biostudies-arrayexpressDavid LindgrenHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15215Bulk RNAseq analysis of mRNA content of human primary astrocytes irradiated with 10 Gy and/or treated with Flunarizine 10uM.biostudies-arrayexpressSample Treatment - one day after seeding, cells were treated with either DMSO or Flunarizine 10uM (MedChemExpress HY-B0358A) and 2 hours later irradiation was performed or not using a Cix1 x-ray irradiator (Xstrahl) at 10Gy. Cells were lysed 24 hours after irradiationSequencing - Library input to sequencing: 0.65 nM PhiX Control input (FC-110-3001, Illumina): 1% Sequencing setup (read one - index reads - read two, bp): 150-10-10-150. Protocol: NovaSeq 6000 Sequencing System Guide (Document # 1000000019358 v11) Reagent/kit: NovaSeq 6000 S4 Reagent Kit, 300 cycles v1.5 (20028312, Illumina). Equipment: NovaSeq 6000 System (20012850, Illumina).Library Construction - Protocol: Illumina Stranded mRNA Prep, Ligation Reference Guide (Document # 1000000124518 v03). Modification of “Enrich DNA Fragment” step: 12 PCR cycles. Reagent/kit: Illumina® Stranded mRNA Prep, Ligation (20091659, Illumina) Indexing: Illumina® RNA UD Indexes Set C, Ligation (96 Indexes, 20091655, Illumina) Equipment: Automatisation of Clean up steps: King Fisher FLEX (18-5400620, ThermoScientific), incubations and PCR: Eppendorf Mastercycler X50s (6311000010, Eppendorf)Sample Collection - The cells used for the experiment are human primary astrocytes (3H Biomedical - SC1800). The cells received either DMSO or Flunarizine treatment at 10uM. 2 hours later, cells have been irradiated or not with 10Gy. 24 hours after irradiation the cells have been lysed and the RNA content extracted for bulk RNAseq analysis. 4 replicates have been made for each condition.Nucleic Acid Extraction - The RNA content of the cells have been extracted RNeasy mini kit (Qiagen) together with the Qiashredder Kit (Qiagen) according to manufacturer’s protocolsGrowth Protocol - Primary human astrocytes (3H Biomedical - SC1800-5) were cultured in astrocyte medium (3H Biomedical, SC1801) supplemented with 2% FBS, 1% PenStrep and astrocyte growth serum (provided by 3H Biomedical).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Paired-end RNA-seq data fastq files were processed using the nf-core/rnaseq pipeline (version 3.14.0) with the --aligner salmon option. Initial quality control of raw FASTQ files was performed using FastQC, and results were summarized with MultiQC. In the nf-core/rnaseq pipeline, transcript-level quantification was carried out using Salmon (v1.10.1) with transcriptome index based on Homo sapiens reference annotation Ensembl release 109. Quantifications were aggregated to the gene level using tximport. The pipeline generated a deseq2.rds object containing gene-level raw count matrices that were imported into R using the DESeq2 package for differential expression and downstream statistical analysis.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAHomo sapiensPauline JeannotDavid LindgrenfalseAstrocytes’ response to Flunarizine combined with irradiationBulk RNAseq analysis of mRNA content of human primary astrocytes irradiated with 10 Gy and/or treated with Flunarizine 10uM.2025-08-19T00:00:00Z2025-08-18T14:36:37.117Z2025-06-09T14:02:56.55ZE-MTAB-15215ERP173285EFO_0002944EFO_0004170EFO_0003789EFO_0005518EFO_0003816EFO_0003738EFO_0003969EFO_0004184