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Roth Lab Protocols
Dr. John R. Roth
Section of Microbiology, College of Biological Sciences
University of California at Davis
Roth Lab Protocols
DNA Preparation
- Bacterial DNA
- Rapid Bacterial DNA
- Improved Alcohol Precipitation of DNA
- Bacterial DNA in Agarose Plugs
- Bacterial DNA from Mucoid Strains
- Plasmid Preps - Alkaline Method
- Plasmid Preps - Boiling Method
- Plasmid Preps - CsCl Method
- Plasmid Preps - LiCl Method
- Plasmid Preps - Qiagen Method
- Plasmid Preps - SDS Method
- Plasmid Preps - TELT Method
- Bacteriophage M13 DNA
- Bacteriophage Lambda Particles
- Bacteriophage Lambda DNA
- Mud-P22 DNA
- Blunt-Ended DNA Fragments
- Single Stranded DNA by Exonuclease Digestion
- RNA Preparation - Bacterial RNA
DNA Purification
- DEAE Nitrocellulaose Membranes.
- Freezing Method
- GeneClean
- Spin Dialysis
- Wizard Columns
- Electroelution
- Removal of γ-32P-ATP from Oligonucleoides
- Manual Detritylation of Oligonucleotides
- Concentration by Butanol Extraction
- Extraction and Precipitation
- Wizard Columns
DNA Reactions
- Standard Taq-Mediated PCR
- Standard Pfu-Mediated PCR
- Cycle Runoffs
- Long PCR
- N Ladders
- Primers
- Primers: Placing in Collection
- Primer Design
- Single Primer ("Semi-Random") PCR
- Terminus PCR
- PCR in Air Cyclers
- Assymetric PCR
- Inverse PCR
- Long Distance PCR
- RNA Reaction - Cycle Runoffs
- Ligation
- Kinasing
- Phosphatasing
- Radiolabeling by Random Priming
- Radiolabeling by Nick Translation
- Polymerase Chain Reaction
- Sequencing Double Stranded Templates - Alkaline Denature
- Sequencing Double Stranded Templates - Nonidet Method
- Sequencing Single Stranded Templates
- Sequencing with Sequenase
- Digestion with Typical Restriction Endonucleases
- Digestion with 4 bp Site Restriction Endonucleases
- Digestion with 8 bp Site Restriction Endonucleases
- Partial Digestion with 4 bp Site Restriction Endonucleases
- Cloning Partial DNA Digests
DNA Electrophoresis
- Agarose Gels for Duplex DNA
- Agarose Gels for Single Stranded DNA
- Polyacrylamide Gels
- Oligonucleotides
- Orienting M13 Bacteriophage Inserts
DNA Transfer
DNA Hybridization
Bacterial Transformations
Microbiology
- Streaking Bacteria for Single Colonies
- Growing Overnight Cultures
- Freezing Bacterial Cultures
- Serial Dilution
- Replica Printing
- Pouring Plates
- Plating in Top Agar
- Using the Anaerobic Chamber
- Maxicells
Genetics
- Quantitation of Bacteriophage P22
- Transduction with Bacteriophage P22
- Use of Bacteriophage P22 with galE Strains
- How Green Plates Work
- Preparation of Bacteriophage P1
- Quantitation of Bacteriophage P1
- Transduction with Bacteriophage P1
- Quantitation of Bacteriophage Lambda
- Amplification of Bacteriophage Lambda
- Preparation of Bacteriophage Mu from Dilysogens
- cis-Transposition of Bacteriophage Mu
- β-Galactosidase Assays
- B12 Bioassays
Mutagenesis
- Bacterial Cells with DES
- Bacteriophage P22 with Hydroxylamine
- Plasmid DNA with Hydroxylamine
- Bochner Selection of Tetracycline Sensitivity
- Making Defective-Tn10 Pools in Salmonella
- Making Defective-Mu Pools in Salmonella
Miscellaneous
- DNA Quantification - TCA Precipitation
- Molecular Weights of DNA Fragments
- Preparation of Polyacrylamide Gels
- Preparation of DEAE Nitrocellulose Membranes
- Common Prehybridization Solutions
- Common Hybridization Solutions
- Salmonella typhimurium Mud-P22 strains
- International Units of Measurement
- Using Units of Measurement
- 50X E Salts and Derivatives
- Green Indicator Plates
- Lambda Plates
- T2 Buffer
- How to Give a Talk
- Mailing Strains First-Class
- Strain Collection
- Strain Collection, Part II: Culture Culture
Old Protocols
DNA
- DNA Electroelution (Method 2)
- DNA from Agarose (Review)
- DNA from P22 Heads (Method 1)
- DNA from P22 Heads (Method 2)
- Magnetic Separation of DNA Strands
- "Quick and Dirty" Chromosomal DNA
Genetic Manipulations
- Bochner Selection
- DES Mutagenesis
- E.coli Genes into Salmonella
- Electroporation
- Electroporation Competent Cells
- Indicator Plates
- HA Mutagenesis (Method 1)
- HA Mutagenesis (Method 2)
- HA Mutagenesis (Method 3)
- Linear Transformation
- Linear Transformation -- Rules for FRT Primers
- MudP22 Mapping
- P1 Transduction into Salmonella
- P1 Transduction Chart 1
- P1 Transduction Chart 2
- P22 Transduction
Insertion Elements
Phage
Proteins
E.coli Immunoprecipitation