Whole blood single cell RNA-seq dataset?
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3.4 years ago
predeus ★ 2.0k

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 • 2.2k 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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Hope you don't get it wrong if I say that, but just because a single marker is not detected in scRNA-seq does not mean it's garbage. The non-detection can be entirely technical, for example poor mappability of the 3'-UTR in end-tagged protocols or modest transcriptional level even of genes that are abundant as proteins in a cell.

The cluster of cells on the bottom of https://www.ebi.ac.uk/gxa/sc/experiments/E-MTAB-9221/results/tsne labelled as neutrophils expresses Il8 receptor, PU.1, G-CSF receptor, CXCR2, CD182...that's clearly a neutrophil.

Sorry for commenting after 2 years but as I am now working in a neutrophil-focused lab this triggered me ;-)

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That's interesting. Back when I posted this I actually went down a list of top 20 markers I obtained from the experiment above (GSE149938), and virtually none were expressed in the neutrophil cluster in E-MTAB-9221. Also, of the 3 genes listed as curated markers in Celltypist encyclopedia, 2 are not visibly expressed, and LCN2 is expressed in the platelet cluster?

I'm not an expert on neutrophils, but this dataset does look problematic.

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Many thanks for your comment about this @predeus

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