RNA library preparation and sequencing: All samples submitted to the New York Genome Center for RNA-seq were prepared for sequencing in randomized batches of 94. The sequencing libraries were prepared using the KAPA Stranded RNA-seq Kit with RiboErase (KAPA Biosystems). rRNA was depleted from 1ug of RNA using the KAPA RiboErase protocol that is integrated into the KAPA Stranded RNA-seq Kit. The insert size and DNA concentration of the sequencing library was determined on Fragment Analyzer Automated CE System (Advanced Analytical) and Quant-iT PicoGreen (ThermoFisher) respectively. A pool of 10 barcoded libraries were layered on a random selection of two of the eight lanes of the Illumina flow cell at appropriate concentration and bridge amplified to ~250 million raw clusters. One-hundred base pair paired end reads were obtained on a HiSeq 2500. Data is provided for those samples that passed all of the following QC filters: samples were required to have had a minimum of 25 million read pairs and less than 5% rRNA alignment. This gives a mean of 56.5 million, median of 56.4 million and maximum of 74.4 million read pairs.
