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Effect of conditional triple-knockout of Jmjd2a/Kdm4a, Jmjd2b/Kdm4b and Jmjd2c/Kdm4c or overexpression of KDM4C/JMJD2C mutants with different phase separation ability on gene expression in mouse embryonic stem cells. [ChIP-Seq]

GSE232845 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 46 samples Submitted 2025/09/29 Platform GPL17021Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 46 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
46 samples: 20 conditions, mostly in duplicateGroups 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.
Summary (written by the submitters)
To investigate the functions of JMJD2/KDM4 family in mouse embryonic stem cells (mESCs), we treat the the conditional triple-knockout mESCs of Jmjd2a/Kdm4a, Jmjd2b/Kdm4b and Jmjd2c/Kdm4c with 4-hydroxytamoxifen (4-OHT) for 72h. Further, to investigate whether JMJD2/KDM4 phase separation affects chromatin binding of YY1, we generated IDR-truncated JMJD2C/KDM4C (Mut) to disrupt its phase separation ability, and rescued it by by fusing two IDRs in other species (hIDR1 and hIDR2).
Read the full summary ↓
We overexpressed those phase separation mutants in the aboved mESCs separately and TKO endogenous Jmjd2 by adding 4-OHT 72h.
This dataset
Open GSE232845 in finder → Find more mouse ChIP / ATAC / CUT&Tag 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 GSE232845_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA974061 and SRA study SRP438475. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
20 conditions, mostly in duplicate
ChIPseq_mESC_Ctrl_H3K27ac ×2 ChIPseq_mESC_Ctrl_H3K27ac_Input ×2 ChIPseq_mESC_JMJD2_TKO_H3K27ac ×2 ChIPseq_mESC_JMJD2_TKO_H3K27ac_Input ×2 ChIPseq_mESC_Ctrl_YY1 ×2 ChIPseq_mESC_Ctrl_YY1_Input ×2 ChIPseq_mESC_JMJD2_TKO_YY1 ×2 ChIPseq_mESC_JMJD2_TKO_YY1_Input ×2 +18 more

Supports a between-group comparison across 40 samples.

How we read this: 20 replicated groups read from 46 sample titles; they account for 40 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

+ 6 more — browse all 46 samples with per-sample file links →

Datasets on a similar topic

Search all mouse ChIP / ATAC / CUT&Tag datasets in GEO →

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