What should I expect to see for chromosome Y gene expression in a male mouse sample?
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3 months ago
gt ▴ 30

I am trying to determine the sex of a mouse for an RNA-seq experiment. If I do CPM normalization using edgeR and observe many chromosome Y genes displaying CPM > 0, then is it safe to assume the mouse is a male?

RNA-seq featureCounts STAR • 281 views
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3 months ago
Gordon Smyth ★ 4.8k

Probably, but the surest way to recognize the sex of the mouse is to examine the expression of Xist on the X chromosome. Xist is very highly expressed in all female cells (regardless of cell type or cell state) and not at all male cells, so it is a sure thing. We use it as a routine check in all our mouse RNA-seq analyses. Xist RPKM is usually >20 (often>100) in females and <1 in males.

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