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Single-cell RNA-Seq analysis of colonic mesenchyme lacking tumor necrosis factor receptor 1

GSE180346 Mus musculus Expression profiling by high throughput sequencing 6 samples Submitted 2025/07/01 Platform GPL19057
Summary
Our study reports a role for tumor necrosis factor receptor 1 (TNFR1) in maintaining colonic mesenchymal cell diversity. Through scRNA-seq profiling, we show that a TNFR1-deficient mesenchyme has a reduced transcriptional diversity of mesenchymal cell populations, with a near complete loss of a cluster enriched in TNF, IFN, and cytokine signaling genes, which include MMP9, CD200, TNFRSF9, and TRAF1. We show that the transcriptional clustering of mesenchymal cells is consistently distinct and unique to the TNFR1-/- genotype. TNFR1-/- mesenchymal cells cluster as a single population, compared to control mesenchymal cells that cluster into 3 sub-populations. Through in vivo immunostaining in control and TNFR1-/- mice we show that the TNF signaling cluster localizes to the sub-epithelial niche and therefore may play an important role in the crosstalk between epithelial stem cells and mesenchyme-driven immune signaling in health and disease.
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Direct links to NCBI, no account and no request form: the whole study as GSE180346_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 6 samples. Raw sequencing reads are also available from ENA.

Also filed as BioProject PRJNA747926 and SRA study SRP328903. Searching any of these in the dataset finder brings you back here.

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