Foundry120 atlas

← IBD spatial transcriptomics

10X Visium Spatial transcriptomics of murine colon at d14 (mucosa healing) in B cell sufficient/deficient mice

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Dataset overview

Participants None
Samples 2
Reuse readiness 5.4/10 evidence-backed score

The spatial transcriptomic landscape of the healing mouse intestine following damage.

Parigi SM, Larsson L, Das S, Ramirez Flores RO, Frede A, Tripathi KP, Diaz OE, Selin K, et al. · Nature communications · 2022

Abstract

The intestinal barrier is composed of a complex cell network defining highly compartmentalized and specialized structures. Here, we use spatial transcriptomics to define how the transcriptomic landscape is spatially organized in the steady state and healing murine colon. At steady state conditions, we demonstrate a previously unappreciated molecular regionalization of the colon, which dramatically changes during mucosal healing. Here, we identified spatially-organized transcriptional programs defining compartmentalized mucosal healing, and regions with dominant wired pathways. Furthermore, we showed that decreased p53 activation defined areas with increased presence of proliferating epithelial stem cells. Finally, we mapped transcriptomics modules associated with human diseases demonstrating the translational potential of our dataset. Overall, we provide a publicly available resource defining principles of transcriptomic regionalization of the colon during mucosal healing and a framework to develop and progress further hypotheses.

doi:10.1038/s41467-022-28497-0 ↗ PMID 35149721 ↗ PMC8837647 ↗

Study facts

Organism
Mus musculus
Platform
10X Visium
Age group
—
Disease groups
—
Anatomical sites
Colon

Data availability

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

File types CSVH5JSONPNGTIFF

Strengths & limitations for reuse

Strengths

  • Raw counts are advertised
  • Processed matrices are advertised
  • Spatial coordinates are advertised
  • Histology images are advertised

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 10X Visium
Using the 10X Visium platform, here, we unbiasedly characterized the spatial transcriptomic landscape of murine colon

Section series_summary, offset —
assay.reference_genome mm10 (Ensembl 93)
Genome_build: mm10 (Ensembl 93)

Section data_processing, offset 420
assay.resolution spot
placed on the already barcoded spots (6.5mm x 6.5mm) on the glass slide

Section extract_protocol, offset 130
assay.sequencing_based True from source
GEO assay type/library strategy: OTHER

Section GEO family SOFT, offset —
assay.whole_transcriptome True inferred
Matrix with raw counts for every gene and every spot

Section data_processing, offset 500

Cohort

FieldValueEvidence
cohort.study_design cross_sectional inferred
On day 14 colonic epithelial cells and stromal cells were sorted by flow cytometry and processed according to 10x Genomics protocol for visium

Section series_overall_design, offset 1900
cohort.treatment_exposure_documented True
mice were treated with 2%DSS via the drinking water followed by 7 days of recovery

Section series_overall_design, offset 1250

Data_Assets

FieldValueEvidence
data_assets.file_manifest True from source
Supplementary files enumerated in family SOFT (ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5726nnn/GSM5726156/suppl/GSM5726156_V19S23-095_C1_S7_filtered_feature_bc_matrix.h5, ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5726nnn/GSM5726156/suppl/GSM5726156_V19S23-095_C1_S7_raw_feature_bc_matrix.h5, ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5726nnn/GSM5726156/suppl/GSM5726156_V19S23-095_C1_S7_tissue_hire

Section GEO family SOFT, offset —
data_assets.histology_images True from source
GEO deposit evidence: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5726nnn/GSM5726156/suppl/GSM5726156_V19S23-095_C1_S7_tissue_hires_image.png.gz

Section GEO family SOFT, offset —
data_assets.open_access True
Public on Dec 10 2021

Section series_status, offset —
data_assets.processed_matrix True from source
GEO deposit evidence: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5726nnn/GSM5726156/suppl/GSM5726156_V19S23-095_C1_S7_filtered_feature_bc_matrix.h5

Section GEO family SOFT, offset —
data_assets.raw_counts True from source
GEO deposit evidence: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5726nnn/GSM5726156/suppl/GSM5726156_V19S23-095_C1_S7_raw_feature_bc_matrix.h5

Section GEO family SOFT, offset —
data_assets.spatial_coordinates True from source
GEO deposit evidence: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5726nnn/GSM5726156/suppl/GSM5726156_V19S23-095_C1_S7_tissue_positions_list.csv.gz

Section GEO family SOFT, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['Colon'] from source
GEO sample source names: Colon

Section GEO family SOFT, offset —
specimens.number_of_samples 2 computed
2 GSM records parsed from GEO family SOFT

Section GEO family SOFT, offset —
specimens.preservation_method frozen in OCT
Mouse colonic tissues (day0 and day14) were cryo-sectioned (10uM) and placed on the already barcoded spots

Section extract_protocol, offset —