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FACT maintains nucleosomes around promoters and opposes to the spreading of chromatin factors, thereby playing a major role in chromatin architecture

GSE314917 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 115 samples Submitted 2026/03/30 Platform GPL34290
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 115 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
115 samples: 39 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.
Summary (written by the submitters)
Amounting evidence suggests nucleosome organization is key for higher levels of chromatin packaging. However, studying it in higher eukaryotes is challenging due to the difficulty to manipulate nucleosomes in vivo and reconstitute their large higher-order chromatin domains in vitro. Facilitates chromatin transcription (FACT) is a H2A/B histone chaperone that displaces and re-assembles histones, being important for processes such as transcription.
Read the full summary ↓
Recent studies report a minor role of FACT in chromatin architecture. Here, we studied chromatin organization upon rapid FACT degradation employing a multidimensional 3C technique with base-pair resolution (MCC-u) and genomic approaches. FACT loss leads to nucleosome depletion around active promoters, nano-scale domain collapse and emergence of larger nucleosome-free regions with increased protein binding. At a larger scale, we detect increased interactions between promoters across topologically associated domains. Thus, we demonstrate FACT plays a major role in chromatin organization and gain insights into the role of nucleosomes in genome architecture.
This dataset
Open GSE314917 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 GSE314917_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 PRJNA1393113 and SRA study SRP657709. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
39 conditions, mostly in triplicate
ATAC, SSRP1-FKBP-E14, DMSO, clone ×3 ATAC, SSRP1-FKBP-E14, dTAG-13 3h, clone ×3 RNA, SSRP1-FKBP-E14, DMSO, clone ×3 RNA, SSRP1-FKBP-E14, dTAG-13 6h, clone ×3 RNA, WT E14, DMSO, ×3 TT-seq, SSRP1-FKBP-E14, DMSO, clone ×3 TT-seq, SSRP1-FKBP-E14, dTAG-13 3h, clone ×3 ChIP, H2A, SSRP1-FKBP-E14, DMSO, clone ×3 +39 more

Supports a between-group comparison across 107 samples.

How we read this: 39 replicated groups read from 115 sample titles; they account for 107 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

+ 75 more — browse all 115 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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