{"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-15273"],"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 on organismal and cellular physiology. Here, we performed bulk RNA-seq on the cerebellum, kidney, liver, lung, muscle, spinal cord, and spleen from 4-month-old homozygous Eif2b1[N208Y] and WT mice, either maintained on a 30 mg/kg 2BAct diet or withdrawn from the diet for 3 days. 2BAct is a small molecule eIF2B activator that can stabilize eIF2B and improve its function. This study also includes WT control mice naive to 2BAct diet."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Paired-end libraries with read length 150 bp were sequenced on an Illumina NovaSeq 6000 sequencer","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)","Nucleic Acid Extraction - Tissues were treated with RNA-later ICE (Invitrogen #AM7030) for 24 hr at -20C and RNA extraction was performed following the MaxMAX total RNA isolation kit (Invitrogen #AM1830)","Sample Collection - Mice were euthanized with CO2, and cerebellum, spinal cord, liver, kidney, lung, muscle and spleen were freshly collected and snap frozen in liquid nitrogen and stored at -80 ℃","Sample Treatment - 2BAct-maintained group: breeders were set up on 2BAct diet, experimental group maintained on 2BAct diet from birth into adulthood. 2BAct-withdrawal group: breeders were set up on 2BAct diet, experimental group maintained on 2BAct diet from birth until 4 months of age, then switched to control diet (0 mg/kg 2BAct) for 3 days prior to tissue collection. 2BAct-naive group: breeders set up on standard chow, experimental animals maintained on standard chow from birth to adulthood"],"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 for protein-coding genes"],"omics_type":["Metabolomics","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 cerebellum, kidney, liver, lung, muscle, spinal cord, and spleen from Eif2b1[N208Y] mice with or without 2BAct treatment","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 on organismal and cellular physiology. Here, we performed bulk RNA-seq on the cerebellum, kidney, liver, lung, muscle, spinal cord, and spleen from 4-month-old homozygous Eif2b1[N208Y] and WT mice, either maintained on a 30 mg/kg 2BAct diet or withdrawn from the diet for 3 days. 2BAct is a small molecule eIF2B activator that can stabilize eIF2B and improve its function. This study also includes WT control mice naive to 2BAct diet.","dates":{"release":"2025-07-10T00:00:00Z","modification":"2025-07-10T12:28:05.421Z","creation":"2025-06-25T15:48:27.506Z"},"accession":"E-MTAB-15273","cross_references":{"ENA":["ERP174042"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}