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FOXO4-SP6 axis controls surface epithelium commitment by mediating epigenomic remodeling [RNA]

GSE280747 Homo sapiens (human) RNA-seq (gene expression) 20 samples Submitted 2025/05/22 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 20 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
20 samples: 10 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
FOXO4-SP6 axis controls surface epithelium commitment by mediating epigenomic remodelingStem cell reports · 2025
Summary (written by the submitters)
Proper development of surface epithelium (SE) is a requisite for the normal development and function of ectodermal appendages; however, the molecular mechanisms underlying SE commitment remain largely unexplored. Here, we developed a KRT8 reporter system and utilized it to identify FOXO4 and SP6 as novel, essential regulators governing SE commitment.
Read the full summary ↓
We found that the FOXO4-SP6 axis governs SE fate and its abrogation markedly impedes SE fate determination. Mechanistically, FOXO4 regulates SE initiation by shaping the SE chromatin accessibility landscape and regulating the deposition of H3K4me3. SP6, as a novel effector of FOXO4, activated SE-specific genes through modulating the H3K27ac deposition across their super enhancers. Our work highlights the regulatory function of the FOXO4-SP6 axis in SE development, contributing to an improved understanding of SE fate decisions and providing a research foundation for the therapeutic application of ectodermal dysplasia.
Published in
FOXO4-SP6 axis controls surface epithelium commitment by mediating epigenomic remodeling
Liu J, Huang H, An F et al. · Stem cell reports 2025 · PMID 40086444 · doi:10.1016/j.stemcr.2025.102445
This dataset
Open GSE280747 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 GSE280747_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 PRJNA1180459 and SRA study SRP542320. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40086444) ↗
Study design
10 conditions, mostly in duplicate
SE initiating cells, scramble_FOXO4, ×2 SE initiating cells, shFOXO4, ×2 SE matutating cells, scramble_FOXO4, ×2 SE matutating cells, shFOXO4, ×2 SE initiating cells, scramble_SP6, ×2 SE initiating cells, shSP6, ×2 SE matutating cells, scramble_SP6, ×2 SE matutating cells, shSP6, ×2 +2 more

Supports a between-group comparison across 20 samples.

How we read this: 10 replicated groups read from 20 sample titles; they account for 20 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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