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single-cell chromatin accessibility profiling of mouse gonads during sex determination [scATAC-seq]

GSE218995 Mus musculus Genome binding/occupancy profiling by high throughput sequencing 4 samples Submitted 2024/04/28 Platform GPL13112
Summary
Gonad development includes sex determination and divergent maturation of the testes and ovaries. Recent advances in measuring gene expression in single cells are providing new insights into this complex process. However, the underlying epigenetic regulatory mechanisms remain unclear. Here, we profiled chromatin accessibility in mouse gonadal cells of both sexes from embryonic day 11.5 to 14.5 using single-cell assay for transposase accessible chromatin by sequencing (scATAC-seq). Our results showed that individual cell types can be inferred by the chromatin landscape, and that cells can be temporally ordered along developmental trajectories. Integrative analysis of transcriptomic and chromatin-accessibility maps identified multiple putative regulatory elements proximal to key gonadal genes Nr5a1, Sox9 and Wt1. We also uncover cell type-specific regulatory factors underlying cell type specification. Overall, our results provide a better understanding of the epigenetic landscape associated with the progressive restriction of cell fates in the gonad.
Published in
The single-cell chromatin landscape in gonadal cell lineage specification
Suen HC, Ou F, Miu KK et al. · BMC genomics 2024 · PMID 38741085 · doi:10.1186/s12864-024-10376-1
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Direct links to NCBI, no account and no request form: the whole study as GSE218995_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.

Also filed as BioProject PRJNA906529 and SRA study SRP410455. Searching any of these in the dataset finder brings you back here.

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