title: GSM5512458: PD1-017-JH_RNA; Homo sapiens; RNA-Seq
library_construction_protocol: Tumor DNA and RNA samples were extracted from formalin-fixed-paraffin-embedded (FFPE) tissue blocks of patients with thymic carcinoma using the DNA/RNA AllPrep Kit (Qiagen, Valencia, CA), as described previously (Petrini et al., 2014). Briefly, FFPE blocks were cut and subjected to hematoxylin and eosin (H&E) staining, and the tumor component was macrodissected from unstained slides that matched to the H&E staining slides. Control DNA for whole exome sequencing was extracted from paired patients' peripheral blood samples using Genfind v2 kit (Beckman Coulter, Brea, CA). The library construction for RNA-seq was performed by Tempus using KAPA HiFi Library Amplification kit (Beaubier et al., 2019). RNA libraries were prepared for sequencing using standard Illumina protocols. The whole exome library construction was performed using The Tempus xE hybrid capture Next-Generation sequencing panel (~20,000 gene) consisting of IDT xGen LockDown probes. The WES panel was sequenced to a depth of at least 150x for tumor and 50x for germline using 126 bp paired end reads on the Illumina HiSeq 4000.