Molecular characterization of glioblatoma tissue samples

Patient-derived glioblastoma tissues were collected from discarded specimens obtained from GBM patients undergoing surgery at UT Health San Antonio under an IRB approved biorepository. The specimens were collected in accordance with the Declaration of Helsinki and approved by the Institutional Review Board (or Ethics Committee) of UT Health San Antonio. Patients provided informed consent for surgery and use of their tissues for research.The RNA was isolated and utilized for RNA-seq analysis. These GBM tissues were subtyped based on established TCGA gene expression-based molecular classifications. Overall design: Patient-derived glioblastoma tissues were obtained from GBM patients undergoing surgery at UT Health San Antonio under an IRB approved biorepository. Total RNA from tissues was isolated using RNeasy mini kit according to the manufacturer's instructions (Qiagen, Valencia, CA). Illumina TruSeq RNA Sample Preparation was performed following the manufacturer's protocol. Samples were run on an Illumina HiSeq 3000. The combined raw reads were aligned to UCSC hg19, and genes were annotated by Tophat. Genes were annotated and quantified by the HTSeq-DESeq pipeline.