Dear crowd,
Can haematopoetic cells sorted by flow cytometry safely be stored in RNAlater for ATAC seq? Any risk of compromising the integrity of nuclei?
Thanks
Need to store the cells immediately after harvesting them so they can be batched. I could freeze in the ATAC lysis buffer, but Im not sure if that affects the assay downstream. Hence, I thought maybe I could store the cells viably, and RNAlater seemed like a possible solution to do this. Thanks for the link, Ill look into it.
Other comments welcome
I would assume that your cells would be fine. As with any freeze thaw process, the integrity may suffer some, but not enough to drastically affect your results. Be sure to be consistent though. If you store your RNA before doing your analysis, make sure to do so for any future replicates to eliminate variability.
I have an answer here FYI to the community: Qiagen does not recommend RNAlater for freezing cells before ATACseq as it may actually damage your cells. They instead recommend RNAprotect.
A better solution kindly provided by Ryan Corces who wrote the paper on Omni-ATAC is to use a serum free cryopreservative (BAM banker media or something similar) and slow freeze. Cells should then be in great shape for ATACseq.
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