Foundry120 atlas

← IBD spatial transcriptomics

IBD CosMx NanoString data from colonic mucosa

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Dataset overview

Participants None
Samples 9
Reuse readiness 7.4/10 evidence-backed score

Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease.

Garrido-Trigo A, Corraliza AM, Veny M, Dotti I, Melón-Ardanaz E, Rill A, Crowell HL, Corbí Á, et al. · Nature communications · 2023

Abstract

Ulcerative colitis and Crohn's disease are chronic inflammatory intestinal diseases with perplexing heterogeneity in disease manifestation and response to treatment. While the molecular basis for this heterogeneity remains uncharacterized, single-cell technologies allow us to explore the transcriptional states within tissues at an unprecedented resolution which could further understanding of these complex diseases. Here, we apply single-cell RNA-sequencing to human inflamed intestine and show that the largest differences among patients are present within the myeloid compartment including macrophages and neutrophils. Using spatial transcriptomics in human tissue at single-cell resolution (CosMx Spatial Molecular Imaging) we spatially localize each of the macrophage and neutrophil subsets identified by single-cell RNA-sequencing and unravel further macrophage diversity based on their tissue localization. Finally, single-cell RNA-sequencing combined with single-cell spatial analysis reveals a strong communication network involving macrophages and inflammatory fibroblasts. Our data sheds light on the cellular complexity of these diseases and points towards the myeloid and stromal compartments as important cellular subsets for understanding patient-to-patient heterogeneity.

doi:10.1038/s41467-023-40156-6 ↗ PMID 37495570 ↗ PMC10372067 ↗

Study facts

Organism
Homo sapiens
Platform
CosMx Spatial Molecular Imaging (SMI)
Age group
adult
Disease groups
—
Anatomical sites
non-IBD colon, UC colon, CD colon

Data availability

  • Raw counts
  • Processed matrix
  • Spatial coordinates
  • Analysis code

File types CSVHTMLTARTXT

  • colon9
AccessionSampleTissueMolecule
GSM7473682 HC a_non-IBD colon colon total RNA
GSM7473683 HC b_non-IBD colon colon total RNA
GSM7473684 HC c_non-IBD colon colon total RNA
GSM7473685 UC a_UC colon colon total RNA
GSM7473686 UC b_UC colon colon total RNA
GSM7473687 UC c_UC colon colon total RNA
GSM7473688 CD a_CD colon colon total RNA
GSM7473689 CD b_CD colon colon total RNA
GSM7473690 CD c_CD colon colon total RNA

Strengths & limitations for reuse

Strengths

  • Raw counts are advertised
  • Processed matrices are advertised
  • Spatial coordinates are advertised
  • Analysis code is available

Limitations

  • 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.number_of_cells_or_spots 415440 computed
corresponding to ~46,160 cells per sample on average

Section sample_data_processing, offset 500
assay.panel_size 1020 computed
1000-plex + 20 custom genes

Section series_overall_design, offset —
assay.platform CosMx Spatial Molecular Imaging (SMI)
CosMxTM technology ... was applied to 9 FFPE samples

Section series_overall_design, offset —
assay.platform_version CosMx Human Universal Cell Characterization RNA Panel (1000-plex) + 20 custom genes
CosMxTM Human Universal Cell Characterization RNA Panel (1000-plex) + 20 custom genes

Section series_overall_design, offset —
assay.resolution cellular
spatial transcriptomics at single-cell resolution

Section series_summary, offset —
assay.segmentation_method Image segmentation to obtain cell boundaries and assign transcripts at the cell level
Images were segmented to obtain cell boundaries, assign transcripts at the cell-level

Section sample_data_processing, offset —
assay.sequencing_based False inferred
RNA target readout on the CosMx SMI instrument

Section Methods—CosMx Spatial Molecular Imager (SMI) instrument run, offset 1500
assay.whole_transcriptome False
CosMx SMI using a multiplex panel of 1000 genes

Section Results—Integration of single-cell RNA sequencing and spatial molecular imaging analysis, offset 6500

Cohort

FieldValueEvidence
cohort.age_group adult from source
GEO age characteristics: 59; 61; 69; 69; 44; 40; 45; 42; 38

Section GEO family SOFT, offset —
cohort.disease_activity_metadata_available True
We applied spatial transcriptomics at single-cell resolution ... to human inflamed and uninflamed intestine.

Section series_summary, offset 4300

Data_Assets

FieldValueEvidence
data_assets.analysis_code True
Full code for analysis of CosMx SMI data can be found at https://github.com/HelenaLC/CosMx-SMI-IBD

Section Code availability, offset 101000
data_assets.file_manifest True
GSE234713_ReadMe_SMI_Data_File.html

Section series_supplementary_file, offset —
data_assets.open_access True from source
Public on Jun 13 2023

Section series_status, offset —
data_assets.participant_metadata True
characteristics: age ... gender ... tissue ... disease

Section samples, offset —
data_assets.processed_matrix True
GSE234713_CosMx_normalized_matrix.txt.gz

Section series_supplementary_file, offset —
data_assets.raw_counts True
GSE234713_RAW.tar

Section series_supplementary_file, offset —
data_assets.sample_metadata True
The following samples are listed with titles, accessions, and characteristics.

Section dataset-authority, offset —
data_assets.segmentation_data True
GSE234713_CosMx_annotation.csv.gz

Section series_supplementary_file, offset —
data_assets.spatial_coordinates True
a.csv, b.csv, c.csv: Spatial transcriptomics polygon data.

Section sample_data_processing, offset 300

Specimens

FieldValueEvidence
specimens.anatomical_sites ['non-IBD colon', 'UC colon', 'CD colon'] from source
GEO sample source names: non-IBD colon; UC colon; CD colon

Section GEO family SOFT, offset —
specimens.inflamed_status_available True
9 FFPE samples: 3 non-IBD healthy controls, 3 CD and 3 UC

Section series_overall_design, offset 1200
specimens.number_of_samples 9 computed
9 GSM records parsed from GEO family SOFT

Section GEO family SOFT, offset —
specimens.preservation_method formalin-fixed paraffin-embedded (FFPE)
CosMxTM technology ... was applied to 9 FFPE samples

Section series_overall_design, offset 1150
specimens.specimen_type resection
For SMI analysis, surgical colon resections were obtained from non-IBD controls ... UC and CD patients

Section Methods—Patient recruitment and sample collection, offset 69000