As we know, the amount of RNA reads per cell obtained from 10X scRNA experiment vary between cells. I wonder if this is effect of technical issues or does the number of RNA reads per cell obtained from the 10X scRNA experiment depend on the amount of mRNA in that cell? For the latter to be the case, we would have to read almost all the mRNA fragments in a cell, which I don't think is likely. Thank you for your replies in advance!
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$\begingroup$ Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer. $\endgroup$– Community BotCommented May 4, 2022 at 19:04
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2 Answers
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I am inclined to agree with you that the reads-per-cell is dependent on the cell type and cell cycle state. In the datasets I have analyzed, I observed that immune cells tend to have far fewer reads than fibroblasts, which have fewer reads than larger epithelial cell types.
EDIT: I have also observed that macrophage populations generally have more RNA than lymphocytes. Granulocytes have even less if you even capture them in your sample.
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The number of reads per cell for any given experiment is largely technical. It depends on sequencing depth. 10X recommend 20K reads per cell for the v3 chemistry (and 50K reads per cell for v2)
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$\begingroup$ Thank you for your answer. I'm aware of that. What I wanted to ask is: If in my data from one 10X experiment and from 1 sequencing I have macrophages cluster that have 100k reads per cell and lymphocytes cluster with 33k reads per cell, can we assume that the amount of mRNA in these lymphocytes cluster was 3times smaller (in living cells, befor 10X exp) than in given macrophages cluster? $\endgroup$ Commented May 13, 2022 at 10:19