RDS file for the seattle Alzheimer’s Disease Brain Cell Atlas

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Hello, I wanted to annotate my single cell RNAseq umap with the seattle Alzheimer’s Disease Brain Cell Atlas, as well as do deconvolution of some spatial data. Is it possible to get the .rds seurat object that belongs to this atlas

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Hi @bmk27e. The RDS Seurat objects for almost all of the data in MTG and DLPFC is available on cellxgene (here). L2/3 IT (and the whole taxonomy) have too many cells to be readable by R and therefore are only stored in h5ad format. It’s worth noting that the metadata is incomplete on cellxgene (we only shared fields to be visualized in the web tool)–for the complete set of data (in h5ad format) and metadata, please see our AWS site (here).

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Hi @jeremyinseattle ,

Is there a way to access the V1C data that are a part of the SEA-AD Cell Atlas? I’ve linked my community post here : V1C data from Seattle Alzheimer's Disease Cell Atlas

Thanks!

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I replied at the above thread. In short: currently only raw data is available on Sage.

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