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A Study of Allostery Within Liganded RARα:RXR Heterodimers at the Genome Scale [CUT&Run]

GSE290328 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 14 samples Submitted 2025/02/24 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 14 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
14 samples: 5 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.
Paper
Genome-wide analysis reveals ligand-dependent allostery in RARα:RXR-mediated transcriptional regulationCell reports · 2026
Summary (written by the submitters)
We provide evidence of coordination between heterodimeric nuclear hormone receptor ligands at the genome scale to reveal three unique transcriptional outcomes. First, when stimulated in pancreatic acinar cells, distinct doubly-liganded complexes of the retinoic acid receptor-α (RARα) and retinoid-X-receptor (RXR) bind divergent DNA hormone response elements (HRE).
Read the full summary ↓
Furthermore, the link between ligand pairs and HRE specificity is correlated with RNA transcript formation. Second, RXR ligands can function as either silent partners or as cooperative effectors on distinct HREs, also with correlated transcriptional outcomes. Third, the absence of unique binding sites on DNA by unliganded RARα:RXR suggests that productive HRE recognition and binding is an exclusive feature of the agonist-bound heterodimer. To achieve the above, DNA-bound heterodimers of RARα:RXR were isolated separately with an RARα-specific antibody, RARα-specific and RXR-specific agonists and the pan-ligand, 9-cis retinoic acid, using the CUT&RUN technique. At each liganded state, transcriptional activity was detected by mRNA sequencing.
Published in
Genome-wide analysis reveals ligand-dependent allostery in RARα:RXR-mediated transcriptional regulation
Hawkins CL, Blaner WS, Fernandez EJ · Cell reports 2026 · PMID 42018440 · doi:10.1016/j.celrep.2026.117280
This dataset
Open GSE290328 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 GSE290328_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 PRJNA1227499 and SRA study SRP565945. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42018440) ↗
Study design
5 conditions, mostly in triplicate
Mouse pancreatic acinar cell line, 9-cis reti… ×3 Mouse pancreatic acinar cell line, CD3254, CU… ×3 Mouse pancreatic acinar cell line, AM+CD, CUT… ×3 Mouse pancreatic acinar cell line, DMSO, CUT&… ×3 Mouse pancreatic acinar cell line, AM580, CUT… ×2

Supports a between-group comparison across 14 samples.

How we read this: 5 replicated groups read from 14 sample titles; they account for 14 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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