{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Tobi Alegbe"],"organism":["Homo sapiens"],"software":["CellRanger v7.2.0"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16986"],"description":["This scRNA-seq data resource contains various clustered and auto-annotated anndata, as well as associated individual and sample metadata, from IBDverse. It consists of over upto 4 million cells from terminal ileal biopsies, rectal biopsies and PMBC samples from 421 individuals, including 125 with Crohn’s disease ."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Single-cell RNA sequencing was performed using 3’ 10X Genomics Chromium kits (v3.0 and v3.1) according to the manufacturer’s instructions.","Sample Collection - 296 individuals without inflammatory bowel disease (IBD) and 125 individuals with Crohn’s disease were recruited at Addenbrooke’s Hospital, Cambridge, UK. CD patients were required to have a history of ileal disease involvement. During routine endoscopy, gastrointestinal biopsies were collected from the rectum and terminal ileum, and blood samples were drawn after the procedure. Terminal ileal biopsies were obtained from 243 individuals without IBD and 119 individuals with Crohn’s disease. Ileal biopsies from CD patients included both inflamed and uninflamed tissue. Rectal biopsies were collected from 275 individuals without IBD. Where possible, rectal and ileal samples were collected from the same healthy individuals, and blood and ileal samples were collected from the same CD patients. Gastrointestinal biopsy processing was performed as previously described76, with an extended collagenase digestion step (15 minutes) for rectal samples due to their fibrotic nature.  Whole blood was collected for single-cell RNA-sequencing from 95 individuals with Crohn’s disease. Peripheral blood mononuclear blood cells (PBMCs) were isolated from the whole blood using the EasySep Direct Human PBMC Isolation Kit (StemCell Technologies).   Because IBD tissue displays increased cellular heterogeneity due to immune infiltration, we targeted 6000 and 3000 cells for CD and healthy biopsies respectively. This is to ensure adequate representation of diverse cell populations and to maintain statistical power for expression quantification and eQTL mapping across annotations. Libraries were sequenced to a target depth of 50,000 reads per cell. CellRanger (v7.2.0) was used to align reads to the GRCh38 human genome reference with Ensembl v93 transcript definitions (GRCh38-3.0.0 reference file provided by 10X Genomics), and to generate cell-by-gene count matrices. The greater number of cells targeted for CD patients is confirmed in the TI samples from the ‘atlasing’ dataset (see ‘Single-cell RNA sequencing quality control and cell clustering’) (wilcoxon p-value<2.2e-16), with no discernable influence on sequencing depth, as indicated by median number of counts per sample (p=0.27) (Supplementary Fig. S6).","Sequencing - Libraries were sequenced using a HiSeq4000 sequencer (Illumina; NCD=20, Ncontrol=4) or NovaSeq S4 XP sequencer (Illumina; NCD=91, Ncontrol=228) with 100bp paired-end reads, targeting 50,000 reads per cell.","Library Construction - All samples sequenced under kit version v3.1 had dual indexes, samples sequenced under kit version v3.0 had either single or dual indexes."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - CellRanger (v7.2.0) was used to align reads to the GRCh38 human genome reference with Ensembl v93 transcript definitions (GRCh38-3.0.0 reference file provided by 10X Genomics), and to generate cell-by-gene count matrices.","Data Transformation - Cell count matrices were initially subset to retain droplets likely to contain cells and corrected for ambient RNA using CellBender v2.190, as previously described76. Scrublet v0.2.191 was then used to identify and remove potential multiplets. All subsequent quality control, normalisation, and clustering steps were performed with Scanpy v1.9.692, including normalising to library sizes of 10,000 total counts using the function sc.pp.normalise_per_cell and log-transformation using sc.pp.log1p to produce the ln[cp10k+1] count matrix."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 4000","3’ 10X Genomics Chromium"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Bradley Harris","Carl Anderson","Tobi Alegbe","Tim Raine"],"additional_accession":[]},"is_claimable":false,"name":"IBDverse: Cell type-resolved genetic variation shapes inflammatory bowel disease risk","description":"This scRNA-seq data resource contains various clustered and auto-annotated anndata, as well as associated individual and sample metadata, from IBDverse. It consists of over upto 4 million cells from terminal ileal biopsies, rectal biopsies and PMBC samples from 421 individuals, including 125 with Crohn’s disease .","dates":{"release":"2026-04-28T00:00:00Z","modification":"2026-04-30T16:18:47.372Z","creation":"2026-04-28T12:22:51.254Z"},"accession":"E-MTAB-16986","cross_references":{"BioStudies":["S-BSST2922"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}