Entering edit mode
3.1 years ago
predeus
★
1.9k
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.
https://www.ebi.ac.uk/gxa/sc/experiments/E-HCAD-8/results/tsne
https://www.ebi.ac.uk/gxa/sc/experiments/E-MTAB-9221/results/tsne <--- probably better of the two
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.
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 ;-)
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.
Many thanks for your comment about this @predeus