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Chemical reprogramming of fibroblasts into functional retinal pigment epithelium cells (cut&tag)

GSE287785 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 40 samples Submitted 2025/10/29 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 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
Mus musculus (mouse)
Samples
40 samples: 15 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
Chemical reprogramming of fibroblasts into retinal pigment epithelium cells for vision restorationNature communications · 2025
Summary (written by the submitters)
Restoring retinal pigment epithelium (RPE) cells is crucial for treating retinal degenerative (RD) diseases, with chemical reprogramming offering a transformative, scalable solution. However, identifying key compounds for generating functional RPE cells remains challenging. Here, we present a two-step chemical reprogramming strategy to convert fibroblasts into functional RPE (ciRPE) cells.
Read the full summary ↓
Leveraging the Single-Cell Reprogramming Compound Finder (scRCF), which integrates transcriptomics-guided predictions with advanced screening, we identified compound cocktails that precisely and efficiently reprogram fibroblasts through an intermediate state into ciRPE cells. These ciRPE cells closely mimic the structure and function of native RPE cells, and upon transplantation into RD rats, they seamlessly integrate into host tissue, protect photoreceptors, and restore visual function. Omics and mechanistic analyses revealed that the identified compounds synergistically activate core transcription factors, including Ascl1 and Olig2, orchestrating the reprogramming process. This work provides a scalable platform for RPE cell generation, advancing cell replacement therapies for RD diseases.
Published in
Chemical reprogramming of fibroblasts into retinal pigment epithelium cells for vision restoration
Li S, Liu H, Pan SH et al. · Nature communications 2025 · PMID 41366246 · doi:10.1038/s41467-025-67104-w
This dataset
Open GSE287785 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 GSE287785_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 PRJNA1214699 and SRA study SRP559372. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41366246) ↗
Study design
15 conditions, mostly in triplicate
H3K27ac_MEF ×3 H3K27ac_D7 ×3 H3K27ac_D18 ×3 H3K27ac_D32 ×3 H3K27ac_P_PRE ×3 H3K4me3_MEF ×3 H3K4me3_D7 ×3 H3K4me3_D18 ×3 +7 more

Supports a between-group comparison across 40 samples.

How we read this: 15 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
Datasets on a similar topic

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