GEO series
Stable maintenance of MERVL-positive embryonic stem cells reveals sustained transcriptional programs and enhancer remodeling
GSE268172
Mus musculus
Genome binding/occupancy profiling by high throughput sequencing
45 samples
Submitted 2026/05/12
Platform GPL21273
Summary
Mouse embryonic stem cells (ESCs) occasionally transit into a rare two-cell-like (2C) state characterized by transient activation of endogenous retroviruses such as MERVL and expression of 2C-specific genes including the Zscan4 cluster. These 2C-like cells (2CLCs) resemble early blastomeres and display expanded developmental potential, but their unstable and sporadic nature has hindered mechanistic studies. Here, we demonstrate the transiently stable maintenance of MERVL-positive ESCs that exhibit persistent MERVL expression and activation of 2C-associated genes. Live-cell imaging revealed uniform and sustained MERVL activity in these MERVL-positive ESCs, contrasting with the heterogeneous and transient expression observed in conventional ESCs. Transcriptome profiling demonstrated robust induction of 2C-specific regulatory networks, and embryoid body differentiation combined with machine learning uncovered increased lineage variability and altered developmental trajectories. Single-cell RNA sequencing revealed clear separation of control ESCs from MERVL-positive populations and redistribution across distinct transcriptional states, with Red and Mosaic lines showing graded shifts within a shared transcriptional manifold. Epigenomic profiling further revealed distinct chromatin states, specialized super-enhancer landscapes, and active enhancer marking at MERVL loci. Together, these findings demonstrate that stable maintenance of MERVL-positive ESCs is achievable in vitro, providing a powerful model to dissect ERV-driven transcriptional regulation, epigenomic remodeling, and 2C-like transcriptional and epigenetic programs.
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE268172_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 45 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1114868 and SRA study SRP509310. Searching any of these in the dataset finder brings you back here.
Study design
18 conditions, mostly in duplicate
1-5 red, ZHBTc4-2c-tcTomato-HisD, H3K4me3 ChI… ×2
1-5 red, ZHBTc4-2c-tcTomato-HisD, H3K27ac ChI… ×2
1-9 red, ZHBTc4-2c-tcTomato-HisD, H3K4me3 ChI… ×2
1-9 red, ZHBTc4-2c-tcTomato-HisD, H3K27ac ChI… ×2
2-10 red, ZHBTc4-2c-tcTomato-HisD, H3K4me3 Ch… ×2
2-10 red, ZHBTc4-2c-tcTomato-HisD, H3K27ac Ch… ×2
2-1 mosaic, ZHBTc4-2c-tcTomato-HisD, H3K4me3 … ×2
2-1 mosaic, ZHBTc4-2c-tcTomato-HisD, H3K27ac … ×2
+14 more
Supports a between-group comparison across 36 samples.
18 replicated groups read from the first 40 of 45 sample titles; they account for 36 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM8287187 1-5 red, ZHBTc4-2c-tcTomato-HisD, H3K4me3 ChIP, rep1
- GSM8287188 1-5 red, ZHBTc4-2c-tcTomato-HisD, H3K4me3 ChIP, rep2
- GSM8287189 1-5 red, ZHBTc4-2c-tcTomato-HisD, H3K27ac ChIP, rep1
- GSM8287190 1-5 red, ZHBTc4-2c-tcTomato-HisD, H3K27ac ChIP, rep2
- GSM8287191 1-9 red, ZHBTc4-2c-tcTomato-HisD, H3K4me3 ChIP, rep1
- GSM8287192 1-9 red, ZHBTc4-2c-tcTomato-HisD, H3K4me3 ChIP, rep2
- GSM8287193 1-9 red, ZHBTc4-2c-tcTomato-HisD, H3K27ac ChIP, rep1
- GSM8287194 1-9 red, ZHBTc4-2c-tcTomato-HisD, H3K27ac ChIP, rep2
- GSM8287195 2-10 red, ZHBTc4-2c-tcTomato-HisD, H3K4me3 ChIP, rep1
- GSM8287196 2-10 red, ZHBTc4-2c-tcTomato-HisD, H3K4me3 ChIP, rep2
- GSM8287197 2-10 red, ZHBTc4-2c-tcTomato-HisD, H3K27ac ChIP, rep1
- GSM8287198 2-10 red, ZHBTc4-2c-tcTomato-HisD, H3K27ac ChIP, rep2
- GSM8287199 2-1 mosaic, ZHBTc4-2c-tcTomato-HisD, H3K4me3 ChIP, rep1
- GSM8287200 2-1 mosaic, ZHBTc4-2c-tcTomato-HisD, H3K4me3 ChIP, rep2
- GSM8287201 2-1 mosaic, ZHBTc4-2c-tcTomato-HisD, H3K27ac ChIP, rep1
- GSM8287202 2-1 mosaic, ZHBTc4-2c-tcTomato-HisD, H3K27ac ChIP, rep2
- GSM8287203 3-1 mosaic, ZHBTc4-2c-tcTomato-HisD, H3K4me3 ChIP, rep1
- GSM8287204 3-1 mosaic, ZHBTc4-2c-tcTomato-HisD, H3K4me3 ChIP, rep2
- GSM8287205 3-1 mosaic, ZHBTc4-2c-tcTomato-HisD, H3K27ac ChIP, rep1
- GSM8287206 3-1 mosaic, ZHBTc4-2c-tcTomato-HisD, H3K27ac ChIP, rep2
- GSM8287207 3-2 mosaic, ZHBTc4-2c-tcTomato-HisD, H3K4me3 ChIP, rep1
- GSM8287208 3-2 mosaic, ZHBTc4-2c-tcTomato-HisD, H3K4me3 ChIP, rep2
- GSM8287209 3-2 mosaic, ZHBTc4-2c-tcTomato-HisD, H3K27ac ChIP, rep1
- GSM8287210 3-2 mosaic, ZHBTc4-2c-tcTomato-HisD, H3K27ac ChIP, rep2
- GSM8287211 ZHBTc4, noDox, H3K4me3-ChIP, rep1
- GSM8287212 ZHBTc4, noDox, H3K4me3-ChIP, rep2
- GSM8287213 ZHBTc4, noDox, H3K27ac-ChIP, rep1
- GSM8287214 ZHBTc4, noDox, H3K27ac-ChIP, rep2
- GSM8287215 ZHBTc4, LIF, Dox, 48h, H3K4me3-ChIP, rep1
- GSM8287216 ZHBTc4, LIF, Dox, 48h, H3K4me3-ChIP, rep2
- GSM8287217 ZHBTc4, LIF, Dox, 48h, H3K27ac-ChIP, rep1
- GSM8287218 ZHBTc4, LIF, Dox, 48h, H3K27ac-ChIP, rep2
- GSM8287219 ZHBTc4, noLIF, Dox, 48h, H3K4me3-ChIP, rep1
- GSM8287220 ZHBTc4, noLIF, Dox, 48h, H3K4me3-ChIP, rep2
- GSM8287221 ZHBTc4, noLIF, Dox, 48h, H3K27ac-ChIP, rep1
- GSM8287222 ZHBTc4, noLIF, Dox, 48h, H3K27ac-ChIP, rep2
- GSM8287223 1-5 red, ZHBTc4-2c-tcTomato-HisD, Input
- GSM8287224 1-9 red, ZHBTc4-2c-tcTomato-HisD, Input
- GSM8287225 2-10 red, ZHBTc4-2c-tcTomato-HisD, Input
- GSM8287226 2-1 mosaic, ZHBTc4-2c-tcTomato-HisD, Input
+ 5 more — browse all 45 samples with per-sample file links →
Similar datasets
- GSE293129 Enhancer rewiring orchestrates inflammation and loss of cell identity during muscle stem cell aging [CUT&RUN] 36 samples
- GSE283906 RXR-Mediated Remodeling of Transcriptional and Chromatin Landscapes in APP Mouse Brain: Insights from Integrated Single-Cell RNA and ATAC Profiling 10 samples
- GSE303384 Mechanism of maintenance and establishment of repression by the Mtg16 tumor suppressor [CUT&RUN, ChIP-Seq] 92 samples
- GSE289108 Neurons undergo IFNγ-driven persistent epigenetic shifts and synaptic remodeling in the inflamed brain [ChIP-Seq] 57 samples
- GSE295340 Polycomb Chromatin Topology Enables Long-Range Enhancer Recruitment during Craniofacial Development [ChIP-seq] 42 samples
- GSE325776 Evolutionary transfer learning enables organism-wide inference of mammalian enhancer landscapes 36 samples
- GSE267882 Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [ChIP-Seq] 34 samples
- GSE324864 HP1B and H3K9me3 Regulate Olfactory Receptor Choice and 2 Transcriptional Identity [ChIP-seq] 28 samples
Share this dataset
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.