Foundry120 atlas

← IBD single-cell transcriptomics

colon stromal

Download from source ↗

Dataset overview

Participants 34
Samples None
Reuse readiness 6.4/10 evidence-backed score

The landscape of immune dysregulation in Crohn's disease revealed through single-cell transcriptomic profiling in the ileum and colon.

Kong L, Pokatayev V, Lefkovith A, Carter GT, Creasey EA, Krishna C, Subramanian S, Kochar B, et al. · Immunity · 2023

Abstract

Crohn's disease (CD) is a chronic gastrointestinal disease that is increasing in prevalence worldwide. CD is multifactorial, involving the complex interplay of genetic, immune, and environmental factors, necessitating a system-level understanding of its etiology. To characterize cell-type-specific transcriptional heterogeneity in active CD, we profiled 720,633 cells from the terminal ileum and colon of 71 donors with varying inflammation status. Our integrated datasets revealed organ- and compartment-specific responses to acute and chronic inflammation; most immune changes were in cell composition, whereas transcriptional changes dominated among epithelial and stromal cells. These changes correlated with endoscopic inflammation, but small and large intestines exhibited distinct responses, which were particularly apparent when focusing on IBD risk genes. Finally, we mapped markers of disease-associated myofibroblast activation and identified CHMP1A, TBX3, and RNF168 as regulators of fibrotic complications. Altogether, our results provide a roadmap for understanding cell-type- and organ-specific differences in CD and potential directions for therapeutic development.

doi:10.1016/j.immuni.2023.01.002 ↗ PMID 36720220 ↗ PMC9957882 ↗

Study facts

Organism
Homo sapiens
Platform
10x
Age group
adult
Disease groups
—
Anatomical sites
ascending colon, caecum lamina propria, colon, colonic epithelium, descending colon, lamina propria of mucosa of colon, sigmoid colon, sigmoid colon epithelium, sigmoid colon lamina propria, transverse colon epithelium, transverse colon lamina propria

Data availability

  • Raw counts
  • Processed matrix

File types H5AD

Strengths & limitations for reuse

Strengths

  • 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 10x 3' v1 from source
assay=10x 3' v1

Section structured repository metadata, offset —
assay.library_chemistry 10x 3' v1, 10x 3' v2, and 10x 3' v3 from source
"assay": [{"label": "10x 3' v1"}, {"label": "10x 3' v2"}, {"label": "10x 3' v3"}]

Section —, offset —
assay.platform 10x from source
"assay": [{"label": "10x 3' v1"

Section —, offset —
assay.sequencing_type scrna_seq from source
sequencing_type=scrna_seq

Section structured repository metadata, offset —

Cohort

FieldValueEvidence
cohort.age_group adult from source
"development_stage": [{"label": "adult stage"

Section —, offset —
cohort.total_participants 34 computed
"donor_id": ["105446", "110204", "1108147", "117351", "124246", "128208", "128400", "128624", "164969", "178961", "197396", "139073", "180844", "106265", "175041", "121881", "114902", "N10", "N11", "N13", "N15", "N16", "N17", "N18", "N20", "N21", "N46", "N51", "N8", "104152", "154787", "107306", "104689", "130084"]

Section —, offset —

Data_Assets

FieldValueEvidence
data_assets.cell_metadata True from source
CELLxGENE dataset exposes cell metadata

Section structured repository metadata, offset —
data_assets.open_access True from source
public CELLxGENE dataset

Section structured repository metadata, offset —
data_assets.processed_matrix True from source
CELLxGENE dataset exposes H5AD

Section structured repository metadata, offset —
data_assets.raw_counts True from source
"raw_data_location": "raw.X"

Section —, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['ascending colon', 'caecum lamina propria', 'colon', 'colonic epithelium', 'descending colon', 'lamina propria of mucosa of colon', 'sigmoid colon', 'sigmoid colon epithelium', 'sigmoid colon lamina propria', 'transverse colon epithelium', 'transverse colon lamina propria'] from source
tissues=ascending colon, caecum lamina propria, colon, colonic epithelium, descending colon, lamina propria of mucosa of colon, sigmoid colon, sigmoid colon epithelium, sigmoid colon lamina propria, transverse colon epithelium, transverse colon lamina propria

Section structured repository metadata, offset —
specimens.number_of_cells 39433 from source
cell_count=39433

Section structured repository metadata, offset —
specimens.participant_to_sample_mapping_available True from source
"donor_id": ["105446", "110204", "1108147"

Section —, offset —