Chromatin activity of IκBα mediates the exit from naïve pluripotency (ChIP-seq Histone marks)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 38 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
- 38 samples: 10 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
- Chromatin activity of IκBα mediates the exit from naïve pluripotencyeLife · 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 GSE239564_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 PRJNA999704 and SRA study SRP452035. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 30 samples.
How we read this: 10 replicated groups read from 38 sample titles; they account for 30 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.
- GSM7667302 H3K9me3_mESCs_WT_rep1 H3K9me3_mESCs_WT
- GSM7667303 H3K9me3_mESCs_WT_rep2 H3K9me3_mESCs_WT
- GSM7667304 H3K9me3_mESCs_WT_rep3 H3K9me3_mESCs_WT
- GSM7667305 H3K9me3_mESCs_KO_rep1 H3K9me3_mESCs_KO
- GSM7667306 H3K9me3_mESCs_KO_rep2 H3K9me3_mESCs_KO
- GSM7667307 H3K9me3_mESCs_KO_rep3 H3K9me3_mESCs_KO
- GSM7667308 H3K9me3_mESCs_WT_input
- GSM7667309 H3K9me3_mESCs_KO_input
- GSM7667310 H3K27me3_mESCs_WT_rep1 H3K27me3_mESCs_WT
- GSM7667311 H3K27me3_mESCs_WT_rep2 H3K27me3_mESCs_WT
- GSM7667312 H3K27me3_mESCs_WT_rep3 H3K27me3_mESCs_WT
- GSM7667313 H3K27me3_mESCs_KO_rep1 H3K27me3_mESCs_KO
- GSM7667314 H3K27me3_mESCs_KO_rep2 H3K27me3_mESCs_KO
- GSM7667315 H3K27me3_mESCs_KO_rep3 H3K27me3_mESCs_KO
- GSM7667316 H3K27me3_mESCs_WT_input
- GSM7667317 H3K27me3_mESCs_KO_input
- GSM7667318 H3K4me3_mESCs_WT_rep1 H3K4me3_mESCs_WT
- GSM7667319 H3K4me3_mESCs_WT_rep2 H3K4me3_mESCs_WT
- GSM7667320 H3K4me3_mESCs_WT_rep3 H3K4me3_mESCs_WT
- GSM7667321 H3K4me3_mESCs_KO_rep1 H3K4me3_mESCs_KO
- GSM7667322 H3K4me3_mESCs_KO_rep2 H3K4me3_mESCs_KO
- GSM7667323 H3K4me3_mESCs_KO_rep3 H3K4me3_mESCs_KO
- GSM7667324 H3K4me3_mESCs_WT_input
- GSM7667325 H3K4me3_mESCs_KO_input
- GSM8238383 H3K27ac_mESCs_WT_rep1 H3K27ac_mESCs_WT
- GSM8238384 H3K27ac_mESCs_WT_rep2 H3K27ac_mESCs_WT
- GSM8238385 H3K27ac_mESCs_WT_rep3 H3K27ac_mESCs_WT
- GSM8238386 H3K27ac_mESCs_KO_rep1 H3K27ac_mESCs_KO
- GSM8238387 H3K27ac_mESCs_KO_rep2 H3K27ac_mESCs_KO
- GSM8238388 H3K27ac_mESCs_KO_rep3 H3K27ac_mESCs_KO
- GSM8238389 H3K4me1_mESCs_WT_rep1 H3K4me1_mESCs_WT
- GSM8238390 H3K4me1_mESCs_WT_rep2 H3K4me1_mESCs_WT
- GSM8238391 H3K4me1_mESCs_WT_rep3 H3K4me1_mESCs_WT
- GSM8238392 H3K4me1_mESCs_KO_rep1 H3K4me1_mESCs_KO
- GSM8238393 H3K4me1_mESCs_KO_rep2 H3K4me1_mESCs_KO
- GSM8238394 H3K4me1_mESCs_KO_rep3 H3K4me1_mESCs_KO
- GSM8238395 H3K4me1_H3K27ac_mESCs_WT_input
- GSM8238396 H3K4me1_H3K27ac_mESCs_KO_input
- GSE241262 Histone marks enable formation of immiscible phase-separated chromatin compartments 35 samples shares chromatin, histone, marks
- GSE272524 Chromatin-dependent motif syntax defines differentiation trajectories [ChIP-seq] 76 samples shares chromatin, chip-seq
- GSE294085 SIRT6 Overexpression Counteracts Chromatin Aging [ChIP-Seq] 74 samples shares chromatin, chip-seq
- GSE295340 Polycomb Chromatin Topology Enables Long-Range Enhancer Recruitment during Craniofacial Development [ChIP-seq] 42 samples shares chromatin, chip-seq
- GSE266022 Nrf2-mediated chromatin activation of hyperosmotic response genes attenuates heat-induced renal injury [ChIP-seq] 24 samples shares chromatin, chip-seq
- GSE306869 The RNA binding protein LIN28A mediates chromatin dynamics during neuronal differentiation 24 samples shares chromatin, mediates
- GSE292285 Depletion of lamin-associated polypeptide 2 alpha leads to chromatin reorganization and redistribution of A-type lamins to open genomic regions [ChIP-seq] 22 samples shares chromatin, chip-seq
- GSE237916 Regulation of T helper cell differentiation by the interplay between histone modification and chromatin interaction 197 samples shares chromatin, histone
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.