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Ldb1 establishes multi-enhancer networks to regulate gene expression [ChIP-Seq]

GSE254377 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 65 samples Submitted 2024/11/27 Platform GPL30172Platform GPL32159
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 65 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
65 samples: 25 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
LDB1 establishes multi-enhancer networks to regulate gene expressionMolecular cell · 2025
Summary (written by the submitters)
How enhancers specifically connect to gene promoters is still unclear. Besides the CTCF/cohesin machinery, only a small set of nuclear factors have been studied for a direct role in physically connecting regulatory elements. Here, we show via acute degradation experiments that LDB1 directly and broadly promotes enhancer-promoter loops.
Read the full summary ↓
Utilizing multiple degron systems, we demonstrate that most endogenous LDB1-mediated contacts can form in the absence of CTCF, cohesin and YY1. Furthermore, an engineered/forced, LDB1-driven chromatin loop can form in the absence of cohesin. Yet, in a fraction of cases cohesin driven extrusion may promote LDB1 anchored loops. Leveraging the dynamic reorganization of nuclear architecture during the transition from mitosis to G1 phase, we establish a relationship between LDB1-dependent interactions in the context of TAD organization and gene activation. Tri-C and Region Capture Micro-C reveal that LDB1 organizes multi-enhancer networks to activate transcription. This establishes LDB1 as direct driver of connectivity between regulatory elements.
Published in
LDB1 establishes multi-enhancer networks to regulate gene expression
Aboreden NG, Lam JC, Goel VY et al. · Molecular cell 2025 · PMID 39721581 · doi:10.1016/j.molcel.2024.11.037
This dataset
Open GSE254377 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 GSE254377_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 PRJNA1070277 and SRA study SRP486399. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39721581) ↗
Study design
25 conditions, mostly in duplicate
SMC3_AID_untreated_RAD21 ×3 SMC3_AID_auxin_RAD21 ×3 SMC3_AID_untreated_LDB1 ×3 SMC3_AID_auxin_LDB1 ×3 LDB1_AID_untreated_POL2 ×3 LDB1_AID_auxin_POL2 ×3 LDB1_prometaphase ×3 LDB1_anatelophase ×3 +21 more

Supports a between-group comparison across 61 samples.

How we read this: 25 replicated groups read from 65 sample titles; they account for 61 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

+ 25 more — browse all 65 samples with per-sample file links →

Datasets on a similar topic

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