Question: Where can I download full transcriptome profiles for specific regions in the human brain?
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gravatar for SpacemanSpiffo
12 months ago by
SpacemanSpiffo10 wrote:

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.

brain rna-seq • 274 views
ADD COMMENTlink modified 12 months ago by Kevin Blighe51k • written 12 months ago by SpacemanSpiffo10

Allen brain atlas has some data available for download.

ADD REPLYlink written 12 months ago by genomax74k

Try ADNI and AMPAD

ADD REPLYlink written 12 months ago by cpad011212k

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

ADD REPLYlink written 12 months ago by Kevin Blighe51k

I think so @ Kevin Blighe

ADD REPLYlink written 12 months ago by cpad011212k
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gravatar for Kevin Blighe
12 months ago by
Kevin Blighe51k
Kevin Blighe51k wrote:

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

ADD COMMENTlink written 12 months ago by Kevin Blighe51k
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