I have some DNA extractions that I would like sequenced to do some population genetics work (GBS or similar). Unfortunately, due to the age of the samples and their storage method (stored in ethanol at room temperature) the DNA I have is low in quantity and highly degraded.
Are there any companies that would accept low-quality/quantity samples for sequencing?
Thanks in advance.
I am unaware about the companies however I would like to ask you, is it only the fragmented DNA you are dealing with or inhibitors too?
If the DNA is just fragmented, you can amplify the DNA by random primers and that DNA could be used for any further downstream applications.
oooohhhhh- good luck with that. What type of organism is the DNA from?
You could try UGA, we sent them some degraded samples for GBS and they were willing to give it a shot, but we did have a lot of DNA to work with at least. They charged us ~$39 per sample for 96 samples and included GBS library prep and sequencing. However, you should the degraded samples did not turn out so well and in my experience with RAD-seq based approaches it is hard to get good data if the samples are degraded since you have to carryout a digest that will further cut your samples down to even smaller size, especially if you do double digest.
If possible I would suggest using a probe based method (i.e. UCE or AHE) or just doing whole genome re-sequencing if your budget allows for it. If you want to stick with a RAD based approach you might want to also check with SNPsaurus (https://www.snpsaurus.com/), which uses a primer based method for RAD-seq (called NextRAD) that might work better with degraded samples. One of the founders of the company is Eric would was one of the inventors of the original RAD-seq and is very knowledge and would probably have some good suggestions.
Hope this helps and good luck!
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