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← IBD spatial transcriptomics

Fragment-sequencing unveils local tissue microenvironments at single cell resolution

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Dataset overview

Participants None
Samples 34
Reuse readiness 6.0/10 evidence-backed score

Fragment-sequencing unveils local tissue microenvironments at single-cell resolution.

Handler K, Bach K, Borrelli C, Piscuoglio S, Ficht X, Acar IE, Moor AE. · Nature communications · 2023

Abstract

Cells collectively determine biological functions by communicating with each other-both through direct physical contact and secreted factors. Consequently, the local microenvironment of a cell influences its behavior, gene expression, and cellular crosstalk. Disruption of this microenvironment causes reciprocal changes in those features, which can lead to the development and progression of diseases. Hence, assessing the cellular transcriptome while simultaneously capturing the spatial relationships of cells within a tissue provides highly valuable insights into how cells communicate in health and disease. Yet, methods to probe the transcriptome often fail to preserve native spatial relationships, lack single-cell resolution, or are highly limited in throughput, i.e. lack the capacity to assess multiple environments simultaneously. Here, we introduce fragment-sequencing (fragment-seq), a method that enables the characterization of single-cell transcriptomes within multiple spatially distinct tissue microenvironments. We apply fragment-seq to a murine model of the metastatic liver to study liver zonation and the metastatic niche. This analysis reveals zonated genes and ligand-receptor interactions enriched in specific hepatic microenvironments. Finally, we apply fragment-seq to other tissues and species, demonstrating the adaptability of our method.

doi:10.1038/s41467-023-43005-8 ↗ PMID 38012149 ↗ PMC10681997 ↗

Study facts

Organism
Homo sapiens; Mus musculus
Platform
GPL24247; GPL24676; GPL25526
Age group
paediatric
Disease groups
—
Anatomical sites
Liver, Spleen, Gut, Colon organoids

Data availability

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

File types CSVJSONMTXPNGRDSTSVTXT

Strengths & limitations for reuse

Strengths

  • Raw counts are advertised
  • Processed matrices are advertised
  • Spatial coordinates are advertised
  • Histology images 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.platform GPL24247; GPL24676; GPL25526
"series_platform_id": "GPL24247\nGPL24676\nGPL25526"

Section series_platform_id, offset 1250
assay.reference_genome GRCh38 from source
GRCh38

Section GEO family SOFT, offset —
assay.sequencing_based True from source
GEO assay type/library strategy: RNA-SEQ

Section GEO family SOFT, offset —
assay.whole_transcriptome True from source
GEO library strategy=['RNA-SEQ']

Section GEO family SOFT, offset —

Cohort

FieldValueEvidence
cohort.age_group paediatric from source
GEO age characteristics: 8-10 weeks old; 8-10 weeks old; 8-10 weeks old; 8-10 weeks old; 8-10 weeks old; 8-10 weeks old; 8-10 weeks old; 8-10 weeks old; 8-10 weeks old; 8-10 weeks old; 8-10 weeks old; 8-10 weeks old; 8-10 weeks old; 8-10 weeks old; 8-10 weeks old; 8-10 weeks old; 8-10 weeks old; 8-10 weeks old; 8-10 weeks o

Section GEO family SOFT, offset —
cohort.treatment_exposure_documented True from source
GEO sample characteristics document treatment/therapy

Section GEO family SOFT, offset —

Data_Assets

FieldValueEvidence
data_assets.analysis_code True from source
GEO deposit evidence: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6661nnn/GSM6661376/suppl/GSM6661376_MetsM1kept_barcodes.txt.gz

Section GEO family SOFT, offset —
data_assets.file_manifest True from source
Supplementary files enumerated in family SOFT (ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6661nnn/GSM6661376/suppl/GSM6661376_MetsM1kept_barcodes.txt.gz, ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6661nnn/GSM6661400/suppl/GSM6661400_Visium4M1_tissue_hires_image.png.gz, ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6661nnn/GSM6661400/suppl/GSM6661400_Visium4M1_tissue_positions_list.csv.gz)

Section GEO family SOFT, offset —
data_assets.histology_images True from source
GEO deposit evidence: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6661nnn/GSM6661400/suppl/GSM6661400_Visium4M1_tissue_hires_image.png.gz

Section GEO family SOFT, offset —
data_assets.open_access True
"license": "cc by"

Section europepmc_record, offset —
data_assets.processed_matrix True from source
GEO deposit evidence: RDS in GEO suppfile types

Section GEO record summary, 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
sample_values_with_sample_counts: title, molecule, organism, source_name, characteristics, and supplementary_files

Section sample_values_with_sample_counts, offset —
data_assets.spatial_coordinates True from source
GEO deposit evidence: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6661nnn/GSM6661400/suppl/GSM6661400_Visium4M1_tissue_positions_list.csv.gz

Section GEO family SOFT, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['Liver', 'Spleen', 'Gut', 'Colon organoids'] from source
GEO sample source names: Liver; Spleen; Gut; Colon organoids

Section GEO family SOFT, offset —
specimens.number_of_samples 34 computed
34 GSM records parsed from GEO family SOFT

Section GEO family SOFT, offset —
specimens.specimen_type mixed inferred
application to metastatic mouse liver (9 replicates), untreated mouse liver (1 replicate), untreated mouse spleen (2 replicates), Crohn?s disease biopsies (2 replicates) and a mix of human and mouse colorectal cancer organoids

Section series_overall_design, offset 1700