Genomic and molecular characterization of the Physical Sciences - Oncology Network Bioresource Core Facility (PBCF) cell lines - Exome 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, Inc. using exome sequencing as described here, as well as using mRNA sequencing and miRNA sequencing. Exome sequencing made use of indexed libraries prepared using the Agilent SureSelectXT2 Human All Exon V5 kit. Library preparation was conducted 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. The libraries were quantified via qPCR with the Kapa kit and/or the Agilent 2100 Bioanalyzer. Indexed libraries were prepared as equimolar pools and loaded onto a MiSeqTM flow cell to generate paired-end 2x50 bp reads. Pooled and validated libraries run on HiSeq2000 (2x100 paired end runs) in order to achieve at least 100X raw data coverage per each sample library. HG19/Build37 was the human reference assembly.