{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Karin Lin"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15247"],"description":["The integrated stress response (ISR) is a conserved signaling pathway triggered by a variety of insults that include ER stress, mitochondrial stress, amino acid deprivation, and viral infection. The essential stress sensor and key effector of this pathway is eIF2B, and loss-of-function mutations in any of its 5 subunits can lead to Vanishing White Matter disease (VWM) in humans. We generated and characterized mouse models harboring different pathogenic mutations to model VWM and to understand the impact of chronic ISR activation. Here, we performed bulk RNA-seq on mouse embryonic fibroblasts (MEFs) isolated from homozygous Eif2b1[N208Y] and WT mouse embryos. MEFs were cultured in 200 nM small molecule eIF2B activator 2BAct, then washed and either maintained in 200 nM 2BAct or switched to 2BAct-withdrawn media (0 nM) to induce an acute ISR."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Paired-end libraries with read length 150 bp were sequenced on an Illumina NovaSeq 6000 sequencer","Sample Treatment - MEFs were seeded in DMEM with 10% FBS with 200 nM 2BAct. Cells were washed 3 times in PBS prior to replacing cells with media containing with or without 200 nM 2BAct for 6 hours.","Library Construction - RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA)","Growth Protocol - Cells were cultured in a 15 cm petri dish housed in an incubator at 37°C, 5% CO2, 3% O2 and passaged every 2-3 days with trypsin","Sample Collection - WT and N208YHOM mouse embryo fibroblasts (MEFs) were isolated from embryos at embryonic day 13.5. Each embryo was individually processed by first removing the liver and heart before mincing into small pieces followed with trypsin digestion. Cells were mechanically dissociated by pipetting before inhibition the trypsin reaction with complete medium (Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Sigma) and 1X antibiotic-antimycotic solution (Gibco) and 200nM 2BAct).","Nucleic Acid Extraction - Cells were collected in RNA lysis buffer (Applied Biosystems A27828) and RNA was extracted following the manufacturer's protocol for bulk RNA sequencing using MaxMAX total RNA isolation kit (Invitrogen #AM1830)"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Reads were mapped using salmon, version 1.9.0, to the transcriptome index derived from the mm10 reference mouse genome and the Encode vM12 primary assembly annotation. Gene level count matrix is provided"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Carmela Sidrauski","Karin Lin"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of mouse embryonic fibroblasts from Eif2b1[N208Y] mice cultured with or without 2BAct","description":"The integrated stress response (ISR) is a conserved signaling pathway triggered by a variety of insults that include ER stress, mitochondrial stress, amino acid deprivation, and viral infection. The essential stress sensor and key effector of this pathway is eIF2B, and loss-of-function mutations in any of its 5 subunits can lead to Vanishing White Matter disease (VWM) in humans. We generated and characterized mouse models harboring different pathogenic mutations to model VWM and to understand the impact of chronic ISR activation. Here, we performed bulk RNA-seq on mouse embryonic fibroblasts (MEFs) isolated from homozygous Eif2b1[N208Y] and WT mouse embryos. MEFs were cultured in 200 nM small molecule eIF2B activator 2BAct, then washed and either maintained in 200 nM 2BAct or switched to 2BAct-withdrawn media (0 nM) to induce an acute ISR.","dates":{"release":"2025-06-30T00:00:00Z","modification":"2025-06-20T11:46:21.538Z","creation":"2025-06-20T11:46:21.538Z"},"accession":"E-MTAB-15247","cross_references":{"ENA":["ERP173819"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}