H9 ESC and HeLa RNA-seq data from fractions exclusively containing polyA− or polyA+ transcripts were analyzed [46]. Transcripts with RNA-seq reads in all four datasets and with FPKM>1 in at least one of the two fractions for each cell type were analyzed for Figure 3B (16,819 NM genes and 127 lincRNAs). For Figure S5, transcripts with reads in both fractions and FPKM>1 in at least one of the two fractions for a specific cell type were included in the analysis of that cell type (20,470 NM genes and 849 lincRNAs in H9 ESCs; 18,294 NM genes and 1,009 lincRNAs in HeLa). The whiskers of the box and whisker plot extend to +/−1.5 times the interquartile range or the most extreme datapoint.
