Foundry120 atlas

← IBD spatial transcriptomics

Performance differences in spatial transcriptomics platforms identify Treg biology in human inflammatory bowel disease [Xenium]

Download from source ↗

Dataset overview

Participants None
Samples 32
Reuse readiness 6.3/10 evidence-backed score

Spatial transcriptomics atlas of inflammatory bowel disease to guide implementation in research consortiums and clinical trials.

Li Y, Wei C, Yang W, Wang H, Robinson A, Peshek I, Yu T, Park J, et al. · Nature communications · 2026

Abstract

Using over 100 intestinal tissue sections from non-diseased controls and patients with ulcerative colitis or Crohn's disease across multiple inflammatory bowel disease consortia, we construct a spatially resolved atlas containing over three million cells and systematically evaluate two imaging-based spatial transcriptomics platforms. Here we show that CosMx tends to achieve higher detection efficiency than Xenium across commercially available panels in both ulcerative colitis and Crohn's disease, whereas Xenium shows reduced performance associated with tissue type, block quality, and panel size. CosMx identifies regulatory T cell associated biology in both disease subtypes, which we validate using independent laboratory experiments and multi-plex spatial multi-omics. CosMx's data quality remains stable across variation in fixation time and sectioning procedures, supporting its operational feasibility for multi-center studies. This study establishes a technical and biological benchmark for the application of single-cell-resolved spatial transcriptomics in gastrointestinal tissue, enabling more reliable application of spatial technologies in translational inflammatory bowel disease research.

doi:10.1038/s41467-026-72482-w ↗ PMID 42049732 ↗ PMC13328602 ↗

Study facts

Organism
Homo sapiens
Platform
Xenium
Age group
—
Disease groups
—
Anatomical sites
human Ileum, human rectum

Data availability

  • Raw counts
  • Spatial coordinates
  • Histology images
  • Analysis code

File types MTXPARQUETTIFFTSV

Strengths & limitations for reuse

Strengths

  • Raw counts are advertised
  • Spatial coordinates are advertised
  • Histology images are advertised
  • Analysis code is available

Limitations

  • Not documented: processed matrices are advertised
  • Not documented: 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.platform Xenium
Performance differences in spatial transcriptomics platforms identify Treg biology in human inflammatory bowel disease [Xenium]

Section series_title, offset —
assay.resolution cellular
imaging-based spatial transcriptomics platforms enable single-cell and/or subcellular resolution

Section Introduction, offset 960
assay.segmentation_method Xenium built-in cell segmentation; the accession includes runs with and without segmentation markers
4 Xenium multi-tissue 377 panel with segmentation... 4 Xenium multi-tissue 377 panel without segmentation

Section series_overall_design, offset 3100
assay.sequencing_based False
imaging-based spatial transcriptomics platforms enable single-cell and/or subcellular resolution profiling

Section Introduction, offset 1000
assay.whole_transcriptome False
Xenium multi-tissue 337 panel

Section series_overall_design, offset —

Cohort

FieldValueEvidence
cohort.disease_activity_metadata_available True
16 Xenium multi-tissue 337 panel (Ileum_CD_Inflamed: 2, Ileum_CD_NonInflamed: 2, Ileum_UC_NonInflamed: 2, Rectum_CD_Noninflamed: 2, Rectum_CD_inflamed: 2, Rectum_UC_inflamed: 4, Rectum_UC_Noninflamed: 2)

Section series_overall_design, offset —
cohort.study_design cross_sectional
All human tissue samples analyzed in this study were collected in a cross-sectional manner, and no post-intervention samples were included.

Section Methods > Sample procurement and preparation, offset —

Data_Assets

FieldValueEvidence
data_assets.analysis_code True
Custom scripts for data processing and quality evaluation are available at https://zenodo.org/records/19006691

Section Code availability, offset —
data_assets.file_manifest True
filelist.txt

Section filelist.txt, offset —
data_assets.histology_images True from source
GEO deposit evidence: TIFF in GEO suppfile types

Section GEO record summary, offset —
data_assets.open_access True
Public on Mar 13 2026

Section series_status, offset —
data_assets.raw_counts True from source
GEO deposit evidence: MTX in GEO suppfile types

Section GEO record summary, offset —
data_assets.sample_metadata True
"title": "Ileum_CD_Inflamed [I0294 ITDF00A Xenium337]" ... "characteristics": {"tissue": "Ileum"}

Section samples, offset —
data_assets.segmentation_data True
4 Xenium multi-tissue 377 panel with segmentation

Section series_overall_design, offset —
data_assets.spatial_coordinates True
we extracted the nuclear and non-nuclear counts from the transcript coordinates file

Section Methods; Extracting nuclear and non-nuclear counts, offset 91000

Specimens

FieldValueEvidence
specimens.anatomical_sites ['human Ileum', 'human rectum'] from source
GEO sample source names: human Ileum; human rectum

Section GEO family SOFT, offset —
specimens.inflamed_status_available True
Rectum_UC_nonInflamed ... Rectum_UC_inflamed ... Ileum_CD_Inflamed ... Ileum_CD_NonInflamed

Section series_overall_design, offset 2600
specimens.number_of_samples 32 computed
32 GSM records parsed from GEO family SOFT

Section GEO family SOFT, offset —
specimens.preservation_method formalin-fixed, paraffin-embedded (FFPE)
Formalin-fixed, paraffin-embedded blocks were cut into sections on positively charged slides

Section extract_protocol, offset —
specimens.specimen_type biopsy
The CosMx multi-tissue panel (950 genes) and the Xenium multi-tissue panel (377 genes) were run on 16 IBD intestinal FFPE blocks (n = 32 mucosal biopsies)

Section Results – CosMx multi-tissue panel versus Xenium multi-tissue panel, offset 3650