Foundry120 atlas

IBD spatial transcriptomics

All published public datasets in this pipeline, ranked by reuse-readiness × participants.

Also see IBD microbiome Also see IBD single-cell transcriptomics

Full catalogue

All published datasets

19 datasets in this domain, ranked by impact.

# Dataset Participants Samples Reuse Impact
1 Digital Spatial Profiling Reveals Functional Shift of Enterochromaffin Cell in Patients with Ulcerative Colitis

NanoString GeoMx Digital Spatial Profiler · unknown

15 23 6.9 /10 103.5
2 Single-Cell and Spatial Multi-omics Reveal Interferon Signaling in the Pathogenesis of Perianal Fistulizing Crohn’s Disease

10X Visium · unknown

15 21 6.6 /10 99.0
3 Single-cell single-molecule spatial transcriptomics using CosMx on colectomy specimens collected during Pouch surgery in IBD patients.

NanoString CosMx Spatial Molecular Imager · unknown

8 8 7.1 /10 56.8
4 Spatial and single cell transcriptomics reveals cellular crosstalk changes in ileal Crohn’s disease during inflammation

10x Genomics Visium · unknown

5 24 7.3 /10 36.5
5 Elucidating the fibrotic niche and cellular dynamics in crohn’s disease-associated fibrostenosis

10x Genomics Visium HD · unknown

2 2 8.4 /10 16.8
6 Granzyme K CD8⁺ T cells with tissue-resident features promote intestinal inflammation in patients with Crohn’s disease

10x Genomics Visium and 10x Genomics Xenium · open

2 45 8.1 /10 16.2
7 Genetic profiles of small intestinal and colonic metaplastic Paneth cells by spatial transcriptomics

10x Genomics Visium HD · unknown

2 2 7.4 /10 14.8
8 Single-cell spatial transcriptomics of formalin-fixed, paraffin-embedded biopsies reveals colitis-associated cell networks [Xenium]

Xenium · open

— 7 7.9 /10 —
9 IBD CosMx NanoString data from colonic mucosa

CosMx Spatial Molecular Imaging (SMI) · open

— 9 7.4 /10 —
10 A necroptotic-to-apoptotic signaling axis underlies inflammatory bowel disease

10x Genomics Xenium · unknown

— 51 6.6 /10 —
11 Single-cell spatial transcriptomics of formalin-fixed, paraffin-embedded biopsies reveals colitis-associated cell networks [Merscope]

MERSCOPE · open

— 1 6.4 /10 —
12 Spatially Resolved Insights Into Fistulating Crohn’s Disease Pathogenesis - Visium Spatial Transcriptomics

10x Genomics Visium FFPE Spatial Gene Expression · unknown

— 36 6.4 /10 —
13 Divergent spatial microdomains drive inflammation and repair in Ulcerative and Immune Checkpoint Therapy Colitis - Spatial Transcriptomics

10x Visium · unknown

— 16 6.1 /10 —
14 The role of DPF2 in mouse radiation-induced intestinal injury by spatial transcriptome

Spatial Transcriptomics · unknown

— 2 5.9 /10 —
15 Creeping fat-derived mechanosensitive fibroblasts drive intestinal fibrosis in Crohn’s disease strictures [Visium]

10x Genomics Visium · unknown

— 2 5.7 /10 —
16 Performance differences in spatial transcriptomics platforms identify Treg biology in human inflammatory bowel disease [Xenium]

Xenium · unknown

— 32 5.7 /10 —
17 Performance differences in spatial transcriptomics platforms identify Treg biology in human inflammatory bowel disease [CosMx]

CosMx · unknown

— 60 5.1 /10 —
18 Creeping fat-derived mechanosensitive fibroblasts drive intestinal fibrosis in Crohn’s disease strictures [Xenium]

10X Genomics Xenium · unknown

— 8 5.0 /10 —
19 Spatiotemporal resolving Crohn's disease fibrosis

10x Genomics Visium Spatial Gene Expression · unknown

— 2 4.4 /10 —

Impact = reuse-readiness mean (0–10) × participants. Sample count is shown for context and does not drive rank. Rows without a reuse-readiness score sort last.