The most likely difference between an scRNA-Seq data and flow cytometry data (assuming) is because there may be a difference in the quantity of transcript for a gene and the amount of protein being measured. Poor correlation is not always unexpected – they are different parts of gene expression stages and so difference could be due to a time delay between level of transcripts and level of protein present. You may also not need a large number of transcripts to make a lot of protein, and the half-life of transcripts and proteins may be different.
There are also potential technical reasons for a why the RNA may not match protein levels. You may have ‘drop-outs’ in detection of the RNA because the reverse transcription was not efficient and/or because we are at the lower detection limit. Detection sensitivity of the protein as a more direct measure may be higher on flow.
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