{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jacqueline Tearle L. E."],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17148"],"description":["Mucosal pinch biopsies from ascending, transverse, descending colon and rectum were obtained from ulcerative colitis (UC), primary sclerosing cholangitis concomitant with colitis (PSC-UC) and healthy control patients during routine endoscopies and cryopreserved. Biopsies were then thawed, digested and subjected to 5' single-cell RNA sequencing with V(D)J TCR analysis."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - TCR cDNA library preparation was carried out according to the 10x Genomics Chromium Single Cell 5' Reagent Kits User Guide.","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.","Sequencing - TCR libraries were loaded onto an S4 flow cell and sequenced on an Illumina NovaSeq 6000."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Processed data files contain per barcode metadata for pooled samples"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["N/A","10x Genomics Chromium","Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Jacqueline Tearle L. E."],"additional_accession":[]},"is_claimable":false,"name":"V(D)J TCR single cell sequencing of frozen mucosal pinch biopsies from patients with ulcerative colitis and primary sclerosing cholangitis concomitant with colitis","description":"Mucosal pinch biopsies from ascending, transverse, descending colon and rectum were obtained from ulcerative colitis (UC), primary sclerosing cholangitis concomitant with colitis (PSC-UC) and healthy control patients during routine endoscopies and cryopreserved. Biopsies were then thawed, digested and subjected to 5' single-cell RNA sequencing with V(D)J TCR analysis.","dates":{"release":"2026-06-29T00:00:00Z","modification":"2026-06-29T14:06:10.653Z","creation":"2026-06-12T10:32:33.979Z"},"accession":"E-MTAB-17148","cross_references":{"ENA":["ERP194965"],"Biostudies":["E-MTAB-14955"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}