Lidstrom:Protocols

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General Lab:

• Health & Safety
• Finding Chemicals
• Dishwasher
• Autoclave
• Sterile technique
• E. coli basics
• Preparing Freezer Cell Stocks
• Pouring Media Plates
• Filtration

Cell Culture:

• Tube Spec
• Bioscreen Setup

Methylotrophs

• media for methylotrophs: MM1/MM2/MM3/HY and NB
• MM1 recipe

E. coli

• E. coli media comparison
• Autoinduction Media
• M9 recipe
• Terrific Broth recipe
• EZ amino acid stock recipe

OD measurements

• Beckmann DU 640B spectrophotometer
• Nano Drop for Cell Cultures

DNA/RNA:

DNA

PCR

• Colony PCR
• PCR (in progress)
• Thermocyclers

Isolation

• QIAquick Gel Extraction Kit Protocol
• Genomic DNA minikit extraction
• Genomic DNA phenol/chloroform extraction

Manipulation

• Intro: Building with DNA (in progress)
• Overlap Extension PCR (in progress)
• Qiagen Buffer Recipes

Fancy Manipulation

• Site-Directed Mutagenesis (in progress)
  • QuikChange Site-Directed Mutagenesis
• λ-Red Mediated Gene Knockouts
• Phage Lysate Prep
• P1 Phage Transduction (in progress)

Restriction Cloning

• Overview of Restriction Enzyme Cloning
• Digestion with Restriction Enzymes
• Ligation (in progress)

Gibson Cloning

• Gibson Assembly (In progress)

Obervation

• Colony PCR
• Agarose Gel Electrophoresis
• Sequencing with GeneWiz

Mutagenesis

• EMS Mutagenesis
• UV Mutagenesis
• GeneMorph II

Misc.

• Loading Dye Recipe
• Purifying DNA (in progress)
• Miniprep (in progress)
• Oligo Orders
• Diluting Primers
• NEB cloning guide

Gene Knockouts

• Gene Knockouts: pCM184, pCM433

Protein

Purification

• His-tag Protein Purification

Analytics

• SDS-PAGE Protein Gels

Protein Concentration Determination

• Choosing a protein concentration quantification method
• BCA assay to determine protein concentration
• NanoDrop for proteins

Chemicals

• Chemical Stability
• Also, see Solution Stock Info

Buffers

• Buffers

E. coli

• E. coli Vector Compatibility (In Progress)
  • origins of replication
• Competent Cell Preparation (in progress)

E. coli transformation

• Chemical Transformation
• Electroporation
• Competent Cell Lines

Lysing & Cells & Clarifying Extract

• French Press
• Sonication
• Bug Buster
• Ultracentrifuge

Assays

General

• Enzyme Assay Basics
• Enzyme Assay Data Analysis
• Solution Stock Info
• Path Length in 96-well plates
• Reducing Agents

Equipment

• Plate readers:
  • Molecular Devices (beige) Plate Reader Setup
  • Tecan (dark grey) Plate Reader
• Cuvette spectrophotometer:
  • UV-2401PC UV-Vis recording spectrophotometer
• Centrifuge:
  • Sorvall centrifuge goes faster than the regular centrifuges that allow 50mL tubes
• Flow Cytometry:
  • Flow Cytometer

in vitro pathway assays (CO₂ project)

• Cell Prep (in progress)
• Crude Extract Prep (in progress)
• Sample Analysis via UPLC-MS/MS (in progress)

Misc

• Assaying enzyme libraries in 96-well plates
• Assaying enzyme libraries

Specific Assays

• Formate Assay via Formate Dehdyrogenase

Metabolomics

• Hot water extraction for in vivo metabolite measurement
• Hot water extraction for in vitro metabolite measurement

Bioreactor

• Bioflo 310 Setup
• Bioreactor GC use

CO2 project

• Measuring 13C Incorporation Into Protein - CO2 Project
  • Lidstrom:13C Incorporation Into Protein - Data Analysis