Median number of expressed genes in lymphoblastoid cell line GM12878

Range translation proteins ~100 splicing regulators ~10 transcription factors ~3 protein copies/cell
Organism Human Homo sapiens
Reference Marinov GK et al., From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing. Genome Res. 2014 Mar24(3):496-510. doi: 10.1101/gr.161034.113 p.503 left column top paragraphPubMed ID24299736
Method Abstract:"Here [investigators] apply the SMART-seq single-cell RNA-seq protocol to study the reference lymphoblastoid cell line GM12878."
Comments p.501 right column bottom paragraph:”Because transcriptional regulators play a crucial role in defining the gene expression state of cells, [investigators] examined the expression of several well-known general transcription factors as well as major regulators of B-cell differentiation (Fig. 3E). Remarkably, except for IRF4, which was usually expressed at several dozen copies, most factors were detected at <10 copies per cell, and were often not detected at all. [Investigators] stress that this does not mean that they are not expressed. Given the 10% psmc of the protocol, these observations are consistent with simple technical failure to detect them. It is also possible that there are no mRNA copies in some cells at the moment of harvest, especially if they are infrequently transcribed. Extending these observations to other functional groups, [they] assessed proteins involved in translation (as a major group of genes with housekeeping functions) (Fig. 3F), splicing regulators (Fig. 3G), and all transcription factors (Fig. 3H). The median number of copies per cell was ~100 for translation proteins, ~10 for splicing regulators, and strikingly, only ~3 for transcription factors. Beyond their biological interest, these large expression differences between functional gene categories mean that quantification is inherently less robust and less informative for some biological functions than it is for others.” Psmc=the number of cells pooled and the single molecule capture efficiency
Entered by Uri M
ID 111780