Question

Where can I download full transcriptome profiles for specific regions in the human brain?

0

Entering edit mode

6.1 years ago

SpacemanSpiffo ▴ 30

I am attempting to make comparisons between the transcriptome of an IPS-derived neural stem cell and that of region-specific samples from external sources. So far I haven't been able to find any such data set available for download. Would anyone have a source to recommend?

TPM format would be preferrable, but any human region-specific transcriptome datasets would be great.

RNA-Seq brain • 985 views

ADD COMMENT • link updated 6.1 years ago by Kevin Blighe 88k • written 6.1 years ago by SpacemanSpiffo ▴ 30

0

Entering edit mode

Allen brain atlas has some data available for download.

ADD REPLY • link 6.1 years ago by GenoMax 147k

0

Entering edit mode

Try ADNI and AMPAD

ADD REPLY • link 6.1 years ago by cpad0112 21k

0

Entering edit mode

ADNI is still controlled access though, right? (I had / have approved access)

ADD REPLY • link 6.1 years ago by Kevin Blighe 88k

0

Entering edit mode

I think so @ Kevin Blighe

ADD REPLY • link 6.1 years ago by cpad0112 21k

score 0 · Answer 1 · 2018-10-23

FANTOM5 profiled neural stem cells that were [I believe] IPS-derived. They have many hundreds of tissues from human and mouse, a large proportion of which are from the central nervous system. Take a look: HERE and HERE.

On the data download page, there are raw counts and RLE counts. RLE relates to the method implemented in DESeq2.

Note that FANTOM utilised CAGE-seq, not RNA-seq. CAGE-seq profiles expression at gene promoters.

Kevin