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Base pair resolution chromosome conformation capture reveals mechanistic insights into the nature of chromatin structure [TT-Seq]

GSE281416 Mus musculus (mouse) RNA-seq (gene expression) 14 samples Submitted 2025/11/26 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 14 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
14 samples: 3 × mES-E14-NANOG-FKBP-DMSO vs 3 × mES-E14-NANOG-FKBP-dTAG vs 2 × mES-E14-MED1-FKBP-DMSO vs 2 × mES-E14-MED1-FKBP-dTAGGroups 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
Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactionsCell · 2025
Summary (written by the submitters)
Chromatin structure is a key determinant of gene expression in eukaryotes but it has not previously been possible to define the full structure of regulatory elements at the scale of the proteins determining gene expression. Here we generate multidimensional chromosome conformation capture (3C) maps at single base-pair resolution using Micro Capture-C (MCC).
Read the full summary ↓
This allows contacts between individual transcription factor binding sites within regulatory elements to be defined. Using degrons-we investigate the structural role of transcription factors and the Mediator complex. We show that the biophysical properties of nucleosomes and DNA can replicate the nanoscale chromatin structures observed with MCC using a detailed chemically specific, molecular dynamics approach. The ultra-high resolution 3C enable molecular dynamics approaches to be linked to larger scale nuclear architecture defined by super-resolution microscopy and allow us to propose a unified model to describe chromatin structure based on these orthogonal approaches.
Published in
Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions
Li H, Dalgleish JLT, Lister G et al. · Cell 2025 · PMID 41197626 · doi:10.1016/j.cell.2025.10.013
This dataset
Open GSE281416 in finder → Find more mouse RNA-seq 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 GSE281416_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1183827 and SRA study SRP544042. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41197626) ↗
Study design
3 × mES-E14-NANOG-FKBP-DMSO vs 3 × mES-E14-NANOG-FKBP-dTAG vs 2 × mES-E14-MED1-FKBP-DMSO vs 2 × mES-E14-MED1-FKBP-dTAG

Supports a between-group comparison across 10 samples.

How we read this: 4 replicated groups read from 14 sample titles; they account for 10 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
Datasets on a similar topic

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