Profiling of MCM2 and phosphorylated MCM2 in MLL3/4 double mutant and control ESCs [ChIP-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
- 12 samples: 12 samples, each with a distinct title — no replicated groupsGroups 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
- Protocol for genome-wide DNA replication timing analysis using click chemistry-based biotinylationSTAR protocols · 2025
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 GSE240512_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 PRJNA1003949 and SRA study SRP454323. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 12 sample titles: 12 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.
- GSM7699267 mESCs, CKO1-IgG
- GSM7699268 mESCs, CKO1-MCM2
- GSM7699269 mESCs, CKO1-pMCM2
- GSM7699270 mESCs, CKO2-IgG
- GSM7699271 mESCs, CKO2-MCM2
- GSM7699272 mESCs, CKO2-pMCM2
- GSM7699273 mESCs, DKO1-IgG
- GSM7699274 mESCs, DKO1-MCM2
- GSM7699275 mESCs, DKO1-pMCM2
- GSM7699276 mESCs, DKO2-IgG
- GSM7699277 mESCs, DKO2-MCM2
- GSM7699278 mESCs, DKO2-pMCM2
- GSE232845 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] 46 samples shares chip-seq, mutant
- GSE242901 An Intrinsically Disordered Region Controlling Condensation of a Circadian Clock Component and Rhythmic Transcription in the Liver [ChIP-seq] 45 samples shares chip-seq, control
- GSE276621 Reciprocal genetic screens identify epigenetics factors controlling epidermal cell activation. [ChIP-Seq] 36 samples shares chip-seq, control
- GSE266686 Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity [ChIP-Seq] 32 samples shares chip-seq, mutant
- GSE261412 Acute hormonal signaling-induced 3D chromatin loop reorganization controls adipocyte thermogenesis [ChIP-Seq mouse, H3K27ac, H3K4me3, H2AZ] 24 samples shares chip-seq, control
- GSE292609 ChIP-seq analysis of control and DOT1L HET cortical nuclei. 18 samples shares chip-seq, control
- GSE309163 P300/CBP inhibition with gilteritinib and venetoclax targets leukemia stem cells in epigenetic mutant AML [ChIP-Seq] 16 samples shares chip-seq, mutant
- GSE291041 Heritable fetal protection against MLL::ENL-driven leukemogenesis depends on MLL3 43 samples shares mll3
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.