Lidstrom:Protocols: Difference between revisions
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*[[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]] | |||
=== Methylotrophs === | |||
*[[Lidstrom:MM1/MM2/MM3/HY|MM1/MM2/MM3/HY]] | |||
===E. coli === | |||
*[[Lidstrom:M9|M9 recipe]] | *[[Lidstrom:M9|M9 recipe]] | ||
*[[Lidstrom:TB|Terrific Broth recipe]] | *[[Lidstrom:TB|Terrific Broth recipe]] | ||
*[[Lidstrom: | *[[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 ==== | |||
*[[Lidstrom:Colony PCR| Colony PCR]] | |||
*[[Lidstrom:PCR| PCR (in progress)]] | |||
*[[Lidstrom:Thermocyclers|Thermocyclers]] | |||
====Isolation ==== | ====Isolation ==== | ||
*[[Lidstrom:QIAquick Gel Extraction Kit Protocol|QIAquick Gel Extraction Kit Protocol]] | *[[Lidstrom:QIAquick Gel Extraction Kit Protocol|QIAquick Gel Extraction Kit Protocol]] | ||
*[[Lidstrom:Genomic DNA extraction|Genomic DNA minikit extraction]] | |||
*[[Lidstrom:Genomic DNA extraction|Genomic DNA phenol/chloroform extraction]] | |||
====Manipulation==== | ====Manipulation==== | ||
*[[Lidstrom:Building with DNA|Intro: Building with DNA (in progress)]] | *[[Lidstrom:Building with DNA|Intro: Building with DNA (in progress)]] | ||
*[[Lidstrom:Overlap Extension PCR| Overlap Extension PCR (in progress)]] | *[[Lidstrom:Overlap Extension PCR| Overlap Extension PCR (in progress)]] | ||
*[[Qiagen_Buffers| Qiagen Buffer Recipes]] | *[[Qiagen_Buffers| Qiagen Buffer Recipes]] | ||
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*[[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 ==== | |||
*[[Lidstrom:Digestion with Restriction Enzymes|Digestion with Restriction Enzymes]] | |||
*[[Lidstrom:Ligation |Ligation (in progress)]] | |||
==== Gibson Cloning ==== | |||
*[[Lidstrom:Gibson Assembly| Gibson Assembly (In progress)]] | |||
====Obervation==== | ====Obervation==== | ||
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====Misc.==== | ====Misc.==== | ||
*[[Lidstrom:Loading Dye Recipe|Loading Dye Recipe]] | *[[Lidstrom:Loading Dye Recipe|Loading Dye Recipe]] | ||
*[[Lidstrom:Purifying DNA|Purifying DNA (in progress)]] | *[[Lidstrom:Purifying DNA|Purifying DNA (in progress)]] | ||
| Line 48: | Line 69: | ||
*[[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== | ||
*[[Lidstrom: SDS-PAGE | SDS-PAGE Protein Gels]] | *[[Lidstrom: SDS-PAGE | SDS-PAGE Protein Gels]] | ||
==E. | === Protein Concentration Determination === | ||
*[[Lidstrom:E. Coli Vector Compatibility| E. | *[[Lidstrom:Choosing a protein concentration quantification method|Choosing a protein concentration quantification method]] | ||
*[[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== | |||
*[[Lidstrom:Buffers|Buffers]] | |||
==E. coli== | |||
*[[Lidstrom:E. Coli Vector Compatibility| E. coli Vector Compatibility (In Progress)]] | |||
*[[Lidstrom:Competent Cell Preparation|Competent Cell Preparation (in progress)]] | *[[Lidstrom:Competent Cell Preparation|Competent Cell Preparation (in progress)]] | ||
=== E. coli transformation === | |||
*[[Lidstrom:Chemical Transformation|Chemical Transformation]] | *[[Lidstrom:Chemical Transformation|Chemical Transformation]] | ||
*[[Lidstrom:Electroporation|Electroporation]] | *[[Lidstrom:Electroporation|Electroporation]] | ||
*[[Lidstrom:Competent Cells|Competent Cell Lines]] | *[[Lidstrom:Competent Cells|Competent Cell Lines]] | ||
== | == Lysing & Cells & Clarifying Extract == | ||
*[[Lidstrom:French Press|French Press]] | |||
*[[Lidstrom:Sonicator|Sonication]] | |||
*[[Lidstrom:Ultracentrifuge|Ultracentrifuge]] | |||
==Assays== | |||
===General=== | ===General=== | ||
*[[Lidstrom: Plate Reader| Plate Reader Setup]] | *[[Lidstrom:Enzyme Assay Basics|Enzyme Assay Basics]] | ||
*[[Lidstrom:Solution Stock Info|Solution Stock Info]] | |||
=== 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]] | |||
== Metabolomics == | == Metabolomics == | ||
Revision as of 17:23, 25 March 2014
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
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 (in progress)
- Phage Lysate Prep
- P1 Phage Transduction (in progress)
Restriction Cloning
Gibson Cloning
Obervation
Misc.
- Loading Dye Recipe
- Purifying DNA (in progress)
- Miniprep (in progress)
- Oligo Orders
- Diluting Primers
- NEB cloning guide
Protein
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 transformation
Lysing & Cells & Clarifying Extract
Assays
General
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)
