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

85 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 6.0 /10 1,194.0
3 IPF Cell Atlas

Illumina HiSeq 4000 · unknown

78 78 7.1 /10 553.8
4 Human CD atlas study between colon and terminal ileum

10x 3' v1 · open

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

GPL24676 and GPL18573 · unknown

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

single-cell-portal-scp548 · open

45 — 6.9 /10 310.5
7 TI epithelial

10x Genomics · open

42 — 6.0 /10 252.0
8 Processed bulk RNA-seq counts and Olink Explore 384 NPX data from tofacitinib-treated patients with ulcerative colitis (TOFA-histology multi-omic substudy)

bulk RNA-seq and Olink Explore 384 proteomics · open

40 — 6.1 /10 244.0
9 TI stromal

10x 3' v2 · open

40 — 5.7 /10 228.0
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 7.1 /10 220.1
11 colon stromal

10x · open

34 — 6.4 /10 217.6
12 Human CD fibrosis study using single cell and spatial data

10x 3' v3 · open

31 61 6.7 /10 207.7
13 colon epithelial

10x · open

34 — 6.0 /10 204.0
14 single-cell RNA sequencing of healthy control, ulcerative colitis, and primary sclerosing cholangitis concomitant with ulcerative colitis colonic mucosa

10x 5' · open

22 — 8.7 /10 191.4
15 colon immune

10x 3' v1 · open

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

Illumina NovaSeq 6000; NextSeq 500; Illumina HiSeq 4000 · unknown

30 34 6.3 /10 189.0
17 IBD and HC 10x Single-cell transcriptomics data

Chromium 10x Genomics platform · open

18 18 9.6 /10 172.8
18 Systemic reprogramming of monocytes in Crohn’s disease promotes their intestinal inflammatory function

10x Genomics Chromium 3′ assay; Illumina NovaSeq 6000 · unknown

20 20 7.7 /10 154.0
19 Transcriptional Survey of Ileal-Anal Pouch Immune Cells from Ulcerative Colitis

10x Genomics Chromium · unknown

26 26 5.7 /10 148.2
20 The reparative immunologic consequences of stem cell transplantation as a cellular therapy for refractory Crohn’s disease

Illumina NovaSeq 6000 · unknown

19 36 7.3 /10 138.7
21 Paediatric Human Gut (4-14y)

10x Genomics Chromium · open

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

Illumina NextSeq500 · unknown

18 — 6.9 /10 124.2
23 Refining Colorectal Cancer Classification and Clinical Stratification Through a Single-Cell Atlas

10X Genomics Single Cell 5' Platform · unknown

16 23 7.0 /10 112.0
24 Single-Cell Analyses Elucidate the Cellular and Molecular Landscape of Ulcerative Colitis

10x Genomics · unknown

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

Illumina HiSeq 4000 · unknown

17 17 5.9 /10 100.3
26 Persistent Inflammation of the Rectum in Perianal-Fisulizing Crohn's Disease Associates with Goblet Cell Function

10X Genomics Chromium · unknown

13 13 7.3 /10 94.9
27 Differential effects of tofacitinib on macrophage activation contribute to lack of response in ulcerative colitis patients

10x Genomics Chromium · unknown

11 23 8.4 /10 92.4
28 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
29 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
30 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
31 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
32 Single-cell transcriptomics reveal cell type-specific molecular changes and altered intercellular communications in chronic obstructive pulmonary disease

Illumina NovaSeq 6000 · unknown

9 9 7.0 /10 63.0
33 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
34 Altered oligodendrocyte heterogeneity in Multiple sclerosis.

Illumina HiSeq 2500 · unknown

9 20 6.0 /10 54.0
35 Dietary induced dedifferentiation of Bmi1 cells and its impact on intestinal mucosal homeostasis

Illumina HiSeq 4000 · unknown

8 8 6.3 /10 50.4
36 Dynamic changes in human single cell transcriptional signatures during fatal sepsis

Illumina NovaSeq 6000 · unknown

7 12 7.0 /10 49.0
37 Intestinal epithelial inositol polyphosphate multikinase protects mice from experimental colitis via governing colonic tuft cell homeostasis

Illumina NextSeq 550 · unknown

8 1,203 6.1 /10 48.8
38 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
39 scRNAseq of sorted stromal cell compartment from patients with Crohn's disease

10x Genomics Chromium · unknown

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

Illumina NovaSeq X Plus · unknown

6 10 7.6 /10 45.6
41 Single cell sequencing data on ileum and mesentery tissue from Crohn's disease patients

10x Genomics Chromium · unknown

5 13 7.9 /10 39.5
42 CD45RA+CD62L- ILCs represent a quiescent local reservoir for the generation of mature ILC in human tissues

Illumina NextSeq 500 · unknown

6 — 6.3 /10 37.8
43 Impact of knocking out Ppargc1a in intestinal stem cells on mucosal homeostasis

Illumina HiSeq 4000 · unknown

6 6 6.1 /10 36.6
44 Single cell and spatial transcriptomics of mouse colon

single-cell-portal-scp2038 · open

6 — 5.1 /10 30.6
45 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
46 Single cell RNA-seq in small intestine

MGISEQ-2000RS · unknown

4 2 7.1 /10 28.4
47 Dictionary of human intestinal organoid responses to secreted niche factors at single cell resolution

10X Chromium X · unknown

3 39 8.7 /10 26.1
48 Multiomic analysis reveals cellular and epigenetic plasticity in intestinal pouches of ulcerative colitis patients [scRNA-seq]

10x Genomics Chromium Single Cell 3' scRNA-seq · unknown

6 — 4.3 /10 25.8
49 Extended - Neural cells

10x 3' v1 · open

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

arrayexpress-e-mtab-9702 · open

3 — 5.0 /10 15.0
51 Concordant B and T Cell Heterogeneity Inferred from the Multiomic Landscape of Peripheral Blood Mononuclear Cells in a Crohn's Disease Cohort

single nucleus multiomic · unknown

3 13 4.6 /10 13.8
52 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
53 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
54 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
55 Extended - All genes

10x 3' v1 · open

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

10x Genomics · open

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

10x Genomics · open

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

10x Genomics Chromium · open

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

10x 3' v2 · open

— — 7.3 /10 —
60 Extended - Myeloid cells

Illumina NovaSeq 6000 · open

— — 7.3 /10 —
61 Spatially Resolved Insights Into Fistulating Crohn’s Disease Pathogenesis - scRNA-Seq

10x Chromium Single Cell platform · unknown

— 62 7.1 /10 —
62 Extended - Myeloid_with_neutrophils

10x 3' v1 · open

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

10x Genomics Chromium · open

— — 6.9 /10 —
64 Extended - Endothelial cells

10x Genomics Chromium · open

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

10x Genomics Chromium · open

— — 6.7 /10 —
66 Gene expression profile at single cell level of patient-derived colon fibroblasts induced by different cytokine cocktails to become inflammation-associated fibroblasts (IAFs)

10x Genomics Chromium Next GEM single cell 3’ HT reagent kit V3.1; Illumina NovaSeq 6000 · unknown

— 8 6.7 /10 —
67 Single-cell RNA sequencing of ovarian, colorectal and breast cancer

10x Genomics Chromium · open

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

10x 3' v1 · open

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

10x Genomics Chromium · open

— — 6.1 /10 —
70 Physiological hypoxia improves growth and functional differentiation of human intestinal epithelial organoids [scRNA-seq]

10x Genomics Chromium Single Cell Platform · unknown

— 4 6.1 /10 —
71 single cell RNA-seq of CD45+ cell from DSS induced colitic

10x Chromium 3′ Reagent Kits v3 · unknown

— 2 6.1 /10 —
72 Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing

Illumina HiSeq 2500; Illumina HiSeq 2000; Illumina NovaSeq 6000 · unknown

— 28 6.0 /10 —
73 Increased neutrophils in inflammatory bowel disease accelerate the accumulation of amyloid plaques in the mouse model of Alzheimer's disease

Illumina NovaSeq 6000 · unknown

— 8 6.0 /10 —
74 Geometric engineering of organoid culture for enhanced organogenesis in a dish

Illumina NovaSeq 6000 · unknown

— 5 5.7 /10 —
75 Gene expression profile at single cell level of periheral blood mono-nucleus cells (PBMC) in response to bacterial protein (PFOR) stimulation

Illumina HiSeq X Ten · unknown

— 2 5.7 /10 —
76 TI immune

10x Genomics · open

— — 5.6 /10 —
77 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 —
78 CD16+ CD163+ monocytes traffic to sites of inflammation in NEC

10x Genomics Chromium · unknown

— 6 5.6 /10 —
79 Acute, reversible dietary effect on the transcriptomic profiles of intestinal epithelial cells

Illumina NovaSeq 6000 · unknown

— 9 5.4 /10 —
80 Deriving human intestinal organoids with functional tissue-resident macrophages all from pluripotent stem cells

10x Genomics Chromium · unknown

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

NextSeq 500 · unknown

— 26 5.1 /10 —
82 Inflammatory transcriptomic signatures and cell type compositions in inflamed and non-inflamed colonic mucosa of ulcerative colitis

Illumina HiSeq 2500 · unknown

— 45 5.1 /10 —
83 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 —
84 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 4.3 /10 —
85 A single-cell atlas of the peripheral immune response to severe COVID-19

Illumina NovaSeq 6000 · unknown

— — 4.1 /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.