and DNA concentration of the sequencing library was determined on Agilent Bioanalyzer and Qubit, respectively. A pool of 10 barcoded libraries were layered on a random selection of two of the eight lanes of the Illumina flow cell bridge amplified to ~250 million raw clusters. One-hundred base pair paired end reads were obtained on a HiSeq 2500. The sequence data were processed for primary analysis to generate QC values (reads were mapped to the human reference genome using TopHat; see “Mapping, QC and quantification of Gene Expression” below). Samples with a minimum of 50 million mapped reads (~25 million paired end reads) and less than 5% rRNA-aligned reads were retained for downstream analysis. We attempted a single round of re-sequencing for samples that failed these QC criteria. In the end, a total of 15 samples did not meet these sequencing criteria (see “Sample QC” below) and were discarded.
