I got some RNA-seq data and want to know whether the cell samples were in good condition or not. Any opinions is greatly appreciated!
If you are asking whether there is some kind of RNA signal that is present in live vs. dead cells (or vice versa), the answer is probably no.
RNA is short-lived even in live cells, but it is constantly made and there is always a good amount of it present. I don't think there would be much difference in RNA content or quality between alive cells and those that have been dead for a short period of time - let's say couple of minutes. Cells that have been dead for tens of minutes or longer will likely have less RNA and molecules will be shorter because of degradation.
All of these are general considerations, and a simple answer to your question is that we probably can't tell whether the cell was alive or not. For example, poor sample handling on a live cell may give a similar result to good sample handling on a dead cell.
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Single-cell or Bulk? In both cases, the highest expressed genes should be mitochondrial genes (if the cells are alive...)
It's bulk data. Thanks for the information, I will check it out.
Ask the person who made the libraries. If they assessed cells under a microscope and measured RIN you might get an idea, and if not then you cannot tell. In single-cell data you can estimate quality by comparing metrics such as % reads mapping to mt or rRNA genes but this is mainly valuable because you can compare each cell to the distribution of all cells. For a bulk sample that is probably not meaningful, and is something the wetlab has to answer.
Given that there are multiple things a cell can die from it is probably not so straightforward as you would have hoped.