Sequencing depth with 10x Genomics
I am planning to do single cell RNA sequencing on the neural progenitor cells of embryonic mice (E11.5) using the 10x Chromium approach. The plan is to perform DE analysis on a mosiac population of the progenitors to understand how their transcriptional profile differs from each other. I'm just wondering what would be the appropriate sequencing depth for an experiment like this? I've read that 20,000 reads/cell is enough for accurate clustering, however as I said the main part of this experiment is the DE analysis of the moasic cells so I believe we would need greater depth. Is there a cap for this sort of experiment using 10x? Has anyone using 10x to sequence mouse neural progenitors before? Thank you in advance!
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