Genomic and molecular characterization of the Physical Sciences - Oncology Network Bioresource Core Facility (PBCF) cell lines - mRNA sequencing

Cell lines provided by Physical Sciences-Oncology Network Bioresource Core Facility (PBCF) originate from the same lot number and passage number of ATCC seed stock. 39 of these cell lines were analyzed by ACGT using mRNA sequencing as described here, as well as using Exome sequencing and miRNA sequencing. mRNA sequencing made use of libraries prepared using the TruSeq Stranded RNA Sample Preparation Kit, and bar-coded with individual tags. Library preparation performed using a semi-automated 96-well plate method, with washing and clean-up/concentration steps performed on the Beckman Coulter Biomek NX platform and with ZR-96 DNA Clean & ConcentratorTM-5 plates, respectively. Appropriate quality control analysis performed at every step, and the libraries quantified via qPCR with the Kapa kit and/or the Agilent 2100 Bioanalyzer. Indexed libraries prepared as equimolar pools and loaded onto MiSeqTM flow cell to generate paired-end 2x50 bp reads. The resulting information used to perform library evaluation and pooling adjustments for the HiSeq2000 dual flow cell loading. Pooled and validated libraries run on HiSeq2000 (2x100 paired end runs) in order to generate at least 30,000,000 paired-end reads per sample library. HG19/Build37 was the human reference assembly.