A case study of novel, breast-specific peak 13741. (a) Browser shot showing expression for a breast cancer sample in the region downstream of ANKRD30A on chromosome 10. The first two tracks show the known genes and RNAs in this locus. The third track shows the peaks identified in this study, including three highly expressed peaks: novel 13741, lncRNA 13742 and novel 13743. The fourth track shows the raw 3SEQ reads (transcript abundance levels) on the forward strand (blue) and reverse strand (red). The final tracks show the longest transcripts that overlap peak 13742, a Scripture-assembled transcript produced using normal breast RNAseq reads from the Illumina BodyMap data set and GENCODE lncRNA ENSG00000235687. (b) Zoom-in browser shot of peak 13741 on chromosome 10 shows the location of the RNA in situ hybridization probe (top track) as well as the raw sequence reads for one breast cancer sample (bottom track). This peak illustrates the shape of a typical 3SEQ peak from a high-expressing transcript. (c) ER staining on an ER+ breast cancer (top left) and an ER-breast cancer (top right). RNA in situ hybridization for peak 13741 performed on the same ER+ breast cancer specimen (bottom left) and same ER- breast cancer (bottom right). Specimens were matched but ER and 13741 stains used different tissue slices. All images are at 400× magnification. 3SEQ, 3'-end sequencing for expression quantification; chr10, chromosome 10; ER, estrogen receptor; lncRNA, long non-coding RNA.
Brunner et al. Genome Biology 2012 13:R75 doi:10.1186/gb-2012-13-8-r75