Transcriptional reprogramming primes CD8+ T cells toward exhaustion in Myalgic encephalomyelitis/chronic fatigue syndrome, 2024, Iu, Hanson et al

Probably not trivial but I wonder if there's a solution involving digesting the tissue like you'd do for scRNA-seq, staining and sorting out the population(s) of interest

 

scATAC-seq on its own is a possibility, the issue would be that the proportion of immune cells in a muscle biopsy sample would already be low, and by doing single cell instead of bulk you’re losing a lot of depth. So your signal of interest would need to be very stark with low variability, which is hard enough to achieve across replicates of genetically identical mice let alone human samples.

I’ve been trying to see if it would be possible to physically sort out immune cells from muscle tissue and then do bulk ATAC-seq—that’s a bit out of my range of expertise though so I need to wait until I can meet with some potential collaborators. It might still leave you with too low of a cell count for bulk unless you’re getting a big hunk of muscle tissue, which requires surgical incision and would be hard to get justification for in a study.