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]] | ||
*[[Lidstrom:Filtration|Filtration]] | |||
==Cell Culture:== | ==Cell Culture:== | ||
*[[Lidstrom:Tube Spec|Tube Spec]] | *[[Lidstrom:Tube Spec|Tube Spec]] | ||
*[[Lidstrom: Bioscreen|Bioscreen Setup]] | *[[Lidstrom: Bioscreen|Bioscreen Setup]] | ||
=== 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]] | ||
*[[Lidstrom: EZ amino acid stock recipe|EZ amino acid stock recipe]] | *[[Lidstrom: EZ amino acid stock recipe|EZ amino acid stock recipe]] | ||
=== OD measurements === | |||
* [[Lidstrom:Beckmann DU 640B spectrophotometer|Beckmann DU 640B spectrophotometer]] | |||
*[[Lidstrom:NanoDrop|Nano Drop for Cell Cultures]] | |||
==DNA/RNA:== | ==DNA/RNA:== | ||
===DNA=== | ===DNA=== | ||
== PCR == | ==== PCR ==== | ||
*[[Lidstrom:Colony PCR| Colony PCR]] | *[[Lidstrom:Colony PCR| Colony PCR]] | ||
*[[Lidstrom:PCR| PCR (in progress)]] | *[[Lidstrom:PCR| PCR (in progress)]] | ||
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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 57: | 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:Oligo Orders | Oligo Orders]] | *[[Lidstrom:Oligo Orders | Oligo Orders]] | ||
*[[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] | |||
==Protein== | ==Protein== | ||
=== Purification === | |||
*[[Lidstrom:His-tag Protein Purification|His-tag Protein Purification]] | |||
=== Analytics === | |||
*[[Lidstrom: SDS-PAGE | SDS-PAGE Protein Gels]] | *[[Lidstrom: SDS-PAGE | SDS-PAGE Protein Gels]] | ||
=== Protein Concentration Determination === | |||
*[[Lidstrom:Choosing a protein concentration quantification method|Choosing a protein concentration quantification method]] | |||
*[[Lidstrom:BCA assay|BCA assay]] to determine protein concentration | *[[Lidstrom:BCA assay|BCA assay]] to determine protein concentration | ||
*[[Lidstrom:NanoDrop#NanoDrop_for_Proteins|NanoDrop for proteins]] | |||
== Chemicals == | |||
*[[Lidstrom:Chemical Stability|Chemical Stability]] | |||
* Also, see [[Lidstrom:Solution Stock Info|Solution Stock Info]] | |||
==Buffers== | ==Buffers== | ||
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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 88: | Line 120: | ||
===General=== | ===General=== | ||
*[[Lidstrom: Molecular Devices Plate Reader| Molecular Devices (beige) Plate Reader Setup]] | *[[Lidstrom:Enzyme Assay Basics|Enzyme Assay Basics]] | ||
*[[Lidstrom: Tecan Plate Reader|Tecan (dark grey) Plate Reader]] | *[[Lidstrom:Enzyme Assay Data Analysis|Enzyme Assay Data Analysis]] | ||
*[[Lidstrom: Flow Cytometer| Flow Cytometer]] | *[[Lidstrom:Solution Stock Info|Solution Stock Info]] | ||
*[[Lidstrom:Path Length in microwell plates|Path Length in 96-well plates]] | |||
*[[Lidstrom:Reducing Agents|Reducing Agents]] | |||
=== Equipment === | |||
*Plate readers: | |||
**[[Lidstrom: Molecular Devices Plate Reader| Molecular Devices (beige) Plate Reader Setup]] | |||
**[[Lidstrom: Tecan Plate Reader|Tecan (dark grey) Plate Reader]] | |||
* Cuvette spectrophotometer: | |||
** [[Lidstrom:UV-2401PC UV-Vis recording spectrophotometer|UV-2401PC UV-Vis recording spectrophotometer]] | |||
* Centrifuge: | |||
**[[Lidstrom:Sorvall Centrifuge|Sorvall centrifuge]] goes faster than the regular centrifuges that allow 50mL tubes | |||
* Flow Cytometry: | |||
**[[Lidstrom: Flow Cytometer| Flow Cytometer]] | |||
===in vitro pathway assays (CO<sub>2</sub> project)=== | ===in vitro pathway assays (CO<sub>2</sub> project)=== | ||
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*[[Lidstrom:in vitro Pathway Assay: Crude Extract Prep| Crude Extract Prep (in progress)]] | *[[Lidstrom:in vitro Pathway Assay: Crude Extract Prep| Crude Extract Prep (in progress)]] | ||
*[[Lidstrom:in vitro Pathway Assay: Sample Analysis via UPLC-MS/MS | Sample Analysis via UPLC-MS/MS (in progress)]] | *[[Lidstrom:in vitro Pathway Assay: Sample Analysis via UPLC-MS/MS | Sample Analysis via UPLC-MS/MS (in progress)]] | ||
==== Misc ==== | |||
*[[Lidstrom:Assaying enzyme libraries in 96-well plates|Assaying enzyme libraries in 96-well plates]] | |||
*[[Lidstrom:Assaying enzyme libraries|Assaying enzyme libraries]] | |||
== 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]] | |||
=== 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]] | ||
Revision as of 06:58, 31 March 2015
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
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
Metabolomics
- Hot water extraction for in vivo metabolite measurement
- Hot water extraction for in vitro metabolite measurement
