We have analyzed six novel RNA-seq datasets generated as part of the Human Epigenome Atlas (http://www.genboree.org/epigenomeatlas/index.rhtml) and 121 previously published RNA-seq datasets representing 23 human tissues under multiple conditions and consisting of over 4.5 billion uniquely mapped reads (Table S1). This set of RNA-seq data allowed for detection of both rare and tissue-specific transcription events that would otherwise be undetectable. In contrast to the limited reach of prior tiling array studies [2]–[5], we analyzed the much larger portion (83.4%) of the genome to which RNA-seq reads can be uniquely mapped thus providing a broader view of the transcriptome. At a threshold of one RNA-seq read, we observed reads mapping to 78.9% of the genome and, if additional evidence of transcription is taken into account including the full structures of known genes, spliced ESTs and cDNAs, we found evidence that 85.2% of the genome is transcribed (Figure 1A). This result closely agrees with the recently published findings from the ENCODE project in which evidence for transcription of 83.7% of the genome was uncovered [14]. Interestingly, even with 4.5 billion mapped reads,
