SL257988_tumor_rnaseq
Tumor RNA sequencing: Sample SL257988
Whole-exome and RNA-sequencing on all tumor and matched normal samples were performed at the HudsonAlpha Institute for Biotechnology. DNA was extracted from germline samples and fresh frozen tissues using the Qiagen QIASymphony method. Total RNA from tumor tissues was extracted using Qiagen RNAeasy plus mini kit. DNA and RNA from all FFPE samples were extracted using the Qiagen All prep FFPE DNA/RNA kit. Each exome was captured using Roche SeqCap EZ Exome v3.0 kit and sequenced on an Illumina HiSeq 4000 platform to a depth a ~100x for germline and ~300x for tumor tissues. RNA libraries were prepared using the Illumina TruSeq RNA Exome protocol and kit reagents and further sequenced on an Illumina HiSeq 4000 with 100 million total reads per sample (50 million paired reads). 
SL257988_tumor_rnaseq
NCI-phs001994
SL257988_tumor_rnaseq
alignment_software
STAR 2.5.3a 