Molecular characterization of patient derived glioblastoma cell line

Patient-derived primary GSCs (GSC082209) was established from discarded specimens obtained from glioblastoma (GBM) patient undergoing surgery at UT Health San Antonio. 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. Deidentified fresh tissue was collected intraoperatively, dispersed into single cells, and cultured briefly in a neurobasal media for expansion and purification followed by intracranial injection in nude mice. Patient derived GSCs were cultured as neurospheres in neurobasal medium (Invitrogen, Carlsbad, CA) supplemented with B27 serum-free supplement, EGF (20 ng/mL), bFGF (20 ng/mL), LIF (10 ng/mL) and heparin (5 µg/mL). The RNA was isolated and utilized for RNA-seq analysis. GSC082209 was subtyped based on established TCGA gene expression-based molecular classifications. Overall design: Total RNA from GSC082209 cells 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.