Figure 5

RNA-Seq of four glioma sphere lines and one human brain sample. Read densities at base pair resolution are shown across a 110 kB region of CHR7 (27,130,000-27,240,00) covering the human HOXA locus. Density of transcripts are presented separately for the minus (black) and plus (gray) strand and are shown as rpm/bp. The RefSeq annotations of the HOXA genes are shown as visual reference below the histograms. The location and structure of the putative HOXA9/10 read-through transcript is indicated in the RefSeq annotation track as a red gene model. See Additional file 1: Figure S12 for a Sashimi plot of RNA-Seq reads which support the presence of the read-through transcript. Locations of CpG islands (UCSC) are indicated by green bars. The gray boxes labelled A/B/D/E show the locations of amplicons used for ChIP-qPCR and methylation-specific clone sequencing (results shown in respective panels of Figure 6).