Is 60,000 estimated cell per sample in sn/scRNASeq too high?

Question

[Tania]

Hi All I am still new to sn/scRNAseq. Is 60000 estimated cell per sample in sn/scRNASeq too high or indicative of somthig? I read in one tutorial the number shoulg be between 500-10000. So it seems too high and weird? Can any one explain please? Thanks

[GenoMax]

See: https://kb.10xgenomics.com/hc/en-us/articles/360001378811-What-is-the-maximum-number-of-cells-that-can-be-profiled-

[Tania]

Thank you genoMax :)

[rpolicastro]

You need to provide us more information, like the method used (10X?), how many cells you aimed for, and how cell number was estimated.

[Tania]

yes, 10X human samples single nuclei, the data is passed to me, I don't know how much was targeted. Cell ranger report shows around 10,000 estimated no. of cells and a warning of law fraction of read and antisene genes warning. However the QC that came with the data says estimated cells is 60000. Thats confusing to me. thank you

[rpolicastro]

This is more of a question for the people that ran the chromium controller, sequenced the data, and provided the QC report. The upper limit on cells per sample is just how much money you want to spend on GEMs and Illumina flow cells.

[Tania]

Got it, thank you so much.