GEO series

Matched single-cell chromatin, transcriptome, and surface marker profiling captures in vivo epigenomic reprogramming during basal-to-luminal transition in the mammary gland [transplantations_OneCell_multiome]

GSE333887 Mus musculus Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing 14 samples Submitted 2026/07/03 Platform GPL16417Platform GPL24247

Summary

Single-cell multi-omics methods enable simultaneous mapping of chromatin states and transcriptomes, offering deep insights into gene regulation. Yet, the full potential of these approaches remains untapped for rare cell populations, as most methods require thousands of cells and are limited in their ability to capture multiple molecular layers comprehensively within the same cell. Here, we introduce OneCell CUT&Tag a user-friendly method that provides matched high-resolution epigenome, full-transcriptome, and surface marker quantification from every cell, with input as low as one cell. Using this approach, we uncovered epigenomic priming of basal cells in the mammary gland and captured the dynamics of basal-to-luminal transdifferentiation. We identified a transitional cell population with intermediate epigenomic profiles—absent in reference populations—and demonstrated a continuous epigenomic progression from basal to luminal states, while transcriptomes exhibited a binary switch. Adaptable to diverse samples and tissues, this method also revealed the role of H3K27me3 in shaping zygotic expression programs. By matching multiple layers of molecular information at single-cell resolution, OneCell CUT&Tag dissects the complementary roles of each omics layer in shaping cellular identity and function, opening new avenues to study rare and complex biological systems.

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Direct links to NCBI, no account and no request form: the whole study as GSE333887_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 14 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 PRJNA1473161 and SRA study SRP705707. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

13 × transplantations_chromatin_p

Supports a between-group comparison across 13 samples.

1 replicated groups read from 14 sample titles; they account for 13 of them. Check it against the sample list below before relying on it.

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