title: Illumina HiSeq 4000 paired end sequencing; Whole Genome Sequencing of Mesothelioma Cell Lines
design: Whole Genome Sequencing of Mesothelioma Cell Lines
library_name: Sample 8_s
library_construction_protocol: Total RNA was isolated by Trizl/Chloroform, and quantity and integrity of the RNA samples was checked on an Agilent 2100 Bioanalyzer. Only samples with a RIN above 8 were selected for microarray analysis.  Total RNA was isolated by Trizl/Chloroform, and quantity and integrity of the RNA samples was checked on an Agilent 2100 Bioanalyzer. Only samples with a RIN above 8 were selected for microarray analysis.  Exome sequencing for all MPM cell models was performed with the Nextera DNA Exome Kit from Illumina (TruSeq Rapid Capture Exome 45Mb, 6 samples per lane HiSeq 4000 2x75 bp paired-end) by the Medical University of Vienna Biomedical Sequencing Facility following the instructions. Sequencing depth was >100x; after removal of duplicates, the achieved mean coverage per base within the target region was 106-fold (range: 98-115). Next generation sequencing (NGS) reads were aligned to the b37 reference genome with BWA MEM. We then applied GATK base quality score recalibration, indel realignment, duplicate removal, and performed SNP and INDEL discovery and genotyping across all samples simultaneously using standard hard filtering parameters or variant quality score recalibration according to GATK Best Practices recommendations.
attributes.tag: Experimental Factor: cell line
attributes.value: Meso208
attributes.tag: Experimental Factor: genotype
attributes.value: wild type genotype