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I need to obtain publicly available RNA-seq + SNP genotyping data for a cohort - ideally one where the RNA-seq data has been sequenced from brain tissue.

I have found CMC and GTEx to be sufficient for my needs, however the procedure to obtaining data from both these sources are extremely long and they request us to share our data with them as well; which we can not do because it is not ours to share.

I was wondering if anyone knows of another resource that can be used for obtaining such data?

Thanks

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    $\begingroup$ Have a look through EGA. It's not public, but you're unlikely to find anything that is. $\endgroup$
    – Devon Ryan
    Apr 18, 2020 at 7:37

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Human RNA-seq data, like genetic data is very sensitive data as it can be used to identify people (and their relatives), so people will likely not distribute it without entering a formal agreement that ensures that people can be held accountable if the data is misused, stolen or made public. Depending on the consent form signed by the patients (or their relatives), they may not be allowed to share it at all. One possibility would be to start a collaboration with a group that has access to such data and ask them to run your analyses on their data. You can then have a shared publication and it's a win for everybody.

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  • $\begingroup$ Could you elaborate on your answer, because at present it is not sufficiently informative? "will likely not distribute it lightly", what does that mean precisely by means of example? $\endgroup$
    – M__ ♦
    Apr 17, 2020 at 21:18
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    $\begingroup$ In most western countries making such data publicly available would be illegal, or at the very least be deemed so ethically problematic that data would be sent to EGA or a similar semi-closed platform. $\endgroup$
    – Devon Ryan
    Apr 18, 2020 at 7:37
  • $\begingroup$ Thank you for your comments. I will take a look at EGA. @citronrose very good suggestion, I thought about it myself. Unfortunately with the current climate, and with everybody working from home, it's not as easy to contact people as it once was, I will give it a go though. $\endgroup$
    – h3ab74
    Apr 18, 2020 at 15:41

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