Count data for Developmental Transcriptome Dataset (RNA-Seq Gencode v10 summarized to genes)

I am working with the Developmental Transcriptome Dataset.
I was wondering if there is the raw count data available for this dataset? I would like to use this normal brain transcriptome data to run a differential expression analysis.
Any help is appreciated.

Thanks for reaching out. We don’t have non-normalized count data at the Allen Institute; however, there may be other ways to access them. If you succeed, please let us know!

First, raw data was uploaded for controlled-access on dbGaP. I’m not sure whether the count matrices are here alongside the fastq files but it may be worth checking. This work was done as part of a collaboration with several other groups (listed at, and I believe the data was generated in the lab of Dr. Nenad Sestan. In addition, at the Human Brain Transcriptome page (run via the Sestan lab), there are some supplementary materials for a couple of papers. I think a large subset of the donors (and possibly data?) from BrainSpan overlap with the Kang 2011 publication, so you may be able to find some of what you need there. Finally, this work was a very small part of a large publication in 2018 in Science, so there may be something useful buried in there. If none of this helps, you could consider reaching out to Dr. Sestan.

Hi Jeremy,
Thanks a lot for your quick reply. This is very helpful information and I will check out the links you provided.