Figure 1.
rRNA-depleted RNA-Seq analysis of HEK-293T cells.
(A) Proportion of reads with a unique match to known genes (left), or known genes supplemented with mRNAs and spliced ESTs (right). Reads were sequentially matched against a non-redundant set of known genes, mRNA and spliced EST data. Any remaining reads were classified as “other”. The known gene set was derived from the UCSC, NCBI, and ENSEMBL genome databases and did not include any lincRNA annotations or processed transcripts. (B) Same as in (A), but considering the total amount of transcribed genomic area. (C) Correlation between RPKB (reads per Kb) for introns and exons of known genes. (D) Relative enrichment of RNA-Seq read frequency in intergenic regions as a function of the distance to 5′ and 3′ ends of annotated genes in the human genome. The median of read frequencies in either orientation between 80 and 100 kb was used as baseline. (E) Rootograms showing the distribution of the total number of RNA-Seq reads per kb of intergenic sequence outside 10-kb gene-flanking regions, compared to the expected random distribution for the same number of reads (red line). (F) Same as (E), but considering only intergenic transcribed regions with single-read coverage (singletons).