Difference between revisions of "Davidson Protocols"
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# [http://gcat.davidson.edu/iGem10/index.html Oligator making dsDNA from oligos] | # [http://gcat.davidson.edu/iGem10/index.html Oligator making dsDNA from oligos] | ||
# [http://gcat.davidson.edu/SynBio12/ The Loligator] | # [http://gcat.davidson.edu/SynBio12/ The Loligator] | ||
| − | # | + | # [http://gcat.davidson.edu/SynBio12/successorater.html How many clones should I screen?] |
# [http://gcat.davidson.edu/IGEM06/oligo.html Lance-olator Oligos for dsDNA assembly] old version, we recommend Oligator now | # [http://gcat.davidson.edu/IGEM06/oligo.html Lance-olator Oligos for dsDNA assembly] old version, we recommend Oligator now | ||
# [http://gcat.davidson.edu/GCATalog Access the GCAT-alog of Davidson and MWSU DNA Freezer Stocks] | # [http://gcat.davidson.edu/GCATalog Access the GCAT-alog of Davidson and MWSU DNA Freezer Stocks] | ||
| Line 74: | Line 74: | ||
# [[Sequencing at Agencourt| Sequencing at Agencourt Bioscience]] | # [[Sequencing at Agencourt| Sequencing at Agencourt Bioscience]] | ||
# [[Davidson Missouri W/CUGI_Seuqencing| Sequencing at CUGI]] | # [[Davidson Missouri W/CUGI_Seuqencing| Sequencing at CUGI]] | ||
| − | # [http://gcat.davidson.edu/GcatWiki/images/3/3b/Ape_protocol.pdf Analyzing Sequences with | + | # [http://gcat.davidson.edu/GcatWiki/images/3/3b/Ape_protocol.pdf Analyzing Sequences with ApE] |
| − | # [[Using | + | # [[Using ApE (A Plasmid Editor)]] |
# [http://72.22.219.205/sequence VeriPart for DNA sequences of Registry Parts] | # [http://72.22.219.205/sequence VeriPart for DNA sequences of Registry Parts] | ||
# [http://gcat.davidson.edu/igem10/opt/opt_index.html The Optimus for optimizing codons] | # [http://gcat.davidson.edu/igem10/opt/opt_index.html The Optimus for optimizing codons] | ||
Revision as of 13:48, 8 August 2012
A. General Lab Information
- How to Keep a Lab Notebook
- Common molecular reagents
- Open Access Libraries
- Standard Assembly
- BioBrick Ends
- Compatibility of Plasmids
- Ethanol Precipitate to clean DNA (short protocol)
- glycerolstocks How to Make Glycerol Stocks of Bacteria
B. Gel Electrophoresis and Purification
- Pouring an agarose gel
- Calculate MWs
- 1kb Plus MW markers
- Macherey-Nagel Gel Purification (improved 260/230 ratios)l
- Qiagen QIAquick Gel Purification
- Qiagen QIAquick Column Regeneration Protocol
- ElectroElute Gel Purification
C. Digestion, Ligation, Transformation
- Digest DNA with restriction enzymes
- Double Digest Guide
- Shrimp Alkaline Phosphatase
- Ligation Protocol
- Choices for Transformation: Heat Shock vs. Zyppy
- Heat Shock Transformation OR Short version of Heat Shock
- Zippy Transformation
- TSS Competent Cell Transformation
- Golden Gate Assembly protocol
D. Minipreps
E. Making New Parts and PCR
- Building dsDNA with Oligos
- The Loligator
- Setting up PCR mixtures
- PCR and Mg2+ concentration
- isolate genomic DNA from a single hair follicle
- Prepare PCR product for sequencing after clean and concentration procedure (for Bio113 lab use)
- Making dsDNA Using Primer Dimers
- Clean and Concentrate DNA with spin column (after PCR, before digestion)
- Colony PCR to Screen for Successful Ligations
- Golden Gate Assembly protocol
- How many clones should I screen?
- TAS2R38 PCR amplification
F. Expression of Phenotypes
- Using degradation tags on proteins such as GFP
- Genomic Insertion Protocol
- When inducing with IPTG, use 3 µL of stock (0.2 g/mL = 20% w/v) to every 1 mL of LB or other liquid.
- When inducing with Arabinose, use "2 µL of stock" (10% w/v L-Arabinose) "to every 1 mL" of LB or other liquid.
- When inducing with 3OC6 (HSL), use a 2000 fold dilution of a 10 mg/mL stock solution. We have dissolved in EtOH which is not the best - degrades with time. Keep this cold.
- List of auto-inducers and their catalog numbers
- Synergy Machine Protocol
G. Golden Gate Shuffling
H. Computer Tools We Use
- Optimize your Gel
- Gene Design (Boeke Lab at JHU)
- Gene Splitting Web Site
- PCR Primers w/ BioBricks
- Promega Tm Calculator
- Oligator making dsDNA from oligos
- The Loligator
- How many clones should I screen?
- Lance-olator Oligos for dsDNA assembly old version, we recommend Oligator now
- Access the GCAT-alog of Davidson and MWSU DNA Freezer Stocks
- Sequencing at MWG Operon
- Sequencing at Agencourt Bioscience
- Sequencing at CUGI
- Analyzing Sequences with ApE
- Using ApE (A Plasmid Editor)
- VeriPart for DNA sequences of Registry Parts
- The Optimus for optimizing codons
- Wiser Optimizer Not working right now
'I. Bio113 Lab Protocols
