Hi everyone, I am about to collect FACS-sorted cells to perform in parallel a transcriptomic and an epigenomic study. To this purpose I need to split my sorted cells into three tubes and perform RNA extraction, genomic DNA extraction and chromatin preparation for low-input ChIP. However, I need to pull several samples to do that in parallel and since I would like to have many biological replicates it is unfeasible to do everything in the same day.
One solution could be to store at -80% the samples in the appropriate lysis buffer but, in order to have higher flexibility could it be possible to just froze cells in liquid nitrogen? In this way I could decide later on, what lysis buffer to use for each application (since I am not still sure about what low-input ChIP protocol I will use) and I will perform all the extraction together avoiding batch effects due to the extraction.
How would that affect the integrity of the RNA, DNA or chromatin? Anyone has already tried to do something similar?
Hi Ilario
For RNA procedure you can freeze your samples using RNA Later. As for DNA the freezing process can lead to strand breaks, maybe you could freeze your cells in freezing media (FBS w/ DMSO) just to keep the cells intact.
Hi, Previously I have actually frozen @ -80 FACS sorted cells for westen blot analyses and DNA extraction for gene amplification. I would not advise LN2 as I think you would suffer a huge casualty interms of viability, BUT if they are robust cells, you may try half and half(?) I used to freeze down in -80 using freezing media.
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