Foundry120 atlas

← IBD single-cell transcriptomics

Reveal the key mediators of inflammation in Crohn's disease undergoing biological treatments

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Dataset overview

Participants 49
Samples 79
Reuse readiness 7.3/10 evidence-backed score

Multiomic analysis reveals cellular, transcriptomic and epigenetic changes in intestinal pouches of ulcerative colitis patients.

Zhao Y, Zhou R, Xie B, Liu CY, Kalski M, Cham CM, Jiang Z, Koval J, et al. · Nature communications · 2025

Abstract

Total proctocolectomy with ileal pouch anal anastomosis is the standard of care for patients with severe ulcerative colitis. We generated a cell-type-resolved transcriptional and epigenetic atlas of ileal pouches using scRNA-seq and scATAC-seq data from paired biopsy samples of the ileal pouch and the ileal segment above the pouch (pre-pouch) from patients (male=4, female=2), and paired biopsies of the terminal ileum and ascending colon from healthy individuals (male=3, female=3) serving as reference. Our study finds an additional population of absorptive and secretory epithelial cells within the pouch but not the pre-pouch. These pouch-specific enterocytes express a subset of colon-specific genes, including CEACAM5 and CD24. However, compared to normal colonocytes, expression of these genes is lower, and these enterocytes also express inflammatory and secretory genes while maintaining expression of some ileal-specific genes. This cell-type-resolved transcriptomic and epigenetic atlas of the ileal pouch establishes a reference for investigating pouch physiology and pathology.

doi:10.1038/s41467-025-56212-2 ↗ PMID 39837850 ↗ PMC11751449 ↗

Study facts

Organism
Homo sapiens
Platform
transcriptomic single cell
Age group
adult
Disease groups
—
Anatomical sites
terminal ileum, ascending colon

Data availability

  • Raw counts
  • Processed matrix

File types TAR

Strengths & limitations for reuse

Strengths

  • Raw reads are advertised
  • Raw counts are advertised
  • Processed matrices are advertised
  • Cell metadata are advertised
  • Participant mapping is available
  • Participant counts are documented
Extraction evidence & provenance

Each extracted field is shown with the source excerpt and location used to resolve it.

Assay

FieldValueEvidence
assay.assay_type transcriptomic single cell
transcriptomic single cell

Section —, offset —
assay.library_chemistry 10x Genomics 3'RNA v3.1
10x Genomics 3'RNA v3.1 library construction protocol

Section —, offset —
assay.reference_genome hg38
Assembly: hg38

Section —, offset —
assay.sequencing_type scrna_seq
scRNA-seq of 79 gut biopsies

Section —, offset —

Cohort

FieldValueEvidence
cohort.age_group adult from source
GEO age characteristics: 52; 52; 58; 58; 55; 55; 75; 75; 57; 57; 63; 63; 50; 50; 27; 62; 31; 31; 51; 66; 66; 45; 45; 45; 33; 33; 24; 21; 21; 29; 29; 53; 53; 61; 61; 34; 34; 37; 37; 50; 50; 49; 49; 45; 45; 43; 48; 48; 38; 38; 31; 40; 40; 74; 74; 70; 70; 27; 27; 51; 51; 51; 51; 49; 49; 32; 32; 63; 63; 38; 38; 24; 24; 21; 21;

Section GEO family SOFT, offset —
cohort.crohns_disease_participants 32
scRNA-seq of 79 gut biopsies in terminal ileum and ascending colon from healthy individuals (n = 17) and Crohn's Disease patients (n = 32)

Section —, offset —
cohort.disease_activity_metadata_available True
"condition": "control", "sample region": "control"

Section —, offset —
cohort.non_ibd_controls 17 computed
GEO characteristics group 'non_ibd_controls': 17 subjects

Section GEO family SOFT, offset —
cohort.total_participants 49 computed
49 distinct subject/participant IDs across GEO samples

Section GEO family SOFT, offset —
cohort.treatment_exposure_documented True from source
GEO sample characteristics document treatment/therapy

Section GEO family SOFT, offset —

Data_Assets

FieldValueEvidence
data_assets.cell_metadata True
"age": "52", "race": "unknown", "tissue": "ascending_colon", "history": "no_IBD", "patient": "HA01", "condition": "control"

Section —, offset —
data_assets.open_access True
Public on Dec 16 2024

Section —, offset —
data_assets.participant_metadata True
"patient": "HA01"

Section —, offset —
data_assets.processed_matrix True
features.tsv.gz (gene features), and matrix.mtx.gz (sparse count matrix)

Section —, offset —
data_assets.raw_counts True
matrix.mtx.gz (sparse count matrix)

Section —, offset —
data_assets.raw_reads True
GSE266616_RAW.tar

Section —, offset —

Processing

FieldValueEvidence
processing.quality_control_reported True
Extract high-quality cells with 200-6000 genes and greater than 1000 UMIs per cell and mitochondria percentage less than 50 using Seurat V4.3

Section —, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['terminal ileum', 'ascending colon']
in terminal ileum and ascending colon

Section —, offset —
specimens.inflamed_status_available True
including non-inflamed, adjacent-to-inflamed, and active inflamed region

Section —, offset —
specimens.number_of_samples 79
scRNA-seq of 79 gut biopsies

Section —, offset —
specimens.participant_to_sample_mapping_available True
"patient": "HA01"

Section —, offset —
specimens.specimen_type biopsy
scRNA-seq of 79 gut biopsies

Section —, offset —