PstI-MspI GBS protocol

The “protocol” that we have been using is available here as a Google doc. I use quotes there because, as you will see, there is no single protocol used by the lab to date. Without analyzed sequence data yet to compare the described protocols, the best advice I can give to you is to pick a sensible pipeline for your needs, taking into consideration the time/effort/desired output that works for you, and apply that pipeline consistently to all samples for the same project. All sets of methods described have resulted in libraries that pass QC and generate a sufficient reads during sequencing. Good luck!

How my PhD was saved by DTT, or: how to get moderate quantities of clean, unsheared DNA from tricky tissues

I have been trying for months to find a high-throughput solution to DNA extraction from lyophilized (freeze-dried) leaf discs of Helianthus argophyllus, a species known for its intransigent polyphenolics and low DNA yields. And I appear to have found one, thanks to Horne et al. 2004 (here) and Dow Chemical!

Continue reading

lab contact information and birthday list

Here is the most up-to-date contact information for the Rieseberg lab, including birthdays, email addresses, and phone numbers. If you want, you can download a word document of this here: Lab Contact Info and Birthday List. If your information changes, either let me know or edit this post and the downloadable document appropriately. Thanks!
(contact: John L)

Continue reading

Turning your SNP table into a STRUCTURE input file (Brook)

I suspect there are probably several homemade versions of this kind of script kicking around, but here is a perl script I’ve written for turning your SNP table into a STRUCTURE input file. To use it, you should change the .txt to a .pl after downloading the script. More on STRUCTURE input files (and so much more!) is in the documentation here.

Continue reading