Hello everyone. I am interested in performing a time-course bulk RNA-seq experiment of FACS sorted cell populations. I will use a live-cell fluorescent for sorting so fixing before sorting is out of the question. I need to sort cells at 0-6h-12h-24h-48h-72h but I want to prepare the RNAs at the same time from each sample. Is it possible to fix the cells after sorting and isolate RNA later? Or is it possible to freeze the cell pellet after sorting and isolate RNA later? Any recommendations by any means (protocol, kits, etc.)?
I would not recommend fixing the cells prior to RNA isolation. You can spin the sorted cells down and flash freeze the cells and isolate RNA later. Some people sort the cells directly into RNA lysis buffer (Trizol, Qiagen lysis buffer, etc). But if you are expecting a low number of cells to be sorted, you would be diluting the lysis buffer with the sheath fluid and might end up with poor lysis.
In addition to Tom's response, another option is to preserve the sorted cells in RNALater, then proceed to freeze them and subsequently isolate RNA.