Been meaning to post this for a while. Anyway, in case you're interested, here is a comparison of mean number of RNA per cell measured by RNA FISH to FPKM as measured by RNA-seq for 26 genes (bulk and also combined single cell RNA-seq). Experimental details in Olivia's paper. We used a standard RNA-seq library prep kit from NEB for the bulk, and used the Fluidigm C1 for the single cell RNA-seq. Cells are primary human foreskin fibroblasts.
|Bulk RNA-seq vs. RNA FISH (avg. # molecules per cell)|
|Single cell RNA-seq vs. RNA FISH (avg. # molecules per cell), linear scale|
Probably could be better with UMIs and so forth, but anyway, for whatever it's worth.