I am working with a cell population that needs to be enriched by cell sorting from fresh tissue. I am wondering what the best way to preserve the cells, after sorting, for downstream single nucleus RNA sequencing and single nucleus ATAC-seq. (I can't snap freeze whole tissue because we cell sort using cell surface markers.)
So far I have been spinning the single cell suspension down at 1000g for 5 minutes, removing as much FACS buffer as possible and then freezing the cell pellet in liquid nitrogen and placing at -80. ((((should I consider resuspending in some sort of RNA protection buffer and then pellet and freeze OR freeze in a suspension of RNA protection buffer?))))
I am wondering if (even using the best methods) the RNA will be too compromised or if I won't be capturing a normal, healthy cell state transcriptomically if I snap freeze as a cell pellet (even though this is with the nuclei). I can't find any information on snRNAseq and/or snATACseq from a snap frozen cell pellet. (((If there is no way good way to do this then I will just do the whole protocol up to the first pause point of 10x but we get tissue late in the afternoon so this isn't ideal)))).
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