{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jacqueline Tearle"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14901"],"description":["Mucosal pinch biopsies from ascending, transverse, descending colon and rectum were obtained from ulcerative colitis (UC) and primary sclerosing cholangitis concomitant with colitis (PSC-UC) patients during routine endoscopies and subjected to 5' single-cell RNA sequencing with V(D)J BCR analysis"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - BCR libraries were loaded onto an S4 flow cell and sequenced on an Illumina NovaSeq 6000.","Nucleic Acid Extraction - Two samples were pooled equally and loaded into the 10x Genomics Chromium Controller according to the manufacturer's protocol at a concentration that would attain between 12,000 cells/chip position.","Library Construction - BCR cDNA library preparation was carried out according to the 10x Genomics Chromium Single Cell V(D)J Reagent Kits User Guide.","Sample Collection - All patients were recruited as part of the Australian IBD Microbiome (AIM) study. All procedures were covered by ethics approval from South Eastern Sydney Local Health District Research Ethics Committee (HREC ref no:18/173) and followed patient consent. 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 endoscopy procedures and immediately transferred to ice-cold RPMI medium containing 10% FBS. Inflammatory state was recorded by treating gastroenterologists during endoscopy and histologically confirmed by anatomical pathologists with subspecialty interest in gastrointestinal pathology. Biopsies from each region were processed separately until pooled for capture. Biopsies were washed in 1x PBS before incubation in 1.5 mL digestion medium (1.16 mL HBSS, 246.9 µL liberase DH, 60 µL hyaluronidase, 36 µL DNase I) in 15 mL tubes with rotation at 600 rpm for 25 minutes at 37°C. Biopsies were homogenised at 10 minutes via trituration and vortexing. Digestions were halted by adding 5 mL ice-cold neutralisation medium (20% FBS in RPMI) and cell suspensions passed through 40 µM cell strainers. Digestion tubes were washed with a further 5 mL neutralisation medium passed through the same strainer to transfer any remaining cells. Cell suspensions were then centrifuged at 300g for 10 minutes at 4°C. Supernatants were discarded and cells resuspended in 1 mL resuspension medium (1% FBS in PBS) and centrifuged again as before. Cells of the right colon (ascending and transverse colon) and left colon (descending colon and rectum) were pooled separately, with hashtag oligos used for in silico deconvolution of discrete anatomical regions for each donor. Supernatants were then discarded and cell pellets resuspended in 45 µL Cell Staining Buffer with 5 µL TruStain Fc Blocking Reagent and incubated for 10 minutes at 4°C to prepare for hashing. TotalSeq C0251 anti-human hashtag 1 and C0252 anti-human hashtag 2 antibody pools were prepared as per the manufacturer’s instructions and added to 50 µL blocked cell suspensions and incubated for 30 minutes at 4°C. Hashed cell suspensions were then washed three times by centrifugation at 400 g at 4°C for 5 minutes with 3 mL Cell Staining Buffer. Cell pellets were then resuspended in 100 µL and counted. Regions were pooled equally for two captures: right colon (containing ascending and transverse colon) and left colon (containing descending and rectum). Demultiplexing based on antibody hashtagging was therefore used for higher-precision mapping to each region (e.g. descending colon vs. rectum). For PSC-2 and PSC-3, regions were pooled across 4 captures and cells demultiplexed using SNP information."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["10x Genomics Chromium Controller","Illumina NovaSeq 6000"],"pubmed_abstract":["Primary sclerosing cholangitis (PSC) is a chronic progressing cholestatic disease that often co-occurs with inflammatory bowel disease (PSC-IBD). PSC-IBD affecting the colon (PSC-UC) is likened clinically to ulcerative colitis (UC), however differences include a right colon dominance, less severe inflammatory presentation and a greater lifetime risk of colorectal cancer. To understand the basis of clinical differences, we combine single-cell mRNA and antigen receptor sequencing, 16S ribosomal DNA analysis and spatial transcriptomics on biopsies from multiple colon regions of both PSC-UC and UC patients in remission or at the time of relapse. We discover disease-specific cell and microbial profiles between these cohorts, highlighting a distinct landscape in the right colon of PSC-UC patients and an epithelial-endothelial cell state that may contribute to intestinal permeability in UC. We show the expansion of an activated mast cell state in both diseases during flare, and demonstrate the requirement of TMEM176B in sustaining this activated state. Together this work demonstrates that PSC-UC and UC are distinct diseases with common cell mechanisms during inflammation, providing cellular and microbial insights to improve treatment of both patient cohorts."],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_title":["The primary sclerosing cholangitis and ulcerative colitis colonic mucosa defined through paired microbial and single-cell RNA sequencing"],"pubmed_authors":["Jacqueline LE Tearle, Fan Zhang, Katherine JL Jackson, Pratibha Malhotra, Paris Tavakoli, Sabrina Koentgen, Joanna Warren, Cameron Williams, Ashraful Haque, Arteen Arzivian, Nicodemus Tedla, Andrew Kim, Hamish W King, Georgina L Hold, Simon Ghaly, Kylie R James","Kylie James","Jacqueline Tearle"],"additional_accession":[]},"is_claimable":false,"name":"V(D)J BCR single cell sequencing of 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) and primary sclerosing cholangitis concomitant with colitis (PSC-UC) patients during routine endoscopies and subjected to 5' single-cell RNA sequencing with V(D)J BCR analysis","dates":{"release":"2026-06-17T00:00:00Z","modification":"2026-06-17T10:35:21.448Z","creation":"2025-03-04T08:54:59.568Z"},"accession":"E-MTAB-14901","cross_references":{"ENA":["ERP169854"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0004184"],"doi":["10.1101/2024.08.12.607536"]}}