Protocols

Below is a list of protocols, both general collections and protocols specific to the class. This list is by no means comprehensive, and you can find a lot more on the web. If you do, and it could be of general interest, please let me know - this collection is an ongoing effort, and could become a valuable resource for our lab and others.

General Collections

• PCR Jump Station - software, protocols and wise words on PCR. Small print, but trustworty.
• Molecular Biology Protocols - huge selection of protocols

Specific for this class

DNA extraction and clean-up

• Salt Precipitation Protocol
• QIAGEN DNeasy - DNA extraction in single tube or 96 well format
• QIAprep Spin Miniprep Kit - plasmid extraction from bacterial cultures. Manual and MSDS sheets.
• QIAGEN Quiaquick - clean up of PCR product before sequencing and genotyping. Single tube, 8-strip tubes or 96 well format.

Cloning and sequencing

• Invitrogen TA cloning manual - cloning of PCR products with Invitrogen kits. Brochure (pretty pictures) and manual (more extensive)
• Cycle Sequencing Kit - specifically designed for MegaBace
• Microsatellite Cloning Protocol - by one of your predecessors, Nick Lowry
• More microsatellite cloning protocols by Travis Glenn, University of Georgia.

Electrophoresis

• Polyacrylamide Gels - general notes and troubleshooting, instructions manual, and Safety Data Sheet
• SybrGold - protocols for basic use, tips and the Material Safety Data Sheets.
• SSCP Protocol from UC Davis. Also a good paper by Sunnucks et al. 2000.

Various

• Protocols and links for t-RFLPs
• Primer design: Primer 3, Webprimer, Codehop

Equipment Manuals

• Pipettes - manual with tips from Rainin. See also useful tips on pipette ergonomics.
• MJResearch DNA Engine - manual
• Eppendorf centrifuge - manual
• Horizontal electrophoresis rigs - manual by Owl Scientific (large file - 5.2 MB - so you may want to look at the hardcopies in the lab)
• Vertical electrophoresis rigs (polyacrylamide) - manual by Owl Scientific, and a manual for the tricky gel caster
• FMBIO II (room 185, 'gel room') - quick guides for general use, DNA fragment sizing and DNA quantification. Full Manual (large file - 5.4 MB) (Do not use without instructions)
• MegaBace (room 272) - General notes on ethanol precipitation for cycle sequencing, fragment analysis and sequencing. (Do not use - give your samples to Ann)