and Laboratory Reference

• • Using the Deep 96-Well Pin Tool
• Population Metagenomics Long Term
• Genome Minimization Growth/Death Assays

See Also

Protocols and Laboratory Reference

• PCR
• Gene and Genomic Sequencing
• Bacterial Genetic Code

• Blast2Seq (NCBI)
• ORF Finder (NCBI)
• EMBOSS Transeq - DNA to protein translation.

Protocols and Laboratory Reference

• Primer Design
• PCR

• Bacterial Genetic Code
• Blast2Seq (NCBI)
• ORF Finder (NCBI)

• Gene Gorging Evolved Alleles
• Gene Knockouts (Datsenko and Wanner Method) (Keio Strain Background)

Experimental Evolution

Bacteria (E. coli)

• Selecting Arabinose Marker Revertants

• • Using the Deep 96-Well Pin Tool
• Population Metagenomics Long Term
• Genome Minimization Growth/Death Assays

See Also

Protocols and Laboratory Reference

Sequence Analysis

• Primer Design

• Making Electrocompetent Cells
• UV Mutagenesis
• E. coli Microarray Experiments

• Cloning and Strain Construction Projects

Genetic Modification

Sequence Analysis

• Making Electrocompetent Cells
• UV Mutagenesis
• E. coli Microarray Experiments

Genetic Modification

Sequence Analysis

• Phage Lysate Preparation (T4,T5,T6) and Determining Phage Titer
• Making Electrocompetent Cells
• UV Mutagenesis

Genetic Modification

• • Using the Deep 96-Well Pin Tool
• Population Metagenomics Long Term
• Genome Minimization Growth/Death Assays

See Also

• OpenWetWare a Wiki of biological protocols

Sequence Analysis

• Common Media Recipes
• Antibiotic Resistance Fluctuation Tests

• Phage Lysate Preparation (T4,T5,T6) and Determining Phage Titer
• Making Electrocompetent Cells
• UV Mutagenesis

Sequence Analysis

• Common Media Recipes
• Antibiotic Resistance Fluctuation Tests

• Making Electrocompetent Cells
• UV Mutagenesis

Sequence Analysis

See Also

• OpenWetWare a Wiki of biological protocols

Sequence Analysis

• PCR
• Gene and Genomic Sequencing
• Bacterial Genetic Code

Sequence Analysis

• Bacterial Genetic Code
• Blast2Seq (NCBI)
• ORF Finder (NCBI)

Microbiology

Sequence Analysis

• Gene and Genomic Sequencing
• Bacterial Genetic Code
• Blast2Seq (NCBI)

Microbiology

Sequence Analysis

Genetic Modification

• Gene Gorging Neutral Markers

• Gene Knockouts (Datsenko and Wanner Method) (Keio Strain Background)

Experimental Evolution

Sequence Analysis

Experimental Evolution

Bacteria (E. coli)

• Long Term Line Competitions
• 96-Well Microplate Competitions
  • Plating Checklist

Sequence Analysis

• Changing Environment Long Terms
• Marker Divergence Long Terms
  • Using the Deep 96-Well Pin Tool

• Genome Minimization Growth/Death Assays

See Also

Sequence Analysis

Bacteria (E. coli)

• Long Term Line Competitions
• 96-Well Microplate Competitions

• Changing Environment Long Terms
• Marker Divergence Long Terms
  • Using the Deep 96-Well Pin Tool

Sequence Analysis

Experimental Evolution

Bacteria (E. coli)

• Long Term Line Competitions

• • Using the Deep 96-Well Pin Tool
• Genome Minimization Growth/Death Assays

Sequence Analysis

• PCR

• Bacterial Genetic Code
• Blast2Seq (NCBI)

Sequence Analysis

• Antibiotic Resistance Fluctuation Tests
• Phage Farming
• Making Electrocompetent Cells

Genetic Modification

Sequence Analysis

• Carbon Source Evolvability Long Term
  • Using the Deep 96-Well Pin Tool
• Genome Minimization Growth/Death Assays

Sequence Analysis

Genetic Modification

• Gene Knockouts (Datsenko and Wanner Method) (Keio Strain Background)

Experimental Evolution

• Carbon Source Evolvability Competitions
• Carbon Source Evolvability Long Term
  • Using the Deep 96-Well Pin Tool

• Genome Minimization Growth/Death Assays

Sequence Analysis

Genetic Modification

• Gene Gorging

Experimental Evolution

Bacteria (E. coli)

Sequence Analysis

• Common Media Recipes
• Antibiotic Resistance Fluctuation Tests
• Phage Farming