organism: Homo sapiens
description: Protocols: GBM cells for functional experiments were obtained following informed consent from patients. Experiments were in accordance with the Research Ethics Board at The Hospital for Sick Children (Toronto, Canada). Access to pathological data was obtained from the institutional review boards. GBM stem cell lines (G797, G729, G411), which were established from mesenchymal GBMs, were cultured using previously established protocols (85) including serum-free NS cell self-renewal media (NS media) consisting of Neurocult NS-A Basal media, supplemented with 2 mmol/L L-glutamine, hormone mix (in house equivalent to N2), B27 supplements, 75 mg/mL BSA, 2 mg/mL Heparin, 10 ng/mL basic FGF and 10 ng/mL human EGF. GBM cell lines were grown adherently on culture plates coated with poly-L-ornithine and laminin and maintained in 37°C tissue culture incubator with 5% CO2. All cell lines were regularly checked for mycoplasma infections by DAPI staining. RNA-seq data was generated in the patient-derived GBM cell line G729 with shRNA targeting GJB2, SCN9A, or non-targeting (NT) shRNA controls, as described above. Total RNA was collected 4 days post lentiviral shRNA transduction using RNeasy Plus Mini Kit (Qiagen #74134). Lentiviral transduction and RNA extraction were performed in triplicates. RNA integrity number (RIN) was determined using Agilent Bioanalyzer. All samples had RIN > 9.8.  Library preparation was performed using NEBNext Ultra II Directional polyA mRNA Library Prep Kit.
identifiers.namespace: BioSample
identifiers.id: SAMEA113563475
attributes.tag: INSDC center name
attributes.value: ONTARIO INSTITUTE FOR CANCER RESEARCH
attributes.tag: Submitter Id
attributes.value: E-MTAB-12859:Sample 1 (729_G5_a)
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell_line
attributes.value: G729
attributes.tag: common name
attributes.value: human
attributes.tag: disease
attributes.value: brain glioblastoma
attributes.tag: genotype
attributes.value: wild type genotype
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: organism part
attributes.value: brain
attributes.tag: sample name
attributes.value: E-MTAB-12859:Sample 1 (729_G5_a)
attributes.tag: scientific_name
attributes.value: Homo sapiens