Whole blood single cell RNA-seq dataset?
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10 months ago
predeus ★ 1.7k

Hello all,

I was wondering if you know of any public single cell RNA-seq datasets that have profiled whole blood, and not just PBMCs? I know this would be quite an unbalanced dataset, so probably some sorted sub-populations? So far I've found this dataset, but it is strange, to say the least.

Would be grateful for any hints, as always.

RNA-Seq scRNA-Seq whole blood single cell • 625 views
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For the benefit of people possibly searching for the data: the E-MTAB-9221 one is complete garbage! The published annotation has about 30% of cells marked as neutrophils, but they don't even express LTF, which is the most prominent marker of a neutrophil.

So far, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149938 is the only dataset that I know of that seems to represent actual whole blood fairly well.

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Many thanks for your comment about this @predeus

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