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Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAs at the Mest-Copg2 locus [RNA-seq]

GSE312072 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2026/01/13 Platform GPL34290Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 18 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
18 samples: 6 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAsbioRxiv : the preprint server for biology · 2025
Summary (written by the submitters)
Genomic imprinting is an epigenetic phenomenon in which genes exhibit restricted or biased expression from one allele according to parental origin. Imprinted gene expression plays a crucial role in the development, including the brain. Higher-order chromatin structure has long been associated with gene regulation, particularly in the context of spatial enhancer-promoter interactions.
Read the full summary ↓
Given the characteristic parental allele-biased expression pattern of imprinted genes, a compelling question is whether the three-dimensional organization of parental genomes plays a role in imprinted gene regulation. Using a capture Hi-C approach, we identifiedparental allele-specific higher-order chromatin structures across multiple imprinted domains in the mouse brain. These allele-specific structural features largely stem from annotated imprinting control regions (ICRs), concomitant with allele-specific binding of CTCF. Detailed analysis suggests that transcriptional start sites (TSS) of active and inactive alleles of imprinted genes form distinct chromatin interactions, differing in degree and/or type. CRISPRi screeningrevealed a distal cis-regulatory element that modulates imprinted expression of the Mest-Copg2locus in neurons, and its regulatory mechanism is tightly associated with allele-specific chromatin interactions. Further investigation revealed that both a cis-acting long non-coding RNA and allele-specific enhancer-promoter architecture modulates Mest-Copg2 imprinted expression. Together, this study highlights the interplay between chromatin structure and regulatory landscapes that modulate allele-specific expression of imprinted genes.
Published in
Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAs
Bae B, Gu K, Loftus D et al. · bioRxiv : the preprint server for biology 2025 · PMID 41531811 · doi:10.64898/2025.12.02.691962
This dataset
Open GSE312072 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE312072_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1372149 and SRA study SRP650337. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41531811) ↗
Study design
6 conditions, mostly in triplicate
RNAseq - CN BxC ×3 RNAseq - CN CxB ×3 RNAseq - NPC neuron LV-Scrb ×3 RNAseq - NPC neuron LV-E105 ×3 mRNAseq - mESC treated with DMSO ×3 mRNAseq - mESC treated with DNMTi ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
Datasets on a similar topic

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