{"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-15295"],"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 single nuclei RNA-seq on the cervical/thoracic spinal cord from 2.5-month-old homozygous Eif2b5[R191H] (n=3) and WT mice (n=3)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - libraries were prepared according to Chromium Next GEM Single Cell 33’ Kit v3.1 instructions (10x Genomics #1000268) to capture 10,000 nuclei per sample.","Sequencing - Libraries were pair-end sequenced on an Illumina NovaSeq 6000 sequencer (Illumina, San Diego, CA) under recommended settings.","Nucleic Acid Extraction - Nuclei were isolated using the Chromium Nuclei Isolation Kit with RNAse Inhibitor (10x Genomics #1000494)","Sample Collection - Mice were euthanized with CO2, and the cervical and thoracic region of each spinal cord was freshly collected and snap frozen in liquid nitrogen and stored in liquid nitrogen"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Illumina output was processed using cellranger count (CellRanger 7.0.0, 10x Genomics) to align reads to the mouse mm10 reference genome (including introns), distinguish nuclei-containing droplets from empty ones, and generate a gene-barcode matrix for each sample.","Data Transformation - Illumina output was processed using cellranger count (CellRanger 7.0.0, 10x Genomics) to align reads to the mouse mm10 reference genome (including introns), distinguish nuclei-containing droplets from empty ones, and generate a gene-barcode matrix for each sample. Samples were concatenated as one object and raw integer counts representing the number of UMIs/reads per gene per cell was exported as a processed counts file"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Mus musculus"],"pubmed_authors":["Carmela Sidrauski","Karin Lin"],"additional_accession":[]},"is_claimable":false,"name":"Single nuclei RNA-seq of spinal cord from Eif2b5[R191H] mice","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 single nuclei RNA-seq on the cervical/thoracic spinal cord from 2.5-month-old homozygous Eif2b5[R191H] (n=3) and WT mice (n=3).","dates":{"release":"2025-07-10T00:00:00Z","modification":"2025-07-10T12:27:28.257Z","creation":"2025-06-30T21:49:32.112Z"},"accession":"E-MTAB-15295","cross_references":{"ENA":["ERP174340"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}