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← IBD single-cell transcriptomics

IBD and HC 10x Single-cell transcriptomics data

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Dataset overview

Participants 18
Samples 18
Reuse readiness 9.6/10 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
Chromium 10x Genomics platform
Age group
—
Disease groups
—
Anatomical sites
mucosa of ascending colon, mucosa of descending colon, mucosa of rectum, mucosa of sigmoid colon, mucosa of transverse colon

Data availability

  • Processed matrix
  • Analysis code

File types H5AD

Strengths & limitations for reuse

Strengths

  • Raw reads are advertised
  • Processed matrices are advertised
  • Cell metadata are advertised
  • Analysis code is available
  • Participant mapping is available
  • Participant counts are documented

Limitations

  • Not documented: raw counts are advertised
Extraction evidence & provenance

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

Assay

FieldValueEvidence
assay.assay_type 10x 3' v2 from source
assay=10x 3' v2

Section structured repository metadata, offset —
assay.library_chemistry 10x Genomics 3′ mRNA single-cell method
10× Genomics 3′ mRNA single-cell method was used

Section Methods / 10× library preparation and sequencing, offset —
assay.platform Chromium 10x Genomics platform
Approximately 7000 cells were loaded onto the Chromium10x Genomics platform

Section Methods / 10× library preparation and sequencing, offset —
assay.reference_genome Gencode release 27, assembly GRCh38 p10
an alignment based on the reference genome (Gencode release 27, assembly GRCh38 p10)

Section Methods / Data processing, offset —
assay.sequencing_type scrna_seq from source
sequencing_type=scrna_seq

Section structured repository metadata, offset —

Cohort

FieldValueEvidence
cohort.crohns_disease_participants 6
CD ( n = 6)

Section Results, offset —
cohort.disease_activity_metadata_available True
active UC and colonic CD patients

Section Results, offset —
cohort.non_ibd_controls 6
HC ( n = 6)

Section Results, offset —
cohort.total_participants 18 computed
ScRNA-seq analysis of colonic biopsies from HC ( n = 6), CD ( n = 6) and UC ( n = 6) active patients

Section Results, offset —
cohort.ulcerative_colitis_participants 6
UC ( n = 6) active patients

Section Results, offset —

Data_Assets

FieldValueEvidence
data_assets.analysis_code True
Full code for scRNAseq analysis is available at https://github.com/ibd-bcn/ibd-bcn_single_cell

Section Code availability, offset —
data_assets.cell_metadata True from source
CELLxGENE dataset exposes cell metadata

Section structured repository metadata, offset —
data_assets.open_access True from source
public CELLxGENE dataset

Section structured repository metadata, offset —
data_assets.participant_metadata True from source
"donor_id": ["HC_1", "CD_1", "CD_2", "UC_1", "UC_2", "HC_2", "CD_3", "CD_4", "HC_3", "HC_4", "HC_5", "HC_6", "CD_5", "CD_6", "UC_3", "UC_4", "UC_5", "UC_6"]

Section —, offset —
data_assets.processed_matrix True from source
CELLxGENE dataset exposes H5AD

Section structured repository metadata, offset —
data_assets.raw_reads True
ScRNA-seq, bulk RNA-seq and CosMx SMI raw data generated in this study have been deposited in the GEO Omnibus database under accession code GSE214695

Section Data availability, offset —

Processing

FieldValueEvidence
processing.batch_correction_reported True
we applied Harmony

Section Methods / Batch correction and cluster annotation, offset —
processing.cell_type_annotation_method Manual annotation based on marker genes; label transfer for spatial data
The annotation of each subcluster from the main cell type was defined by the marker genes

Section Methods / Identification of cell types, offset —
processing.doublet_detection_reported True
doublets were assessed using the scDblFinder R package and removed

Section Methods / Data processing, offset —
processing.normalization_method Logarithmic normalization
Then, we logarithmically normalized, obtained the highly variable genes, and scaled the counts

Section Methods / Data processing, offset —
processing.quality_control_reported True
Low-quality cells were then filtered out based on mitochondrial RNA percentage and number of genes per cell

Section Methods / Data processing, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['mucosa of ascending colon', 'mucosa of descending colon', 'mucosa of rectum', 'mucosa of sigmoid colon', 'mucosa of transverse colon'] from source
tissues=mucosa of ascending colon, mucosa of descending colon, mucosa of rectum, mucosa of sigmoid colon, mucosa of transverse colon

Section structured repository metadata, offset —
specimens.inflamed_status_available True
colon biopsies from active areas of UC and CD patients

Section Methods / Patient recruitment and sample collection, offset —
specimens.number_of_cells 46700 from source
cell_count=46700

Section structured repository metadata, offset —
specimens.number_of_samples 18
Two cohorts of colonic samples including active Crohn’s disease (CD), active ulcerative colitis (UC) and healthy controls (HC) were processed by scRNA-seq ( n = 18 samples)

Section Results, offset —
specimens.participant_to_sample_mapping_available True from source
"donor_id": ["HC_1", "CD_1", "CD_2", "UC_1", "UC_2", "HC_2", "CD_3", "CD_4", "HC_3", "HC_4", "HC_5", "HC_6", "CD_5", "CD_6", "UC_3", "UC_4", "UC_5", "UC_6"]

Section —, offset —
specimens.specimen_type biopsy
Colon samples were collected to perform scRNAseq

Section Methods / Patient recruitment and sample collection, offset —