{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":[null],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-12007"],"description":["The introduction in the 1960s of the glucocorticoids-based therapy for the management of the vasogenic edema forming in brain tumour patients is considered as a revolution in the history of neurosurgery. Since then, although it is impossible to deny the ability of glucocorticoids to reduce mortality and morbidity of brain tumour patients worldwide, many scientific papers have highlighted the controversial effects that they can exert on glioma cells, for instance in terms of enhanced proliferation and interference with chemotherapeutics drugs. Among synthetic glucocorticoids, the most widely used is Dexamethasone (Dex). Using 4 different Glioblastoma Patient-Derived Xenograft (PDX) cell lines, we treated them with or without Dex 0.1 µM in order to look at the drug-related changes in the transcriptome of the cells. Each experiment has produced 8 samples (1 CTR sample and 1 DEX-treated sample for each cell line) and the experiment has been repeated 3 times, thus giving a total of 24 samples."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - The libraries were run on the Illumina NextSeq 500 using the HighOutput 75 cycles kit (2 × 36 cycles,paired-end reads, single index). Fastq files were generated from the sequencer output using illumina’s bcl2fastq and quality checks on the raw data were done using FastQC and Fastq Screen.","Library Construction - Libraries for cluster generation and DNA sequencing were prepared using Illumina TruSeq RNA Library Preparation Kit. Quality and quantity of the DNA libraries were assessed on an Agilent 2200 TapeStation (D1000 screentape) and Qubit (Thermo Fisher Scientific), respectively.","Sample Collection - GBM patient-derived cell lines were obtained as described in \\\\\"Oudin, A. et al. Protocol for derivation of organoids and patient-derived orthotopic xenografts from glioma patient tumors. STAR Protocols 2, 100534, doi:10.1016/j.xpro.2021.100534 (2021).\\\\\". Intracortical implantation of organoids in immunodeficient mice is performed to induce tumor growth in vivo and to establish PDOX models method was used. Animals must be housed in individually ventilated cages in a Specific Pathogen Free (SPF) facility, under controlled environment (temperature 22 ± 2°C, humidity between 45% and 65% and 12 h light / 12 h dark cycle) with free access to autoclaved and acidified water and irradiated food ad libitum.","Nucleic Acid Extraction - Samples were processed using the QIAshredder/RNeasy Mini Kit (Qiagen)","Growth Protocol - GBM naive cells were seeded at different densities in 6-well plates and cultured in Plasmax.","Sample Treatment - 24h after seeding, media were renewed with fresh Plasmax, supplemented with vehicle or dexamethasone 0.1 uM, and cells were incubated for 72 hours at 21% O2. Cells were then harvested for RNA extraction."],"figure_sub":["MINSEQE Score","Assays and Data","Processed Data","organisation","MAGE-TAB Files"],"data_protocol":["Data Transformation - Quality control of the raw RNA-seq data files was performed by FastQC and fastq_screen. Then, RNA-seq reads were aligned to the human genome (GRCh38.75) and resulting bam files were processed with htseq_count.","Sequence Alignment - Alignment of the RNA-Seq paired-end reads was to the GRCh38 version of the human genome and annotation using Hisat2."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 500"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"additional_accession":["ERP139987"],"pubmed_authors":["Saverio Tardito"]},"is_claimable":false,"name":"RNA-seq of 4 naive GBM cell lines upon dexamethasone (0.1 uM) treatment","description":"The introduction in the 1960s of the glucocorticoids-based therapy for the management of the vasogenic edema forming in brain tumour patients is considered as a revolution in the history of neurosurgery. Since then, although it is impossible to deny the ability of glucocorticoids to reduce mortality and morbidity of brain tumour patients worldwide, many scientific papers have highlighted the controversial effects that they can exert on glioma cells, for instance in terms of enhanced proliferation and interference with chemotherapeutics drugs. Among synthetic glucocorticoids, the most widely used is Dexamethasone (Dex). Using 4 different Glioblastoma Patient-Derived Xenograft (PDX) cell lines, we treated them with or without Dex 0.1 µM in order to look at the drug-related changes in the transcriptome of the cells. Each experiment has produced 8 samples (1 CTR sample and 1 DEX-treated sample for each cell line) and the experiment has been repeated 3 times, thus giving a total of 24 samples.","dates":{"release":"2025-10-30T00:00:00Z","modification":"2025-10-30T02:02:13.483Z","creation":"2022-08-01T18:35:03.071Z"},"accession":"E-MTAB-12007","cross_references":{"ENA":["ERP139987"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0003816","EFO_0005518","EFO_0003738","EFO_0004184","EFO_0003969"]}}