FOXO4-SP6 axis controls surface epithelium commitment by mediating epigenomic remodeling [ATAC]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 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
- Homo sapiens (human)
- Samples
- 12 samples: 6 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
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE280745_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1180452 and SRA study SRP542319. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 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.
- GSM8605295 hESC, ATAC, Rep1 hESC, ATAC,
- GSM8605296 hESC, ATAC, Rep2 hESC, ATAC,
- GSM8605297 SE initiating cell, ATAC, Rep1 SE initiating cell, ATA…
- GSM8605298 SE initiating cell, ATAC, Rep2 SE initiating cell, ATA…
- GSM8605299 SE initiating cell, scramble_F, ATAC, Rep1 SE initiating cell, scr…
- GSM8605300 SE initiating cell, scramble_F, ATAC, Rep2 SE initiating cell, scr…
- GSM8605301 SE initiating cell, shFOXO4, ATAC, Rep1 SE initiating cell, shF…
- GSM8605302 SE initiating cell, shFOXO4, ATAC, Rep2 SE initiating cell, shF…
- GSM8605303 SE initiating cell, scramble_S, ATAC, Rep1 SE initiating cell, scr…
- GSM8605304 SE initiating cell, scramble_S, ATAC, Rep2 SE initiating cell, scr…
- GSM8605305 SE initiating cell, shSP6, ATAC, Rep1 SE initiating cell, shS…
- GSM8605306 SE initiating cell, shSP6, ATAC, Rep2 SE initiating cell, shS…
- GSE271384 The APOE isoforms differentially shape the transcriptomic and epigenomic landscapes of human microglia in a xenotransplantation model of Alzheimer’s disease [ATAC-seq] 20 samples shares atac, epigenomic
- GSE256345 SMARCA4 controls state plasticity in small cell lung cancer through regulation of neuroendocrine transcription factors and REST splicing [ATAC-seq] 13 samples shares atac, controls
- GSE323981 MEF2C controls lysosomal and lipid clearance programs linked to Alzheimer’s disease risk in macrophages [ATAC-seq] 8 samples shares atac, controls
- GSE307363 3D epigenomic landscape of human retinal pigment epithelium [CUT&Tag] 40 samples shares epithelium, epigenomic
- GSE341236 3D epigenomic landscape of human retinal pigment epithelium 69 samples shares epithelium, epigenomic
- GSE235715 Multi-scaled transcriptomics of chronically inflamed nasal epithelium reveals immune-epithelial dynamics and tissue remodeling in nasal polyp formation 60 samples shares epithelium, remodeling
- GSE291386 Chromatin accessibility profiling of HSPC-derived erythroblast differentiation [ATAC-seq] 165 samples shares atac
- GSE289805 Histone H4 lysine 20 tri-methylation safeguards breast cancer lineage fidelity and unfolded protein response [ChIP-seq/ATAC-seq] 126 samples shares atac
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.