Determine sex/ gender of a mouse cell line via sequencing data
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5 days ago
cwwong13 ▴ 10

Noted that the STAR Methods required by Cell Press require reporting the degender of cell lines used. While I order the cells from ATCC, they do not have such information available. I also tried going back to the reference/ patent/ reference, but none of them mentioned the gender/ sex of the cell line. Therefore, I am looking for a quick way to determine the sex of the cell line: using some online publicly available data.

While this question can be more general and theoretical -- if I can determine the sex of a cell line by any sequencing data and how reliable is it (given that I do not really have extra resources by doing wet-lab experiments for this authentication), I am specifically looking for if I can determine the sex of cell line by ChIP-seq data.

After downloading the ChIP peak calling output from "control" IP conditions, such as H2A, H3K4Me2, H3K27Ac. I just do a grep "chrY" Peaks.txt | head.

My rationale is that if there is any peak mapped to chromosome Y, the sample must be a male. On the other hand, if there is no peak mapped to chromosome X, the sample is highly likely to be a female (while it is not 100% certain).

May I know if this is correct? Or it would be nice if you can suggest a method that is more rigorous. Thanks!

sequencing line cell • 287 views
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Entering edit mode
5 days ago

I wouldn't necessarily go by whether there is a peak or not, but the coverage/reads on the Y chromosomes versus the other chromosomes. Just because of the limitations of short read sequencing and alignment you could get some reads incidentally mapping to the Y chromosome in some regions even without a Y chromosome present, but you should only get appreciable coverage if the chromosome is actually there.