Foundry120 atlas

IBD single-cell transcriptomics

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

Also see IBD spatial transcriptomics Also see IBD microbiome

Full catalogue

All published datasets

67 datasets in this domain, ranked by impact.

# Dataset Participants Samples Reuse Impact
1 IBDverse multitissue atlasing cohort

10x Genomics Chromium · open

421 732 8.9 /10 3,746.9
2 Single-cell analysis of Crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy

Illumina HiSeq 2000 · unknown

199 199 5.6 /10 1,114.4
3 Human CD atlas study between colon and terminal ileum

10x 3' v1 · open

71 — 6.7 /10 475.7
4 Reveal the key mediators of inflammation in Crohn's disease undergoing biological treatments

10x Genomics Chromium · unknown

49 85 7.6 /10 372.4
5 An immune-cell signature of bacterial sepsis (Patient PBMCs)

single-cell-portal-scp548 · open

45 — 6.9 /10 310.5
6 TI epithelial

10x Genomics · open

42 — 6.0 /10 252.0
7 TI stromal

10x 3' v2 · open

40 — 5.7 /10 228.0
8 colon stromal

10x · open

34 — 6.4 /10 217.6
9 colon epithelial

10x · open

34 — 6.0 /10 204.0
10 TL1A-activated Tcells as upstream regulators of perianal fistulizing disease-associated changes in the rectum of Crohn's Disease patients [scRNA-seq]

10x Genomics · unknown

31 29 6.4 /10 198.4
11 Human CD fibrosis study using single cell and spatial data

10x 3' v3 · open

31 61 6.4 /10 198.4
12 colon immune

10x 3' v1 · open

34 — 5.6 /10 190.4
13 Single-cell RNA-sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis

10X 5' Gene Expression (GEX) · unknown

30 34 6.3 /10 189.0
14 IPF Cell Atlas

geo-gse136831 · unknown

78 — 2.3 /10 179.4
15 IBD and HC 10x Single-cell transcriptomics data

Chromium 10x Genomics platform · open

18 18 9.6 /10 172.8
16 Transcriptional Survey of Ileal-Anal Pouch Immune Cells from Ulcerative Colitis

10x Genomics Chromium · unknown

26 26 5.7 /10 148.2
17 single-cell RNA sequencing of healthy control, ulcerative colitis, and primary sclerosing cholangitis concomitant with ulcerative colitis colonic mucosa

10x Genomics · open

22 — 6.3 /10 138.6
18 Paediatric Human Gut (4-14y)

10x Genomics Chromium · open

15 15 9.0 /10 135.0
19 Longitudinal single cell RNA-seq of the inflamed colon

NextSeq 500 · unknown

18 — 6.6 /10 118.8
20 The reparative immunologic consequences of stem cell transplantation as a cellular therapy for refractory Crohn’s disease

10x Genomics Chromium iX; Illumina NovaSeq 6000 · unknown

19 — 6.1 /10 115.9
21 Refining Colorectal Cancer Classification and Clinical Stratification Through a Single-Cell Atlas

10X Genomics Single Cell 5' Platform · unknown

16 23 6.7 /10 107.2
22 Single-Cell Analyses Elucidate the Cellular and Molecular Landscape of Ulcerative Colitis

10X Genomics · unknown

16 103 6.6 /10 105.6
23 Single-Cell Transcriptomic Analysis of Human Lung Reveals Complex Multicellular Changes During Pulmonary Fibrosis II

10x Genomics Chromium Single Cell Controller · unknown

17 17 5.9 /10 100.3
24 Differential effects of tofacitinib on macrophage activation contribute to lack of response in ulcerative colitis patients

Chromium 10x Genomics · unknown

11 23 7.9 /10 86.9
25 Single-cell transcriptome analysis of human skin identifies novel fibroblast subpopulation and enrichment of immune subsets in atopic dermatitis

10x Genomics Chromium; Illumina HiSeq 2500 · unknown

12 17 7.0 /10 84.0
26 Single-cell RNA sequencing to identify 51248 single cells from periodontal tissues of healthy humans and periodontitis patients with or without treatment

BD Rhapsody system · unknown

12 12 6.7 /10 80.4
27 Single-cell transcriptomics and bulk T-cell receptor beta-chain sequencing of peripheral blood mononuclear cells from patients with inflammatory bowel disease (Crohn's disease and ulcerative colitis) and healthy controls I

BD Rhapsody Targeted Analysis; Illumina NovaSeq 6000 · unknown

12 2 6.3 /10 75.6
28 Single-cell RNA sequencing of healthy mouse colon and mouse colon with acute or chronic colitis induced by DSS

10x Genomics Chromium · unknown

10 10 7.1 /10 71.0
29 Selective oxidative protection leads to tissue topological changes orchestrated by macrophage during ulcerative colitis

10x Genomics Chromium Controller · unknown

8 12 7.6 /10 60.8
30 Single-cell transcriptomics reveal cell type-specific molecular changes and altered intercellular communications in chronic obstructive pulmonary disease

BD Rhapsody · unknown

9 9 6.7 /10 60.3
31 Metadata for scDrugPrio analysis of individual Crohn's disease (CD) patients' scRNA-sequencing data

datacite-10.25452-figshare.plus.22344127.v1 · open

11 — 4.3 /10 47.3
32 Dynamic changes in human single cell transcriptional signatures during fatal sepsis

10x Genomics Chromium · unknown

7 12 6.6 /10 46.2
33 scRNAseq of sorted stromal cell compartment from patients with Crohn's disease

10x Genomics Chromium · unknown

7 13 6.6 /10 46.2
34 Accute and repeated DSS exposure induce distinct immune responses with differential relevance to human Ulcerative Colitis

Illumina NovaSeq X Plus · unknown

6 10 7.3 /10 43.8
35 Single cell sequencing data on ileum and mesentery tissue from Crohn's disease patients

Illumina NovaSeq 6000 · unknown

5 — 7.1 /10 35.5
36 Single cell and spatial transcriptomics of mouse colon

single-cell-portal-scp2038 · open

6 — 5.1 /10 30.6
37 Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn’s Disease

Illumina NextSeq 500 · unknown

5 — 6.1 /10 30.5
38 Dictionary of human intestinal organoid responses to secreted niche factors at single cell resolution

10X Chromium X · unknown

3 249 8.7 /10 26.1
39 Extended - Neural cells

10x 3' v1 · open

2 — 7.6 /10 15.2
40 scRNAseq of monocytes from Trained immunity experiments

arrayexpress-e-mtab-9702 · open

3 — 5.0 /10 15.0
41 Single-cell RNA-sequencing analysis of the IL-10 dependent response of human CD14+ monocytes to LPS

10x Genomics Chromium Controller with Illumina HiSeq 4000 · unknown

2 4 6.3 /10 12.6
42 Inflammatory signaling differentially changes chromatin accessibility and gene expression of the PD-associated kinase LRRK2 between human and mice [snRNA-Seq human]

10x Genomics Single Cell 3′ Gene Expression · unknown

2 4 4.4 /10 8.8
43 Bioengineered Extracellular Vesicles Co-delivering PD-L1 and miR-27a-3p Synergistically Reprogram T cells To Treat Inflammatory Bowel Disease [scRNA-Seq]

single-cell RNA sequencing · unknown

3 — 2.9 /10 8.7
44 Extended - All genes

10x 3' v1 · open

— — 7.6 /10 —
45 Extended - Small intestine (adult/pediatric)- 18485genes

10x Genomics · open

— — 7.4 /10 —
46 Extended - Small intestine (adult/pediatric)

10x Genomics · open

— — 7.4 /10 —
47 Total - Cells of the human intestinal tract mapped across space and time

10x Genomics Chromium · open

— 164 7.4 /10 —
48 Extended - Large Intestine (adult/pediatric)

10x 3' v2 · open

— — 7.3 /10 —
49 Extended - Myeloid cells

Illumina NovaSeq 6000 · open

— — 7.3 /10 —
50 Extended - Myeloid_with_neutrophils

10x 3' v1 · open

— — 7.0 /10 —
51 Extended - B and B plasma cells

10x Genomics Chromium · open

— — 6.9 /10 —
52 Extended - Endothelial cells

10x Genomics Chromium · open

— — 6.9 /10 —
53 Spatially Resolved Insights Into Fistulating Crohn’s Disease Pathogenesis - scRNA-Seq

10x Chromium Single Cell platform · unknown

— — 6.9 /10 —
54 Extended - T and NK cells

10x Genomics Chromium · open

— — 6.7 /10 —
55 Single-cell RNA sequencing of ovarian, colorectal and breast cancer

10x Genomics Chromium · open

— 49 6.4 /10 —
56 Extended+ - 18485 genes

10x 3' v1 · open

— — 6.3 /10 —
57 Extended - Mesenchymal (adult/pediatric)

10x Genomics Chromium · open

— — 6.1 /10 —
58 single cell RNA-seq of CD45+ cell from DSS induced colitic

10x Chromium 3′ Reagent Kits v3 · unknown

— 2 6.1 /10 —
59 TI immune

10x Genomics · open

— — 5.6 /10 —
60 Single-cell Transcriptomics Combined With Interstitial Fluid Proteomics Defines Cell Type-Specific Immune Regulation in Atopic Dermatitis

Illumina HiSeq 3000 · unknown

— 15 5.6 /10 —
61 CD16+ CD163+ monocytes traffic to sites of inflammation in NEC

10x Genomics Chromium · unknown

— 6 5.6 /10 —
62 Deriving human intestinal organoids with functional tissue-resident macrophages all from pluripotent stem cells

10x Genomics Chromium · unknown

— 5 5.4 /10 —
63 Gene expression profile at single cell level from the colorectal cancer (CRC)

NextSeq 500 · unknown

— 26 4.9 /10 —
64 Inflammatory transcriptomic signatures and cell type compositions in inflamed and non-inflamed colonic mucosa of ulcerative colitis

Illumina NovaSeq 6000 · unknown

— 45 4.9 /10 —
65 CD45RA+CD62L- ILCs represent a quiescent local reservoir for the generation of mature ILC in human tissues

Illumina NextSeq 500 · unknown

— — 4.6 /10 —
66 Gene expression at single cell level of stromal cells from the distal colon of normal sites of colorectal cancer and inflamed sites of ulcerative colitis.

DNBSEQ-G400 · unknown

— 13 4.6 /10 —
67 TL1A-activated Tcells as upstream regulators of perianal fistulizing disease-associated changes in the rectum of Crohn's Disease patients [RNA-seq]

Illumina NovaSeq X · unknown

— 28 4.0 /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.