Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation [MNase-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 18 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
- 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
- Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiationNature communications · 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 GSE268717_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 PRJNA1118314 and SRA study SRP510886. Searching any of these in the dataset finder brings you back here.
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.
- GSM8297436 mnase_d0_rep1 mnase_d0
- GSM8297437 mnase_d0_rep2 mnase_d0
- GSM8297438 mnase_d0_rep3 mnase_d0
- GSM8297439 mnase_d008_rep1 mnase_d008
- GSM8297440 mnase_d008_rep2 mnase_d008
- GSM8297441 mnase_d008_rep3 mnase_d008
- GSM8297442 mnase_d016_rep1 mnase_d016
- GSM8297443 mnase_d016_rep2 mnase_d016
- GSM8297444 mnase_d016_rep3 mnase_d016
- GSM8297445 mnase_d1_rep1 mnase_d1
- GSM8297446 mnase_d1_rep2 mnase_d1
- GSM8297447 mnase_d1_rep3 mnase_d1
- GSM8297448 mnase_d2_rep1 mnase_d2
- GSM8297449 mnase_d2_rep2 mnase_d2
- GSM8297450 mnase_d2_rep3 mnase_d2
- GSM8297451 mnase_d4_rep1 mnase_d4
- GSM8297452 mnase_d4_rep2 mnase_d4
- GSM8297453 mnase_d4_rep3 mnase_d4
- GSE283958 Cohesin recruitment to promoters and enhancers by general transcription factors and chromatin regulators 47 samples shares transcription, factors
- GSE326173 Nuclear receptor Nur77 resolves the inflammatory response of macrophages primarily by regulating expression of AP-1 transcription factors and their target genes [ChIP-seq] 42 samples shares transcription, factors
- GSE269913 The pioneer transcription factor PBX as a downstream target of MNX1 [ATAC] 10 samples shares transcription, pioneer
- GSE314917 FACT maintains nucleosomes around promoters and opposes to the spreading of chromatin factors, thereby playing a major role in chromatin architecture 115 samples shares nucleosome, factors
- GSE283382 N6-methyladenosine modulate second cell fate decision by enhancing mRNA stability of pivotal transcription factors during primitive endoderm development [TBLC_RNAseq] 98 samples shares transcription, factors
- GSE282280 DNA methylation-sensitive transcription factors and bivalency orchestrate transposon expression in the absence of DNA methylation. 93 samples shares transcription, factors
- GSE269910 The pioneer transcription factor PBX as a downstream target of MNX1 [ACT] 55 samples shares transcription, pioneer
- GSE281037 Large-scale transcriptomic analyses reveal downstream target genes of ZFY1 and ZFY2 transcription factors in male germ cells 48 samples shares transcription, factors
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.