Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation [ChIP-Seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 96 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
- 96 samples: 45 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.
- 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 GSE269897_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 PRJNA1124086 and SRA study SRP514011. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 90 samples.
How we read this: 45 replicated groups read from 96 sample titles; they account for 90 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.
- GSM8329738 esrrb_d0_rep1 esrrb_d0
- GSM8329739 esrrb_d0_rep2 esrrb_d0
- GSM8329740 esrrb_d008_rep1 esrrb_d008
- GSM8329741 esrrb_d008_rep2 esrrb_d008
- GSM8329742 esrrb_d016_rep1 esrrb_d016
- GSM8329743 esrrb_d016_rep2 esrrb_d016
- GSM8329744 esrrb_d1_rep1 esrrb_d1
- GSM8329745 esrrb_d1_rep2 esrrb_d1
- GSM8329746 esrrb_d2_rep1 esrrb_d2
- GSM8329747 esrrb_d2_rep2 esrrb_d2
- GSM8329748 esrrb_d4_rep1 esrrb_d4
- GSM8329749 esrrb_d4_rep2 esrrb_d4
- GSM8329750 gata6_d0
- GSM8329751 gata6_d008_rep1 gata6_d008
- GSM8329752 gata6_d008_rep2 gata6_d008
- GSM8329753 gata6_d016_rep1 gata6_d016
- GSM8329754 gata6_d016_rep3 gata6_d016
- GSM8329755 gata6_d1_rep1 gata6_d1
- GSM8329756 gata6_d1_rep2 gata6_d1
- GSM8329757 gata6_d2_rep1 gata6_d2
- GSM8329758 gata6_d2_rep2 gata6_d2
- GSM8329759 gata6_d4_rep1_2
- GSM8329760 gata6_d4_rep1 gata6_d4
- GSM8329761 gata6_d4_rep2 gata6_d4
- GSM8329762 gata6_xen_rep1 gata6_xen
- GSM8329763 gata6_xen_rep2 gata6_xen
- GSM8329764 input_d0_rep1 input_d0
- GSM8329765 input_d0_rep2 input_d0
- GSM8329766 input_d008_rep1 input_d008
- GSM8329767 input_d008_rep2 input_d008
- GSM8329768 input_d016_rep1 input_d016
- GSM8329769 input_d016_rep2 input_d016
- GSM8329770 input_d1_rep1 input_d1
- GSM8329771 input_d1_rep2 input_d1
- GSM8329772 input_d2_rep1 input_d2
- GSM8329773 input_d2_rep2 input_d2
- GSM8329774 input_d4_rep1 input_d4
- GSM8329775 input_d4_rep2 input_d4
- GSM8329776 input_xen_rep1 input_xen
- GSM8329777 input_xen_rep2_2
+ 56 more — browse all 96 samples with per-sample file links →
- 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, chip-seq, factors
- GSE283958 Cohesin recruitment to promoters and enhancers by general transcription factors and chromatin regulators 47 samples shares transcription, factors
- GSE324864 HP1B and H3K9me3 Regulate Olfactory Receptor Choice and 2 Transcriptional Identity [ChIP-seq] 28 samples shares transcription, chip-seq
- GSE339012 Mega-Enhancers Compartmentalize Transcriptionally Active Long Genes in the Brain [ChIP-Seq] 22 samples shares transcription, chip-seq
- GSE281685 Transcription factor occupancy is affected by genetic variation in the white adipose tissue of C57BL6/j and 129S1/SvImJ mice [ChIP-seq] 16 samples shares transcription, chip-seq
- GSE305064 FOXP3 Expression Depends on Cell-Type Specific Cis-Regulatory Element and Transcription Factor Circuitry [mouse_Tconv_ChIP-seq] 15 samples shares transcription, chip-seq
- GSE315062 Smad4-p65 interactions drive BMP-mediated protection against inflammatory cell death [ChIP-Seq] 10 samples shares interactions, chip-seq
- GSE269913 The pioneer transcription factor PBX as a downstream target of MNX1 [ATAC] 10 samples shares transcription, pioneer
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.