Foundry120 atlas

← IBD single-cell transcriptomics

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

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Dataset overview

Participants 12
Samples 2
Reuse readiness 6.4/10 evidence-backed score

(untitled)

PMID 42262895 ↗

Study facts

Organism
Homo sapiens
Platform
Illumina NovaSeq 6000
Age group
—
Disease groups
—
Anatomical sites
peripheral blood

Data availability

  • Raw counts
  • Processed matrix

File types CSVRDS

Strengths & limitations for reuse

Strengths

  • Raw reads are advertised
  • Raw counts are advertised
  • Processed matrices are advertised
  • Cell metadata are advertised
  • Participant mapping is available
  • 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.assay_type BD Rhapsody Targeted Analysis
BD Rhapsody Targeted Analysis with Parse Evercode WT v2.

Section samples.extract_protocol, offset —
assay.library_chemistry Parse Evercode WT v2
BD Rhapsody Targeted Analysis with Parse Evercode WT v2.

Section samples.extract_protocol, offset —
assay.platform Illumina NovaSeq 6000
Sequenced on Illumina NovaSeq 6000 (paired-end, 150bp).

Section samples.extract_protocol, offset —
assay.reference_genome GRCh38
Assembly: GRCh38

Section samples.data_processing, offset —
assay.sequencing_type scrna_seq
using single-cell RNA sequencing

Section summary, offset —

Cohort

FieldValueEvidence
cohort.total_participants 12
12 donors multiplexed across 2 libraries

Section series_overall_design, offset —

Data_Assets

FieldValueEvidence
data_assets.cell_metadata True
VDJ_perCell.csv: per-cell VDJ chain assignments.

Section samples.data_processing, offset —
data_assets.open_access True
Public on May 24 2026

Section series.series_status, offset —
data_assets.processed_matrix True
GSE330122_integrated_seurat_object_all12donors.rds

Section filelist.txt, offset —
data_assets.raw_counts True
DBEC_MolsPerCell.csv: DBEC-corrected molecule counts per cell

Section samples.data_processing, offset —
data_assets.raw_reads True
GSE330122_RAW.tar

Section filelist.txt, offset —

Processing

FieldValueEvidence
processing.quality_control_reported True
PBMCs counted and viability assessed by trypan blue exclusion.

Section samples.extract_protocol, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['peripheral blood']
peripheral blood mononuclear cells (PBMCs)

Section summary, offset —
specimens.number_of_samples 2
"n_samples": 2

Section geo_record_summary, offset —
specimens.participant_to_sample_mapping_available True
Donor demultiplexing via BD Sample Tags.

Section samples.data_processing, offset —