ATpoint what if we have few genes and want to isolate the cells that express all those genes. basically we know there should be a small population of cells in our dataset which can be isolated in FACS. I want to take those cells. in my scRNAseq data when I do DEG analysis and make the dot plot, I will ge few DEGs but based on the dotplot, they are not expressed in the proportion of cells. I want to isolate the cells that have those genes in comon.
Detection of unknown sub cells in a population of cells using DEGs from scRNAseq data
1 answer
Given that these DEGs form a geneset that is enriched or specific in your "sub cells" you simply run clustering (with parameters set go get a lot of small clusters) and then simply color clusters by expression of these genes. Either the geneset as a score, or individual genes, and see whether one or some clusters are indeed convincingly expressing these genes highly. No magic here I would say.
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