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Mus musculus strain:C57BL/6J Raw sequence reads

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Dataset overview

Participants None
Samples 2
Reuse readiness 4.6/10 evidence-backed score

miR147 promotes mucosal integrity and healing in intestinal inflammation.

Czopik AK, Dabiri A, Tung CH, Vaughn V, Huang X, Wang J, Li H, Moreno NF, et al. · JCI insight · 2025

Abstract

The intestinal mucosal epithelium forms a barrier between luminal contents and the body. MicroRNAs (miRNAs) regulate mucosal homeostasis by controlling inflammatory responses and structural integrity. Here, we discovered a protective role for miR147 in intestinal inflammation using a miR147tdTomato reporter mouse. miR147 was enriched in the intestines, with the highest expression in the colonic epithelial cells at the luminal surface, with prominent expression in differentiated enterocytes. Mice with general or intestinal epithelial deletion of miR147 showed increased intestinal inflammation and diminished mucosal healing during colitis. RNA sequencing of miR147-deficient cells showed dysregulated immune signaling, with upregulated proinflammatory cytokine pathways and reduced type I interferon responses and revealed Ndufa4 as a likely miR147 target. Ndufa4, a mitochondrial protein regulating energy metabolism and inflammation, was elevated at the crypt base, inversely correlating with miR147. Mice lacking the miR147 binding site in Ndufa4's 3'-UTR phenocopied miR147-deficient mice during colitis. Spatial and single-cell transcriptomic analyses in murine and human colons showed mutually exclusive miR147 and Ndufa4 expression, consistent with a regulatory relationship in epithelial differentiation and metabolism. These findings underscore miR147's role in intestinal homeostasis and mucosal healing, suggesting it as a therapeutic target for inflammatory bowel disease.

doi:10.1172/jci.insight.190466 ↗ PMID 40956617 ↗ PMC12581662 ↗

Study facts

Organism
Mus musculus
Platform
Illumina Genome Analyzer II
Age group
—
Disease groups
—
Anatomical sites
—

Data availability

Specific data assets have not been resolved from the source yet — see the source repository below for the full file listing.

Strengths & limitations for reuse

Strengths

  • Raw reads are advertised
  • Sample counts are documented

Limitations

  • Not documented: feature/otu tables are advertised
  • Not documented: taxonomic tables are advertised
  • 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.paired_end True inferred
Sequencing was conducted on an Illumina NovaSeq 6000 (43 bp read 1, 50 bp read 2, 10 bp i7/i5 sample indexes).

Section Spatial transcriptomics, offset 20100
assay.platform Illumina Genome Analyzer II from source
ENA instrument_model=Illumina Genome Analyzer II

Section ENA study report, offset —

Cohort

FieldValueEvidence
cohort.disease_activity_metadata_available True
Colonic tissues from healthy (n981_healthy; 386,865 pseudo-cells) and DSS-treated (n2_DSS; 421,574 pseudo-cells; 3% DSS for 3 days) mice

Section Spatial transcriptomics, offset 19000
cohort.treatment_exposure_documented True
Colonic tissues from healthy (n981_healthy; 386,865 pseudo-cells) and DSS-treated (n2_DSS; 421,574 pseudo-cells; 3% DSS for 3 days) mice

Section Spatial transcriptomics, offset 19000

Data_Assets

FieldValueEvidence
data_assets.open_access True
Raw sequencing data for the spatial transcriptomics study are available at the NCBI Sequence Read Archive (SRA) under BioProject accession PRJNA1284556

Section Data availability, offset 24500
data_assets.qc_or_negative_controls_reported True
Data quality was assessed by standard metrics, including gene counts and mitochondrial content, with consistent filtering thresholds applied to both samples

Section Spatial transcriptomics, offset 19180
data_assets.raw_reads True
Raw sequencing data for the spatial transcriptomics study are available at the NCBI Sequence Read Archive (SRA) under BioProject accession PRJNA1284556

Section Data availability, offset 24500

Specimens

FieldValueEvidence
specimens.body_site colon
Colonic tissues from healthy (n981_healthy; 386,865 pseudo-cells) and DSS-treated (n2_DSS; 421,574 pseudo-cells; 3% DSS for 3 days) mice

Section Spatial transcriptomics, offset 19000
specimens.inflamed_status_available True
Colonic tissues from healthy (n981_healthy; 386,865 pseudo-cells) and DSS-treated (n2_DSS; 421,574 pseudo-cells; 3% DSS for 3 days) mice

Section Spatial transcriptomics, offset 19000
specimens.number_of_samples 2 from source
ENA sample_count=2

Section ENA study report, offset —