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The LHX1 Gene Regulatory Network Represses Pluripotency and Modulates Multiple Signaling Pathways to Specify the Embryonic Head [Embryo_ATAC-seq]

GSE280128 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 12 samples Submitted 2025/10/01 Platform GPL17021
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
12 samples: 3 × ATAC-seq, E7.25, control, vs 3 × ATAC-seq, E7.25, Lhx1-epiCKO, vs 3 × ATAC-seq, E7.75, control, vs 3 × ATAC-seq, E7.75, Lhx1-epiCKO,Groups 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)
The development of the embryonic head in mice relies on the activity of the transcription factor LIM homeobox 1 (LHX1) in the anterior epiblast. In this study, we sought to unravel the molecular role of LHX1 during and immediately following gastrulation. We utilized CRISPR-Cas9 gene editing in embryo models as well as DamID-seq, RNA-seq, and ATAC-seq in mouse embryos.
Read the full summary ↓
These techniques enabled us to reveal the genome wide targets of LHX1 for the first time in gastrulation stage mouse embryos. Integrated analysis of the omics datasets uncovered that LHX1 is instrumental in decommissioning the pluripotency network and determining the anterior fate of the precursor tissue of the embryonic head. We found that LHX1 directly binds to and regulates genes involved in WNT and FGF signaling pathway inhibition. We also identified a downstream target of LHX1, Kctd1, expressed in the anterior tissue, which acts to modulate canonical WNT activity. These findings identified a component of the gene regulatory network anchored by LHX1 that governs the development of the embryonic head.
This dataset
Open GSE280128 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 GSE280128_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 PRJNA1176513 and SRA study SRP540359. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × ATAC-seq, E7.25, control, vs 3 × ATAC-seq, E7.25, Lhx1-epiCKO, vs 3 × ATAC-seq, E7.75, control, vs 3 × ATAC-seq, E7.75, Lhx1-epiCKO,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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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