{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Jacqueline Tearle L. E."],"instrument_platform":["N/A","10x Genomics Chromium Controller","Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16401"],"description":["Single cell sequencing of frozen mucosal pinch biopsies from four colonic regions of patients with ulcerative colitis and primary sclerosing cholangitis concomitant with colitis, as well as one healthy control. Pinch biopsies from each region were thawed, digested and pooled with 3 other donor biopsies and subjected to 5' 10x Chromium Next GEM cell RNA sequencing."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - GEX cDNA library preparation was carried out according to the 10x Genomics Chromium Single Cell 5' Reagent Kits User Guide.","Sequencing - GEX libraries were loaded onto an S4 flow cell and sequenced on an Illumina NovaSeq 6000.","Sample Collection - Mucosal pinch biopsies were collected from the ascending colon, transverse colon, descending colon and rectum of patients with either UC or PSC-UC (classified as resembling UC at the clinical level) during routine colonoscopy procedures. Prior to colonoscopy, Picoprep bowel preparation was used, which contains active ingredients sodium picosulfate, magnesium carbonate hydrate, and citric acid. All patients were Australian and of typically white European descent and had undergone no antibiotic use in the 28 days prior to colonoscopy. Inflammatory state was recorded by the treating gastroenterologists during colonoscopy and histologically confirmed by anatomical pathologists with subspecialty interest in gastrointestinal pathology. Mucosal pinch biopsies were immediately transferred to ice-cold RPMI medium containing 10% heat-inactivated (HI) FBS. All procedures were covered by ethics approval from South Eastern Sydney Local Health District Research Ethics Committee (Australian IBD Microbiome (AIM) study; HREC ref no:18/173) or St Vincent's Hospital Human Research Ethics Committee (2024/ETH01125) and followed patient consent.","Nucleic Acid Extraction - Mucosal pinch biopsies were thawed, enzymatically digested and washed to generate single cell suspensions. Individual regional samples from 4 donors were pooled equally and loaded into the 10x Genomics Chromium Controller according to the manufacturer's protocol at a concentration that would attain 15,000 cells/chip position."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Jacqueline Tearle L. E."],"additional_accession":[]},"is_claimable":false,"name":"Single cell sequencing of frozen mucosal pinch biopsies from patients with ulcerative colitis and primary sclerosing cholangitis concomitant with colitis","description":"Single cell sequencing of frozen mucosal pinch biopsies from four colonic regions of patients with ulcerative colitis and primary sclerosing cholangitis concomitant with colitis, as well as one healthy control. Pinch biopsies from each region were thawed, digested and pooled with 3 other donor biopsies and subjected to 5' 10x Chromium Next GEM cell RNA sequencing.","dates":{"release":"2026-06-26T00:00:00Z","modification":"2026-06-26T08:36:47.401Z","creation":"2025-12-16T10:14:07.674Z"},"accession":"E-MTAB-16401","cross_references":{"ENA":["ERP186610"],"Biostudies":["E-MTAB-14955"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0004184"]}}