{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Daniel Borshagovski"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14662"],"description":["Mesenchymal cells and the extracellular matrix (ECM) support epithelium during homeostasis and regeneration. We modeled epithelial regeneration by culturing intestinal epithelium on decellularized small intestinal scaffolds (iECM), and identify Asporin (Aspn), an ECM bound proteoglycan, as a critical mediator of epithelial fetal-like reprogramming. To investigate its role in modulating intestinal epithelial cell states, we performed RNA sequencing (RNAseq) on small intestinal organoids treated with recombinant Aspn. This dataset provides a transcriptional profile of Aspn-treated intestinal epithelial cells, highlighting gene expression changes associated with fetal-like reprogramming and regenerative processes. The analysis offers insights into how Aspn influences epithelial signaling pathways, including TGF-beta signaling, underlying epithelial plasticity and the ECM's role in coordinating tissue responses to injury."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - An Ovation Universal RNA-seq System kit was used for Illumina library preparations (NuGEN Technologies Inc., CA, USA), with rRNA removal according to the kit manual. Libraries were purified with AMPure XP beads.","Sequencing - The libraries were sequenced on a NextSeq500 using a 75bp single read kit (Illumina, CA, USA).","Sample Collection - Freshly isolated small intestinal crypts were cultured as organoids in 60% matrigel for 48 hours, with or without recombinant asporin. Organoids were collected from matrigel and total RNA was extracted from them.","Nucleic Acid Extraction - Total RNA was isolated using RNeasy Mini Kit (Qiagen) according to the Manufacturer's instructions with on-column DNAse digestion."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Genes were quantified with QoRTs 1.3.0. Unnormalized counts are provided.","Sequence Alignment - STAR 2.5.3a"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 500"],"study_type":["RNA-seq of total RNA"],"species":["Mus musculus"],"pubmed_authors":["Sharif Iqbal","Daniel Borshagovski"],"additional_accession":[]},"is_claimable":false,"name":"Fetal-like reversion in the regenerating intestine is regulated by mesenchymal Asporin","description":"Mesenchymal cells and the extracellular matrix (ECM) support epithelium during homeostasis and regeneration. We modeled epithelial regeneration by culturing intestinal epithelium on decellularized small intestinal scaffolds (iECM), and identify Asporin (Aspn), an ECM bound proteoglycan, as a critical mediator of epithelial fetal-like reprogramming. To investigate its role in modulating intestinal epithelial cell states, we performed RNA sequencing (RNAseq) on small intestinal organoids treated with recombinant Aspn. This dataset provides a transcriptional profile of Aspn-treated intestinal epithelial cells, highlighting gene expression changes associated with fetal-like reprogramming and regenerative processes. The analysis offers insights into how Aspn influences epithelial signaling pathways, including TGF-beta signaling, underlying epithelial plasticity and the ECM's role in coordinating tissue responses to injury.","dates":{"release":"2025-11-27T00:00:00Z","modification":"2025-11-27T02:01:36.648Z","creation":"2024-12-02T22:00:55.25Z"},"accession":"E-MTAB-14662","cross_references":{"ENA":["ERP166721"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}