Foundry120 atlas

← IBD microbiome

10x Visium HD spatial transcriptomics of full-thickness colon from medically refractory ulcerative colitis and healthy controls

Download from source ↗

Dataset overview

Participants 6
Samples 6
Reuse readiness 6.3/10 evidence-backed score

A full-thickness spatial transcriptomics atlas of medically refractory ulcerative colitis identifies niche signatures associated with biologic non-response

Bai Q, Li R, Liu Z, Zhang Y, He X, Yao J, Wu S, Huang J, et al. · Frontiers in immunology · 2026

PMC13650985 ↗

Study facts

Organism
—
Platform
Illumina NovaSeq 6000
Age group
—
Disease groups
Non-IBD controls, Ulcerative colitis
Anatomical sites
—

Data availability

Specific data assets have not been resolved from the source yet — see the source repository below for the full file listing.

Strengths & limitations for reuse

Strengths

  • Participant-to-sample mapping is available
  • Participant counts are documented
  • Sample counts are documented

Limitations

  • Not documented: raw reads are advertised
  • Not documented: feature/otu tables are advertised
  • Not documented: taxonomic tables are advertised
Extraction evidence & provenance

Each extracted field is shown with the source excerpt and location used to resolve it.

Assay

FieldValueEvidence
assay.platform Illumina NovaSeq 6000 from source
ENA instrument_model=Illumina NovaSeq 6000

Section ENA study report, offset —

Cohort

FieldValueEvidence
cohort.disease_activity_metadata_available True
Detailed sample-level clinical and demographic characteristics ... (gender, age, height, weight, body mass index [BMI], Mayo score and endoscopic Mayo subscore)

Section Human subjects and tissue collection, offset 5900
cohort.non_ibd_controls 3
including 3 non-IBD surgical controls

Section Human subjects and tissue collection, offset 5700
cohort.study_design cross_sectional
Third, the cross-sectional design of spatial transcriptomics precludes direct assessment of the dynamic temporal progression

Section Discussion, offset 63500
cohort.total_participants 6
including 3 non-IBD surgical controls ... and 3 severe, treatment-refractory UC tissues

Section Human subjects and tissue collection, offset 5700
cohort.treatment_exposure_documented True
3 severe, treatment-refractory UC tissues (Mayo score ≥ 10)

Section Human subjects and tissue collection, offset 5820
cohort.ulcerative_colitis_participants 3
3 severe, treatment-refractory UC tissues (Mayo score ≥ 10)

Section Human subjects and tissue collection, offset 5700

Data_Assets

FieldValueEvidence
data_assets.open_access True
"isOpenAccess": "Y"

Section publication metadata, offset —
data_assets.pipeline_or_tool_versions True
All analyses were performed in Python 3.11 using Scanpy ... v1.10, Squidpy ... v1.4 ... pySCENIC ... v0.12.1

Section Software environment and statistical analysis, offset 25100
data_assets.qc_or_negative_controls_reported True
Quality control removed bins with <50 counts or >25% mitochondrial gene fraction

Section Spatial transcriptomics data preprocessing and quality control, offset 8900
data_assets.sample_metadata True
Detailed sample-level clinical and demographic characteristics for all six specimens ... are provided in Supplementary Table S1

Section Human subjects and tissue collection, offset 5750

Specimens

FieldValueEvidence
specimens.body_site colon
Human colon tissues were obtained from Zhongshan Hospital of Xiamen University

Section Human subjects and tissue collection, offset 5580
specimens.inflamed_status_available True
confirmed histologically normal ... and three severe, treatment-refractory UC tissues (Mayo score ≥ 10)

Section Human subjects and tissue collection, offset 5650
specimens.longitudinal_sampling False
the cross-sectional design of spatial transcriptomics precludes direct assessment of the dynamic temporal progression

Section Discussion, offset 63500
specimens.number_of_samples 6 from source
ENA sample_count=6

Section ENA study report, offset —
specimens.participant_to_sample_mapping_available True
Detailed sample-level clinical and demographic characteristics for all six specimens

Section Human subjects and tissue collection, offset 5750