{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Filip Horvat"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14858"],"description":["Glioblastoma (GBM) is the deadliest type of brain cancer, exhibiting resistance not only to traditional treatments like radiation and chemotherapy but also to modern immunotherapy. GBM is classified as an immunologically cold tumor with an immunosuppressive microenvironment. Radio- and chemotherapy have been shown to alter the tumor microenvironment and trigger an anti-tumor immune response in various cancers, including breast, lung, and colorectal cancer, via the cGAS/STING and type I interferon (IFN-I) pathway. Additionally, STING agonists and inhibitors of DNA damage response and cell cycle checkpoints, which promote the accumulation of immunostimulatory cytoplasmic dsDNA, have been found to enhance the effects of radiation. Here we examined the immunogenic response of four different GBM cell lines (U251, T98G, GB-1, KALS-1) exposed to hypofractionated X-ray radiation (3x8 Gy) in combination with a STING agonist or with inhibitors targeting immune signaling (PARP7). We performed RNA-seq analysis of all four GBM cell lines treated with 3x8 Gy, PARP7i, diABZI alone or in combination with 3x8 Gy."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - GBM cells were mixed with 10% mouse embryonic fibroblasts (MEFs) as a spike-in control prior to RNA isolation. Cells were washed 1x in PBS, detached using trypsin-EDTA solution (Sigma) and pelleted by centrifugation at 500g for 5min.","Growth Protocol - The Human GBM cell lines U251 and T98G cell lines were cultured in Dulbecco’s Modified Eagle Medium (DMEM) medium (Gibco, 41965-039), supplemented with 10% fetal bovine serum (FBS) (Sigma, F7524-500ml) and 1% penicillin/streptomycin (P/S) (Gibco, 15140-122). GB1 and KALS1 cell lines were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Gibco, 21875-034), supplemented with 10 % FBS, 1% P/S and 1 % LGlutamine (Gibco, 25030-024). All cell lines were maintained at 37 °C in a humidified atmosphere with 95% air and 5% CO2. Cells were grown to 70-80% of confluency at time of irradiation. Prior to irradiation, cell culture flasks were filled air-bubble free with unsupplemented medium to accommodate the vertical flask positioning in both irradiation workflows, which was replaced immediately after irradiation with fresh, supplemented medium.","Library Construction - RNA-seq libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions using 600 ng total RNA as input.","Sequencing - Sequencing was performed at the VBCF NGS facility on a NovaSeq X sequencing system (Illumina) in readmode SR100.","Nucleic Acid Extraction - Cell pellets were resuspended in 1 mL TRAzol (Neo-biotech). 200 µL chloroform (Applichem) was added and the lysate was vortexed and centrifuged at maximum speed (21100xg) for 15 min at 4°C. The aqueous layer was transferred to a new tube and precipitated with 0.5 mL isopropanol. The RNA pellet was isolated by centrifugation for 30 min at 4°C, washed with 1 mL 75% ethanol, re-centrifuged for 10 min, dried and resuspended in 70 µL RNase free water. 20 µg RNA was treated with 40 U DNaseI (Roche) for 30 min at 37°C and subsequently purified by phenol-chloroform extraction and ethanol precipitation.","Sample Treatment - X-ray irradiations were administered using a horizontal irradiation cabinet (YXLON, TU32-D03, 20 mA, 5.5FOC, filtration: 3 mm Be + 3 mm Al + 0.5 mm Cu). Dedicated irradiation set-ups for all flask types used (Nunc™ Lab-Tek™ ChamberFlasks (170920), T25 (169900) and T75 (156800; all Sarstedt) were developed to accommodate the horizontal beam geometry and ensure standardized positioning. Cells were irradiated with 8 Gy. Fractionation regimen of 3x8 Gy was implemented for the X-ray experiments. PARP7 inhibitor KMR-206 was used in concentration of 300 nM, and the STING agonist diABZI was used in concentration of 100nM."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Luca Lippert","Dea Slade","Filip Horvat"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of four glioblastoma (GBM) cell lines treated with irradiation, PARP7i, diABZI alone or in combination with irradiation","description":"Glioblastoma (GBM) is the deadliest type of brain cancer, exhibiting resistance not only to traditional treatments like radiation and chemotherapy but also to modern immunotherapy. GBM is classified as an immunologically cold tumor with an immunosuppressive microenvironment. Radio- and chemotherapy have been shown to alter the tumor microenvironment and trigger an anti-tumor immune response in various cancers, including breast, lung, and colorectal cancer, via the cGAS/STING and type I interferon (IFN-I) pathway. Additionally, STING agonists and inhibitors of DNA damage response and cell cycle checkpoints, which promote the accumulation of immunostimulatory cytoplasmic dsDNA, have been found to enhance the effects of radiation. Here we examined the immunogenic response of four different GBM cell lines (U251, T98G, GB-1, KALS-1) exposed to hypofractionated X-ray radiation (3x8 Gy) in combination with a STING agonist or with inhibitors targeting immune signaling (PARP7). We performed RNA-seq analysis of all four GBM cell lines treated with 3x8 Gy, PARP7i, diABZI alone or in combination with 3x8 Gy.","dates":{"release":"2026-01-01T00:00:00Z","modification":"2026-01-01T02:02:05.541Z","creation":"2025-02-18T11:14:08.71Z"},"accession":"E-MTAB-14858","cross_references":{"ENA":["ERP169314"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003738","EFO_0004184","EFO_0003969"]}}