GEO series

Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodeling [RNA-seq]

GSE280704 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/06/16 Platform GPL18573

At a glance

RNA-seq (gene expression) · human · 12 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: Homo sapiens (human)
Samples: 12 samples: 3 × rna.ta1.ctrl vs 3 × rna.ta1.dox vs 3 × rna.wt.ctrl vs 3 × rna.wt.doxGroups 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: Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodelingNucleic acids research · 2025

Summary (written by the submitters)

The mechanistic details by which pioneer transcription factors interact with partner transcription factors and chromatin modification/remodeling enzymes to activate enhancers remains an emerging area of study. Here, we utilize inducible expression of the pioneer factor GATA3 and study cofactor association and structural alterations in local chromatin.

Read the full summary ↓

ATAC-seq analysis and footprinting revealed co-occurrence of GATA3 with other transcription factors, including AP-1, in newly accessible chromatin. GATA3 and AP-1 co-localize at primed enhancers with p300 and BRG1 where nucleosome positioning is responsive to GATA3 location, not to AP-1. Genetic inhibition of AP-1 binding alters chromatin opening at some, but not most, GATA3-bound loci. Pharmacologic inhibition of SWI/SNF ATPase function results in loss of GATA3-dependent chromatin accessibility, binding, and alterations in local chromatin architecture. We conclude that GATA3-dependent gains in chromatin accessibility require chromatin remodeling and that accessibility at some loci is facilitated by a partner transcription factor, in this case AP-1.

Published in

Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodeling

Orlando KA, Grimm SA, Wade PA · Nucleic acids research 2025 · PMID 40479714 · doi:10.1093/nar/gkaf473

This dataset

Open GSE280704 in finder → Find more human 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 GSE280704_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 PRJNA1180068 and SRA study SRP542192. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40479714) ↗

Study design

3 × rna.ta1.ctrl vs 3 × rna.ta1.dox vs 3 × rna.wt.ctrl vs 3 × rna.wt.dox

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

GSM8604429 rna.ta1.ctrl.rep1 rna.ta1.ctrl
GSM8604430 rna.ta1.ctrl.rep2 rna.ta1.ctrl
GSM8604431 rna.ta1.ctrl.rep3 rna.ta1.ctrl
GSM8604432 rna.ta1.dox.rep1 rna.ta1.dox
GSM8604433 rna.ta1.dox.rep2 rna.ta1.dox
GSM8604434 rna.ta1.dox.rep3 rna.ta1.dox
GSM8604435 rna.wt.ctrl.rep1 rna.wt.ctrl
GSM8604436 rna.wt.ctrl.rep2 rna.wt.ctrl
GSM8604437 rna.wt.ctrl.rep3 rna.wt.ctrl
GSM8604438 rna.wt.dox.rep1 rna.wt.dox
GSM8604439 rna.wt.dox.rep2 rna.wt.dox
GSM8604440 rna.wt.dox.rep3 rna.wt.dox

Datasets on a similar topic

GSE171817 SUMOylation Regulates Super-Enhancers Through Transcription Factor TFAP2C Binding on Chromatin 30 samples shares transcription, enhancers, chromatin
GSE196619 Synthetic transcription factor overrides persistent repressive chromatin marks 120 samples shares transcription, chromatin
GSE296192 Hypoxic regulation of chromatin and gene transcription 98 samples shares transcription, chromatin
GSE302930 Epigenetic Atlas of Bladder Cancer Reveals Master Transcription Factors and Risk-Associated Regulatory Elements in Luminal and Basal-Squamous Molecular Subtypes 92 samples shares transcription, factors
GSE301298 Functional redundancy between UTY and UTX in regulating the localization of transcription factors involved in pluripotency 88 samples shares transcription, factors
GSE296190 Hypoxic regulation of chromatin and gene transcription [ChIP-seq] 84 samples shares transcription, chromatin
GSE275721 Lineage master regulator and cancer-selective partner transcription factors rewire 3D genome topology for tumor-specific gene control 72 samples shares transcription, factors
GSE293334 Allelic topological centering by transcription factors drives oncogenic multi-enhancer transcriptional regulation [ChIP-seq] 60 samples shares transcription, factors

Search all human RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.