Single Cell Count about brca_cell_atlas

[johnyaku]

Basically, I believe that this was a result of filtering. I'll let the authors point you to the filtering conditions that led to this reduction, but in the meantime I have placed the raw unfiltered counts on the Broad's Single Cell Portal: https://singlecell.broadinstitute.org/single_cell/study/SCP1039/a-single-cell-and-spatially-resolved-atlas-of-human-breast-cancers#study-download
The file in question is brca_mini_atlas_raw_unfiltered.zip

[Ethan-Earlie]

I see, thank you for your quick reply!

[sunnyzwu]

Hi Ethan, our final dataset that we uploaded to the the Broad single-cell portal (~100k cells) was following the removal of all poor quality clusters after sub-clustering and detailed sub-annotation of our major cell types (Epithelial, CAFs, Endothelial, Perivascular, T-cells, Myeloid, B-cells). These filtered small clusters were predominantly driven by low genes, UMIs or high mitochondrial content, as well as those which showed features of doublets (expressing markers of other cell lineages).