GEO series

Differential chromatin accessibility, gene expression and mRNA splicing between developing cochlear inner and outer hair cells [ATAC-Seq]

GSE288376 Mus musculus Genome binding/occupancy profiling by high throughput sequencing 4 samples Submitted 2025/09/08 Platform GPL19057

Summary

The mammalian cochlea has two types of low abundance and highly specialized inner (IHC) and outer (OHC) mechanosensory hair cells. Their malfunction or death are common causes of congenital and acquired deafness. We separately collected developing IHCs and OHCs to identify their mRNAs and chromatin state. We examined their transcriptomes by RNA-seq to reveal differences in gene expression and alternative mRNA splicing. We examined their chromatin conformation by ATAC-seq to reveal open vs closed promoter and enhancer elements. Combining both approaches we find that developing IHCs and OHCs have differentially accessible promoters in differentially expressed genes, differ in both levels of gene expression, extent of mRNA splicing and transcription start sites, and utilize unique promoters and mRNA isoforms absent in other cell types. We provide a resource for the identification of promoter and mRNA isoforms of every gene expressed by IHCs or OHCs.

Published in

Differential Chromatin Accessibility, Gene Expression, and mRNA Splicing Between Developing Cochlear Inner and Outer Hair Cells

Foo CZ, Duggan A, Bartom ET et al. · Journal of the Association for Research in Otolaryngology : JARO 2025 · PMID 40911150 · doi:10.1007/s10162-025-01005-z

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Direct links to NCBI, no account and no request form: the whole study as GSE288376_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 4 samples. Raw sequencing reads are also available from ENA.

Whole study · RAW.tar ↓ Series matrix ↓ All supplementary files ↗ Raw reads on ENA ↗

Also filed as BioProject PRJNA1217049 and SRA study SRP560645. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40911150) ↗

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