Lab Protocols

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Microsatellite Related

1. BLASTing loci: Checking the loci you are using (or have developed) are unique.

2. Using Standalone Blast: Stand alone BLASTing to check for duplicate loci

3. Microsatellite Library Problem Solving: Common problems observed with microsatellite primers due to poor microsatellite library construction; includes some fundamental checks to establish why primers may be failing to amplify.

4. Unenriched library preparation: Preparing an unenriched microsatellite library (draft!)

DNA Extraction

5. Ammonium acetate DNA extraction (as used with bird blood)

6. Chelex DNA extraction from hair

7. Chelex DNA extraction from hair contaminated with Mycobacterium bovis (e.g. Badger)

8. Silica-based high-throughput DNA extraction

8.5. Guidlelines for taking bird and mammal samples for DNA extraction

DNA Quality and Concentration Estimation

9. Assessing DNA quality using agarose gel

10. Calculating DNA concentration: using markers of known concentration on agarose gel along with a fluorimeter

Other Technical Guides

11. Performing PCR (with PCR recipes)

12. Preparing acrylamide gels and silver staining (coming soon)

13. Molecular sexing of birds (see also SMGF Bird sex-typing using genetic markers)

14. Semi-automated fluorescent genotyping

15. Semi-automated fluorescent genotyping (full method, starting from the blood/tissue)

16. Sequencing Protocol (draft!)

Data Analysis

17. Sequential Bonferoni correction

Protocols From Other Sources

Protocols online

Disclaimer

We have provided these protocols as a courtesy, in the hope that this will help you in your research. Although we have taken great care to record them accurately, we do not accept any responsibility for the accuracy or for any costs or damages that you might suffer as a consequence of mistakes in these protocols. If you use these protocols it is implicit that you accept the conditions of this disclaimer.

Please acknowledge the Biomolecular Analysis Facility at Sheffield and the Natural Environmental Research Council when using these protocols.

Example acknowledgement:
"The laboratory work was assisted by the protocols provided by the Biomolecular Analysis Facility at Sheffield which is funded by the Natural Environmental Research Council, UK."


We would be grateful for suggested corrections / improvements to any of these protocols. Please contact Dr Deborah Dawson.

email : d.a.dawson@sheffield.ac.uk