Histone marks enable formation of immiscible phase-separated chromatin compartments
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 35 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Mus musculus (mouse)
- Samples
- 35 samples: 28 distinct titles, 4 of them repeatedGroups 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
- Histone marks enable formation of immiscible phase-separated chromatin compartmentsCell reports · 2025
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE241262_RAW.tar (it can run to tens of gigabytes).
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.
What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1007600 and SRA study SRP456090. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 35 sample titles: 28 distinct titles with little repetition. 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.
- GSM7720210 3T3_RNA_WT_batch1
- GSM7720211 3T3_RNA_C5_batch1
- GSM7720212 3T3_RNA_WT_batch2
- GSM7720213 3T3_RNA_C5_batch2
- GSM7720214 3T3_RNA_WT_batch3
- GSM7720215 3T3_RNA_C3_batch3
- GSM7720216 3T3_RNA_C4_batch3
- GSM7720217 3T3_RNA_WT_batch4
- GSM7720218 3T3_RNA_C3_batch4
- GSM7720219 3T3_RNA_C4_batch4
- GSM7720220 3T3_RNA_C5_batch4
- GSM7720221 3T3_H3K9me3_WT_rep1
- GSM7720222 3T3_H3K9me3_C3_rep1
- GSM7720223 3T3_H3K9me3_C4_rep1
- GSM7720224 3T3_H3K9me3_C5_rep1
- GSM7720225 3T3_H3K27me3_WT_rep1
- GSM7720226 3T3_H3K27me3_C3_rep1
- GSM7720227 3T3_H3K27me3_C4_rep1
- GSM7720228 3T3_H3K27me3_C5_rep1
- GSM7720229 3T3_H2AK119Ub_WT_rep1
- GSM7720230 3T3_H2AK119Ub_C3_rep1
- GSM7720231 3T3_H2AK119Ub_C4_rep1
- GSM7720232 3T3_H2AK119Ub_C5_rep1
- GSM7720233 3T3_H3K4me3_WT_rep1
- GSM7720234 3T3_H3K4me3_C3_rep1
- GSM7720235 3T3_H3K4me3_C4_rep1
- GSM7720236 3T3_H3K4me3_C5_rep1
- GSM7720237 3T3_CBX7_WT_rep1
- GSM7720238 3T3_CBX7_C3_rep1
- GSM7720239 3T3_CBX7_C4_rep1
- GSM7720240 3T3_CBX7_C5_rep1
- GSM7720241 3T3_HiC_WT_rep1
- GSM7720242 3T3_HiC_C3_rep1
- GSM7720243 3T3_HiC_C4_rep1
- GSM7720244 3T3_HiC_C5_rep1
- GSE225898 An RNA-dependent and phase-separated active subnuclear compartment safeguards repressive chromatin domains 31 samples shares phase-separated, chromatin
- GSE332710 Splice isoforms of the histone variants macroH2A1 differentially regulate hippocampal gene expression and memory formation 33 samples shares formation, histone
- GSE273309 Chromatin remodeler CHD4 establishes chromatin states required for ovarian reserve formation, maintenance, and germ cell survival 30 samples shares formation, chromatin
- GSE256073 De novo formation of cis-regulatory contacts in the absence of NIPBL-driven chromatin loop extrusion 30 samples shares formation, chromatin
- GSE243402 Multi-omics approaches for identification of novel dynamic regulators in transcriptional landscape and chromatin accessibility changes in liver regeneration and hepatocyte organoid formation 27 samples shares formation, chromatin
- GSE291987 Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization [RNA-Seq] 23 samples shares formation, chromatin
- GSE281416 Base pair resolution chromosome conformation capture reveals mechanistic insights into the nature of chromatin structure [TT-Seq] 14 samples shares formation, chromatin
- GSE281414 Base pair resolution chromosome conformation capture reveals mechanistic insights into the nature of chromatin structure [ATAC-Seq] 12 samples shares formation, chromatin
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.