GEO series

3D epigenomic landscape of human retinal pigment epithelium [CUT&Tag]

GSE307363 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 40 samples Submitted 2026/07/26 Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 40 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: 40 samples: 16 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.

Summary (written by the submitters)

Retinal pigment epithelium (RPE) serves as a vital guardian of visual function, with its dysfunction driving pathogenesis in various retinal diseases, including age-related macular degeneration and inherited retinal disorders. While ongoing RPE cells transplantation clinical trials worldwide, the absence of standardized quality metrics for stem cell-derived RPE represents a significant gap.

Read the full summary ↓

In this study, we aim to systematically dissect epigenomic divergence among human primary RPE (hRPE), induced pluripotent stem cell-derived RPE (iPSC-RPE), and immortalized ARPE-19 cells through multi-omic analyses. Our study elucidated the distinct functional characteristics of the three types of RPE and their underlying epigenetic regulatory mechanisms, with a particular focus on the development and functional maturation of iPSC-RPE. We further revealed cell-type-specific regulatory blueprints: hRPE exhibits strong extracellular matrix (ECM) organization capacity through 3D-epigenomic (3D genome folding and epigenomic state) regulation, as exemplified by the enrichment of the RUNX1 motif, whereas iPSC-RPE retains signatures of RPE development and weak ECM function, marked by transcription factors such as Hand1, OTX2, PAX6, and ECM-associated genes. On the other hand, ARPE-19 exhibits greater cell proliferation ability and specifically regulated by transcription factors such as KLF5. Together, our data greatly advance our understanding of RPE biology and provide a robust foundation for optimizing iPSC-RPE differentiation protocols and developing innovative therapeutic strategies for retinal diseases.

This dataset

Open GSE307363 in finder → Find more human 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 GSE307363_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 PRJNA1316513 and SRA study SRP617613. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

16 conditions, mostly in duplicate

hRPE_H3K4me3, ×4 hRPE_H3K4me1, ×4 hRPE_H3K27ac, ×4 hRPE_H3K27me3, ×4 iPSC-RPE_H3K4me3, ×2 iPSC-RPE_H3K4me1, ×2 iPSC-RPE_H3K27ac, ×2 iPSC-RPE_H3K27me3, ×2 +8 more

Supports a between-group comparison across 40 samples.

How we read this: 16 replicated groups read from 40 sample titles; they account for 40 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

GSM9222813 hRPE_H3K4me3,rep1 hRPE_H3K4me3,
GSM9222814 hRPE_H3K4me3,rep2 hRPE_H3K4me3,
GSM9222815 hRPE_H3K4me1,rep1 hRPE_H3K4me1,
GSM9222816 hRPE_H3K4me1,rep2 hRPE_H3K4me1,
GSM9222817 hRPE_H3K27ac,rep1 hRPE_H3K27ac,
GSM9222818 hRPE_H3K27ac,rep2 hRPE_H3K27ac,
GSM9222819 hRPE_H3K27me3,rep1 hRPE_H3K27me3,
GSM9222820 hRPE_H3K27me3,rep2 hRPE_H3K27me3,
GSM9222821 iPSC-RPE_H3K4me3,rep1 iPSC-RPE_H3K4me3,
GSM9222822 iPSC-RPE_H3K4me3,rep2 iPSC-RPE_H3K4me3,
GSM9222823 iPSC-RPE_H3K4me1,rep1 iPSC-RPE_H3K4me1,
GSM9222824 iPSC-RPE_H3K4me1,rep2 iPSC-RPE_H3K4me1,
GSM9222825 iPSC-RPE_H3K27ac,rep1 iPSC-RPE_H3K27ac,
GSM9222826 iPSC-RPE_H3K27ac,rep2 iPSC-RPE_H3K27ac,
GSM9222827 iPSC-RPE_H3K27me3,rep1 iPSC-RPE_H3K27me3,
GSM9222828 iPSC-RPE_H3K27me3,rep2 iPSC-RPE_H3K27me3,
GSM9222829 ARPE-19_H3K4me3,rep1 ARPE-19_H3K4me3,
GSM9222830 ARPE-19_H3K4me3,rep2 ARPE-19_H3K4me3,
GSM9222831 ARPE-19_H3K4me1,rep1 ARPE-19_H3K4me1,
GSM9222832 ARPE-19_H3K4me1,rep2 ARPE-19_H3K4me1,
GSM9222833 ARPE-19_H3K27ac,rep1 ARPE-19_H3K27ac,
GSM9222834 ARPE-19_H3K27ac,rep2 ARPE-19_H3K27ac,
GSM9222835 ARPE-19_H3K27me3,rep1 ARPE-19_H3K27me3,
GSM9222836 ARPE-19_H3K27me3,rep2 ARPE-19_H3K27me3,
GSM9222837 iPSC_H3K4me3,rep1 iPSC_H3K4me3,
GSM9222838 iPSC_H3K4me3,rep2 iPSC_H3K4me3,
GSM9222839 iPSC_H3K4me1,rep1 iPSC_H3K4me1,
GSM9222840 iPSC_H3K4me1,rep2 iPSC_H3K4me1,
GSM9222841 iPSC_H3K27ac,rep1 iPSC_H3K27ac,
GSM9222842 iPSC_H3K27ac,rep2 iPSC_H3K27ac,
GSM9222843 iPSC_H3K27me3,rep1 iPSC_H3K27me3,
GSM9222844 iPSC_H3K27me3,rep2 iPSC_H3K27me3,
GSM9883412 hRPE_H3K4me3,rep3 hRPE_H3K4me3,
GSM9883413 hRPE_H3K4me3,rep4 hRPE_H3K4me3,
GSM9883414 hRPE_H3K4me1,rep3 hRPE_H3K4me1,
GSM9883415 hRPE_H3K4me1,rep4 hRPE_H3K4me1,
GSM9883416 hRPE_H3K27ac,rep3 hRPE_H3K27ac,
GSM9883417 hRPE_H3K27ac,rep4 hRPE_H3K27ac,
GSM9883418 hRPE_H3K27me3,rep3 hRPE_H3K27me3,
GSM9883419 hRPE_H3K27me3,rep4 hRPE_H3K27me3,

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