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Swarbricklab-code / BrCa_cell_atlas

Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".
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Single Cell Count #14

Closed Ethan-Earlie closed 2 years ago

Ethan-Earlie commented 2 years ago

Hello, I have a question about the number of cells present in the published analyses. In the Figure 1.A legend there are ~130k cells quoted for the UMAP. However, in the published data on the Broad Single Cell Portal there seem to be ~100k cells. Would you please be able to help clarify this discrepancy and how many cells were used to generate the main Fig.1.A UMAP.

Thank you!

johnyaku commented 2 years ago

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 commented 2 years ago

I see, thank you for your quick reply!

sunnyzwu commented 2 years ago

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).