Absolute expression levels at the single-cell level. FPKM values converted to estimated copies per cell using the spike-in quantification standards are shown. (A) Distribution of expression levels of RefSeq protein-coding genes in estimated copies per cell in single cells and pool/split experiments. (B) Distribution of expression levels of GENCODE v13 lncRNA protein-coding genes in estimated copies per cell in single cells and pool/split experiments. (C) Total number of mRNA copies per cell in single cells. (D) Total number of mRNA copies in pool/split experiments. (E) Expression levels of housekeeping and highly expressed genes (GAPDH, CD74, left panel), and general (CTCF, REST, YY1) and B-cell regulatory (PAX5, EBF1, BCL11A, ETS1, IRF4, IKZF1, PBX3, POU2F2, RUNX3, TCF3, TCF12) transcription factors (right panel). Upper and middle panels show the estimated copies-per-cell numbers for single cells and pool/splits, respectively. The lower panel shows FPKM values for cell pools and bulk RNA libraries. (F–H) Distribution of absolute expression levels in copies per cell in single cells for translation initiation, elongation, and termination proteins (F), splicing regulators (G), and transcription factors (H). The list of translation proteins was retrieved from the corresponding GO category annotations downloaded from FuncAssociate 2.0 (Berriz et al. 2009). The list of splicing regulators was obtained from the SpliceAid-F database of human splicing factors (Giulietti et al. 2013). The list of transcription factors used was the one from Vaquerizas et al. (2009). Note that only values ≥0.1 estimated copies per cell were included in these plots, i.e., libraries in which the genes were not detected were excluded.
