Data Updates - December 13, 2023

The Allen Brain Cell Atlas (ABC Atlas) has been updated with new data!

Mouse Whole-Brain Transcriptomic Cell Type Atlas Data Updates

In conjunction with the publication of an associated paper in Nature, we have made some minor updates to the Merscope and 10x data sets. In addition, 7 new neighborhood embeddings are now fully explorable in the ABC Atlas:

Check out our GitHub resources to learn more and download data.

As always, thank you for being part of the AIBS community. Please let us know how we can improve the ABC Atlas to better serve your needs.

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hello, than you for putting together such a nice dataset

in the was container, i noticed that there are .h5ad files for atac and rna data of the mtg cells. is there any chance that they can be made available for the dlpfc cells as well?

thank you

@shawnfan19: if you are referring to the human SEA-AD work, all of the single nucleus -omics data from DLPFC and MTG (and spatial transcriptomics data from MTG) are available on AWS.

yes i am aware of that

in the aws bucket you provided the .h5ad files for MTG cells at sea-ad-single-cell-profiling/MTG/ATACseq/SEAAD_MTG_ATACseg_all-nuclei.2024-02-13.h5ad and sea-ad-single-cell-profiling/MTG/RNAseq/SEAAD_MTG_RNAseq_all-nuclei.2024-02-13.h5ad.

i was wondering if similar .h5ad files can be made available for the DLPFC cells as well

thank you

The are already available for DLPFC. Let us know if you have any more issues.

i found sea-ad-single-cell-profiling/DLPFC/RNAseq/SEAAD_DLPFC_RNAseq_all-nuclei.2024-02-13.h5ad but could not find any .h5ad files in sea-ad-single-cell-profiling/DLPFC/ATACseq.

is there a .h5ad file for ATACseq data?

Correct, for ATAC-Seq h5ad files are available only for MTG, as we have not yet analyzed DLPFC this way. For RNA-seq h5ad files are available in both regions. Sorry for the confusion.


Do you plan to analyze the DLPFC ATAC-Seq data in the same way soon? To have an idea if I can expect to have DLPFC ATAC-Seq h5ad files in the near future. Thank you in advance and have a nice day

Hi @jerem. These ATAC-seq data are actively being analyzed. While we don’t currently have a timeline for release, we will post to the Community Forum when these (or other SEA-AD) data become available.