How do I access raw RNA-Seq data (e.g., FASTQ, bam)?

Links to raw data for each project will eventually be posted on the Transcriptional Landscape of the Brain “Explore” page after they become available. Current publications and data available for download follow:

  • Single cell / nucleus RNA-Seq collected as through BICCN is available through BCDC (and via link above).
  • Aging, Dementia, and TBI Study raw data is on NIAGADS (see link above).
  • BrainSpan Atlas of the Developing Human Brain: download raw data from RNA-seq and several other modalities is available through dbGaP, here.
  • Read more about single nucleus RNA-Seq data availability in this Forum post.
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Raw data for a few mouse pre-BICCN studies is available through GEO/SRA:

For the mouse VISp data from Tasic et al., Nature Neuroscience (2016), raw data are available on GEO at GSE71585.

For mouse VISp and ALM data from Tasic et al., Nature (2018), raw data is available at GSE115746. If you’re going for one dataset for VISp, I would recommend this one due to the use of newer RNA-seq chemistry with better gene detection.

Additional mouse VISp data from Daigle et al., Cell (2018) is available at GSE112846.

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Due to concerns of donor identification, raw data is currently unavailable for RNA-seq data from the Allen Human Brain Atlas (231 samples from donors H0351.2001 and H0351.2002), from RNA-seq data from our IVY Glioblastoma Atlas Project, and for most of our human snRNA-seq data (the nuclei not collected through BCDC). We will update this link if and when these data become available.

UPDATE: Some controlled access data is now available through the NeMO Archive and more will be available soon. Directions for requesting data access are found at the same link. At present, any available controlled-access single cell/nucleus RNA-seq data will be found on NeMO and nowhere else.


Update: controlled access data for the human SMART-Seq data sets listed on the Allen Cell Types Database is now available through the NeMO Archive. This includes data from our published study on human middle temporal gyrus.

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