Online brain RNA-Seq database

Question

[Victoria]

Hi, I have some RNA-Seq datasets from patients and am looking for online brain RNA-Seq datasets to use them as controls. Does anyone have any suggestions for that?

Thanks!

Answer 1

[jared.andrews07]

The Allen Brain Map is probably the best resource out there. Expression, histology, and genetics.

[Victoria]

Thanks for your answer. But on their brain RNA-Seq webpage, there are only two human brains with RNA-Seq data. http://human.brain-map.org/static/download Are there other databases with more samples?

[jared.andrews07]

They break it up by anatomical structures (and have microarray data as well). You can certainly find other sets on GEO, but "brain" samples is pretty vague. It is not at all a homogeneous organ.

[Victoria]

To be more specific, I am looking for healthy thalamus RNA-Seq data. Found some on BRAINSPAN, but they provided FPKM data. I prefer raw counts. Any comments would be appreciated!

[jared.andrews07]

RNA-seq is tough to find for healthy, hard to acquire tissues. Found a few studies on GEO that might be helpful, but they are arrays: 1, 2, 3. Will keep an eye out for others.

[Victoria]

Thanks for your response; at this point I am mainly looking for RNA-Seq data. I will look more as well; thanks!