Lidstrom:Protocols: Difference between revisions
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*[[Lidstrom:Autoclave |Autoclave]] | *[[Lidstrom:Autoclave |Autoclave]] | ||
*[[Lidstrom:Sterile Technique | Sterile technique]] | *[[Lidstrom:Sterile Technique | Sterile technique]] | ||
*[[Lidstrom:E. | *[[Lidstrom:E. coli basics|E. coli basics]] | ||
*[[Lidstrom:Preparing Freezer Cell Stocks| Preparing Freezer Cell Stocks]] | *[[Lidstrom:Preparing Freezer Cell Stocks| Preparing Freezer Cell Stocks]] | ||
*[[Lidstrom:Pouring Media Plates|Pouring Media Plates]] | *[[Lidstrom:Pouring Media Plates|Pouring Media Plates]] | ||
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=== Methylotrophs === | === Methylotrophs === | ||
*[[Lidstrom:MM1/MM2/MM3/HY|MM1 | *[[Lidstrom:media for methylotrophs|media for methylotrophs: MM1/MM2/MM3/HY and NB]] | ||
*[[Lidstrom:MM1_recipe|MM1 recipe]] | |||
===E. coli === | ===E. coli === | ||
*[[Lidstrom:E. coli media comparison|E. coli media comparison]] | |||
*[[Lidstrom:Autoinduction Media|Autoinduction Media]] | |||
*[[Lidstrom:M9|M9 recipe]] | *[[Lidstrom:M9|M9 recipe]] | ||
*[[Lidstrom:TB|Terrific Broth recipe]] | *[[Lidstrom:TB|Terrific Broth recipe]] | ||
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=====Fancy Manipulation===== | =====Fancy Manipulation===== | ||
*[[Lidstrom:Site-Directed Mutagenesis|Site-Directed Mutagenesis (in progress)]] | *[[Lidstrom:Site-Directed Mutagenesis|Site-Directed Mutagenesis (in progress)]] | ||
*[[Lidstrom:λ-Red Mediated Gene Knockouts|λ-Red Mediated Gene Knockouts | ** [[Lidstrom:QuikChange Site-Directed Mutagenesis|QuikChange Site-Directed Mutagenesis]] | ||
*[[Lidstrom:λ-Red Mediated Gene Knockouts|λ-Red Mediated Gene Knockouts]] | |||
*[[Dorman:P1_phage_%28lysogenic%29|Phage Lysate Prep]] | *[[Dorman:P1_phage_%28lysogenic%29|Phage Lysate Prep]] | ||
*[[Lidstrom:P1 Phage Transduction|P1 Phage Transduction (in progress)]] | *[[Lidstrom:P1 Phage Transduction|P1 Phage Transduction (in progress)]] | ||
==== Restriction Cloning ==== | ==== Restriction Cloning ==== | ||
*[[Lidstrom:Overview of Restriction Enzyme Cloning|Overview of Restriction Enzyme Cloning]] | |||
*[[Lidstrom:Digestion with Restriction Enzymes|Digestion with Restriction Enzymes]] | *[[Lidstrom:Digestion with Restriction Enzymes|Digestion with Restriction Enzymes]] | ||
*[[Lidstrom:Ligation |Ligation (in progress)]] | *[[Lidstrom:Ligation |Ligation (in progress)]] | ||
| Line 62: | Line 68: | ||
*[[Lidstrom: Agarose Gel Electrophoresis|Agarose Gel Electrophoresis]] | *[[Lidstrom: Agarose Gel Electrophoresis|Agarose Gel Electrophoresis]] | ||
*[[Lidstrom:Sequencing with GeneWiz|Sequencing with GeneWiz]] | *[[Lidstrom:Sequencing with GeneWiz|Sequencing with GeneWiz]] | ||
====Mutagenesis==== | |||
*[[Lidstrom:EMS Mutagenesis|EMS Mutagenesis]] | |||
*[[Lidstrom:UV Mutagenesis|UV Mutagenesis]] | |||
*[[Lidstrom:GeneMorph_II| GeneMorph II]] | |||
====Misc.==== | ====Misc.==== | ||
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*[[Lidstrom:Diluting Primers | Diluting Primers]] | *[[Lidstrom:Diluting Primers | Diluting Primers]] | ||
*[https://www.neb.com/~/media/NebUs/Files/Brochures/Cloning_Guide_1113.pdf NEB cloning guide] | *[https://www.neb.com/~/media/NebUs/Files/Brochures/Cloning_Guide_1113.pdf NEB cloning guide] | ||
==Gene Knockouts== | |||
*[[Lidstrom:Gene_Knockouts|Gene Knockouts]]: pCM184, pCM433 | |||
==Protein== | ==Protein== | ||
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=== Analytics === | === Analytics === | ||
*[[Lidstrom: SDS-PAGE | SDS-PAGE Protein Gels]] | *[[Lidstrom: SDS-PAGE | SDS-PAGE Protein Gels]] | ||
=== Protein Concentration Determination === | === Protein Concentration Determination === | ||
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==E. coli== | ==E. coli== | ||
*[[Lidstrom:E. | *[[Lidstrom:E. coli Vector Compatibility| E. coli Vector Compatibility (In Progress)]] | ||
** origins of replication | |||
*[[Lidstrom:Competent Cell Preparation|Competent Cell Preparation (in progress)]] | *[[Lidstrom:Competent Cell Preparation|Competent Cell Preparation (in progress)]] | ||
=== E. coli transformation === | === E. coli transformation === | ||
*[[Lidstrom:Chemical Transformation|Chemical Transformation]] | *[[Lidstrom:Chemical Transformation|Chemical Transformation]] | ||
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*[[Lidstrom:French Press|French Press]] | *[[Lidstrom:French Press|French Press]] | ||
*[[Lidstrom:Sonicator|Sonication]] | *[[Lidstrom:Sonicator|Sonication]] | ||
*[[Lidstrom:Bug Buster|Bug Buster]] | |||
*[[Lidstrom:Ultracentrifuge|Ultracentrifuge]] | *[[Lidstrom:Ultracentrifuge|Ultracentrifuge]] | ||
| Line 108: | Line 124: | ||
===General=== | ===General=== | ||
*[[Lidstrom:Enzyme Assay Basics|Enzyme Assay Basics]] | *[[Lidstrom:Enzyme Assay Basics|Enzyme Assay Basics]] | ||
*[[Lidstrom:Enzyme Assay Data Analysis|Enzyme Assay Data Analysis]] | |||
*[[Lidstrom:Solution Stock Info|Solution Stock Info]] | *[[Lidstrom:Solution Stock Info|Solution Stock Info]] | ||
*[[Lidstrom:Path Length in microwell plates|Path Length in 96-well plates]] | *[[Lidstrom:Path Length in microwell plates|Path Length in 96-well plates]] | ||
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==== Misc ==== | ==== Misc ==== | ||
*[[Lidstrom:Assaying enzyme libraries in 96-well plates|Assaying enzyme libraries in 96-well plates]] | *[[Lidstrom:Assaying enzyme libraries in 96-well plates|Assaying enzyme libraries in 96-well plates]] | ||
*[[Lidstrom:Assaying enzyme libraries|Assaying enzyme libraries]] | |||
==== Specific Assays ==== | |||
*[[Lidstrom:Formate Assay via Formate Dehdyrogenase|Formate Assay via Formate Dehdyrogenase]] | |||
== Metabolomics == | == Metabolomics == | ||
*[[Lidstrom:Hot water extraction | Hot water extraction for ''in vivo'' metabolite measurement]] | |||
*[[Lidstrom:Hot water extraction in vitro | Hot water extraction for ''in vitro'' metabolite measurement]] | |||
== Bioreactor == | |||
*[[Lidstrom: Bioflo 310 Setup | Bioflo 310 Setup]] | |||
*[[Lidstrom: Bioreactor GC use | Bioreactor GC use]] | |||
=== CO2 project === | === CO2 project === | ||
*[[Lidstrom:Measuring 13C Incorporation Into Protein - CO2 Project|Measuring 13C Incorporation Into Protein - CO2 Project]] | *[[Lidstrom:Measuring 13C Incorporation Into Protein - CO2 Project|Measuring 13C Incorporation Into Protein - CO2 Project]] | ||
** [[Lidstrom:13C Incorporation Into Protein - Data Analysis]] | ** [[Lidstrom:13C Incorporation Into Protein - Data Analysis]] | ||
Latest revision as of 12:05, 30 November 2016
Back home: Lidstrom
General Lab:
- Health & Safety
- Finding Chemicals
- Dishwasher
- Autoclave
- Sterile technique
- E. coli basics
- Preparing Freezer Cell Stocks
- Pouring Media Plates
- Filtration
Cell Culture:
Methylotrophs
E. coli
- E. coli media comparison
- Autoinduction Media
- M9 recipe
- Terrific Broth recipe
- EZ amino acid stock recipe
OD measurements
DNA/RNA:
DNA
PCR
Isolation
- QIAquick Gel Extraction Kit Protocol
- Genomic DNA minikit extraction
- Genomic DNA phenol/chloroform extraction
Manipulation
Fancy Manipulation
- Site-Directed Mutagenesis (in progress)
- λ-Red Mediated Gene Knockouts
- Phage Lysate Prep
- P1 Phage Transduction (in progress)
Restriction Cloning
Gibson Cloning
Obervation
Mutagenesis
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
Analytics
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
E. coli
- E. coli Vector Compatibility (In Progress)
- origins of replication
- Competent Cell Preparation (in progress)
E. coli transformation
Lysing & Cells & Clarifying Extract
Assays
General
- Enzyme Assay Basics
- Enzyme Assay Data Analysis
- Solution Stock Info
- Path Length in 96-well plates
- Reducing Agents
Equipment
- Plate readers:
- Cuvette spectrophotometer:
- Centrifuge:
- Sorvall centrifuge goes faster than the regular centrifuges that allow 50mL tubes
- Flow Cytometry:
in vitro pathway assays (CO2 project)
- Cell Prep (in progress)
- Crude Extract Prep (in progress)
- Sample Analysis via UPLC-MS/MS (in progress)
Misc
Specific Assays
Metabolomics
- Hot water extraction for in vivo metabolite measurement
- Hot water extraction for in vitro metabolite measurement
