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.
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SpacemanSpiffo •
1 answer
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
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Allen brain atlas has some data available for download.
Try ADNI and AMPAD
ADNI is still controlled access though, right? (I had / have approved access)
I think so @ Kevin Blighe