{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Laura Pikkupeura"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15918"],"description":["The intestinal epithelium constitutes a vital absorptive barrier that protects the host organism against luminal bacteria. Following tissue damage, intestinal epithelial cells are reprogrammed into a state characterized by YAP1 activation to facilitate barrier restoration. We demonstrate that mechanical fragmentation of intestinal organoids induces transient regenerative reprogramming, driving the formation of spheroid morphology, nuclear YAP1 accumulation, and the expression of regeneration-associated markers. We identify ALK4/ALK5 signaling as a regulator of the regenerative response and dissect the effects of the specific ALK4 and ALK5 ligands, Activin and TGF-β, thereby illustrating the importance of organoid models in dissecting regenerative responses and identifying novel signaling p"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - scraped adult crypts were harvested from the proximal parts of the small intestine using EDTA (2mM), embedded in Matrigel droplets and cultured in advanced DMEM/F12 with GlutaMAX, Hepes and Penicillin/Streptomycin supplemented with recombinant EGF (Peprotech; 50 ng/ml), recombinant Noggin (Peprotech; 100ng/mL), R-spondin1 (RSPO1) conditioned medium at 10%. Mouse small intestinal organoids were passaged every 4 days using mechanical disruption. This encompassed rigorous pipetting of the pelleted organoid culture 30x with a p1000 pipette followed by centrifugation and rigorous pipetting of the pelleted organoid culture 30x with a p200 pipette followed by centrifugation and resuspension in Matrigel. Recombinant mouse Activin A (R&D Systems or Peprotech) and recombinant mou","Nucleic Acid Extraction - RNA was collected from three biological replicates using RNAeasy Microkit (Qiagen).","Library Construction - Sequencing libraries were generated by Genewiz using their standard mRNA-seq workflow with polyA selection of RNAs.","Sequencing - Sequencing was done by Genewiz with 2x150bp paired end sequencing with Illumina HiSeq."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw counts from featureCounts are supplied as processed data without normalisation or transformation.","Sequence Alignment - Mapping and quantification of fastq files were performed via the Rsubread package. Reads were mapped to the mm10 genome assembly using the align-function with default settings. Mapped reads were quantified across RefSeq gene models using the featureCounts-function with default settings."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 2000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Hjalte Larsen","Kim Jensen","Laura Pikkupeura"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of mouse intestinal regenerative reprogramming","description":"The intestinal epithelium constitutes a vital absorptive barrier that protects the host organism against luminal bacteria. Following tissue damage, intestinal epithelial cells are reprogrammed into a state characterized by YAP1 activation to facilitate barrier restoration. We demonstrate that mechanical fragmentation of intestinal organoids induces transient regenerative reprogramming, driving the formation of spheroid morphology, nuclear YAP1 accumulation, and the expression of regeneration-associated markers. We identify ALK4/ALK5 signaling as a regulator of the regenerative response and dissect the effects of the specific ALK4 and ALK5 ligands, Activin and TGF-β, thereby illustrating the importance of organoid models in dissecting regenerative responses and identifying novel signaling p","dates":{"release":"2026-10-01T00:00:00Z","modification":"2026-10-01T01:00:39.511Z","creation":"2025-10-29T16:07:43.979Z"},"accession":"E-MTAB-15918","cross_references":{"ENA":["ERP183310"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}