{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Francesco Rusconi"],"organism":["Mus musculus"],"software":["STAR, featureCount"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15221"],"description":["This RNA-seq experiment investigates hippocampal transcriptional responses to chronic social stress in mice, aiming to uncover molecular signatures of behavioral resilience and susceptibility. Male C57BL/6J mice were subjected to a 10-day Chronic Social Defeat Stress (CSDS) protocol. At the end of the paradigm, animals were stratified into resilient (RES) and susceptible (SUS) groups using a dual behavioral index: the Social Ratio, which incorporates both interaction time and avoidance behavior in the presence of a novel CD1 aggressor. Hippocampal tissue was collected 7 hours after the final defeat session to capture transcriptional changes associated with the adaptive or maladaptive response to stress.  RNA was extracted and processed for bulk RNA-seq on the Illumina platform. Analysis of differentially expressed genes revealed a marked transcriptional asymmetry in SUS mice, characterized by a widespread and selective upregulation of activity-dependent and stress-responsive genes.  This dataset enables the exploration of gene expression dynamics and alternative splicing events underlying individual differences in stress adaptation."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Defeated and control animals underwent a final defeat session and were euthanized by decapitation 7 hours after sensory interaction to preserve brain tissue integrity. Hippocampi were dissected and snap-frozen in liquid nitrogen","Library Construction - Universal Plus mRNA-Seq kit (Tecan Genomics, Redwood City, CA) has been used for library preparation following the manufacturer’s instructions (library type: fr-secondstrand). RNA samples were quantified and quality tested by Agilent 2100 Bioanalyzer RNA assay (Agilent technologies, Santa Clara, CA) or Caliper (PerkinElmer, Waltham, MA). Final libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay or Caliper (PerkinElmer, Waltham, MA).","Sequencing - Libraries were then prepared for sequencing and sequenced on paired-end 150 bp mode on NovaSeq 6000 (Illumina, San Diego, CA), obtaining an average of 47M reads (SD 12M). Base calling, demultiplexing and adapter masking were performed with Illumina BCL Convert v3.9.3.","Nucleic Acid Extraction - Total RNA was extracted from hippocampal extract with TRIzol Reagent (Invitrogen) following manufacturer protocol and resuspended in DEPC water. RNA concentration and quality was assessed by 4200 Tape Station (Agilent)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The genes-by-samples count matrix was filtered to keep only genes with at least 3 counts per million in 4 samples, obtaining a total of 13’093 genes.","Sequence Alignment - Sequencing reads were aligned against mouse reference genome GRCm39 using STAR, and quantified thorugh featureCount and annotation file “Mus_musculus.GRCm39.110.gtf” from Ensembl, resulting in a mean of assigned reads per sample of 85.7% (SD 0.97%)."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Francesco Rusconi"],"additional_accession":[]},"is_claimable":false,"name":"Hippocampal Transcriptomic Signatures of Stress Resilience and Susceptibility in the CSDS Mouse Model 7 hours after the last stress","description":"This RNA-seq experiment investigates hippocampal transcriptional responses to chronic social stress in mice, aiming to uncover molecular signatures of behavioral resilience and susceptibility. Male C57BL/6J mice were subjected to a 10-day Chronic Social Defeat Stress (CSDS) protocol. At the end of the paradigm, animals were stratified into resilient (RES) and susceptible (SUS) groups using a dual behavioral index: the Social Ratio, which incorporates both interaction time and avoidance behavior in the presence of a novel CD1 aggressor. Hippocampal tissue was collected 7 hours after the final defeat session to capture transcriptional changes associated with the adaptive or maladaptive response to stress.  RNA was extracted and processed for bulk RNA-seq on the Illumina platform. Analysis of differentially expressed genes revealed a marked transcriptional asymmetry in SUS mice, characterized by a widespread and selective upregulation of activity-dependent and stress-responsive genes.  This dataset enables the exploration of gene expression dynamics and alternative splicing events underlying individual differences in stress adaptation.","dates":{"release":"2026-01-01T00:00:00Z","modification":"2026-01-02T02:02:32.388Z","creation":"2025-06-12T13:36:35.517Z"},"accession":"E-MTAB-15221","cross_references":{"ENA":["ERP173423"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}