GEO series

Comparative single-cell analysis of multiple models of retinitis pigmentosa reveals common pro-survival mechanisms activated in photoreceptors

GSE296646 Mus musculus (mouse) Single-cell RNA-seq 13 samples Submitted 2026/07/31 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 13 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 13 samples: 10 distinct titles, 3 of them repeatedGroups 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)

Retinitis pigmentosa (RP) is a group of inherited retinal diseases marked by the progressive degeneration of photoreceptors, ultimately leading to severe vision loss or blindness. The vast genetic heterogeneity of RP results in highly variable disease phenotypes, yet the identification of shared, mutation-independent mechanisms could provide a foundation for broadly applicable therapeutic strategies.

Read the full summary ↓

To explore such mechanisms, we generated scRNA-seq datasets across three key timepoints in two RP mouse models, rd10 and P347S, and integrated them with public datasets from rd1 and AdipoR1-KO models. Time-course differential expression and gene regulatory network analyses revealed a conserved transcriptional response to retinal degeneration across photoreceptor types and disease models. Transcription factors such as Cebpd, Stat3, and E2f6 emerged as central regulators, consistently upregulated and potentially mediating pro-survival mechanisms. IEGs like Junb, Fosb, and Egr1 were consistently activated, configuring an early response to stress associated to apoptotic responses. Furthermore, we identified epigenetic regulators such as Dnmt1 and Atf7 upregulated across models, pointing to a role for chromatin remodeling in retinal degeneration. These findings support the existence of a core stress-induced regulatory program in RP and highlight promising targets for the development of mutation-independent, disease-modifying therapies.

This dataset

Open GSE296646 in finder → Find more mouse 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 GSE296646_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1260435 and SRA study SRP583852. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

10 distinct titles, 3 of them repeated

Optic cup, P347S, P10, biol ×2 Optic cup, WT, P30, biol ×2 Optic cup, WT, P60, biol ×2

How we read this: Read from 13 sample titles: 10 distinct titles with little repetition. 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

GSM8974152 Optic cup, WT, P10, biol replicate 1
GSM8974153 Optic cup, rd10, P10, biol replicate 1
GSM8974154 Optic cup, P347S, P10, biol replicate 1
GSM8974155 Optic cup, P347S, P10, biol replicate 2
GSM8974156 Optic cup, WT, P18, biolreplicate 1
GSM8974157 Optic cup, rd10, P18, biol replicate 1
GSM8974158 Optic cup, WT, P30, biol replicate 1
GSM8974159 Optic cup, WT, P30, biol replicate 2
GSM8974160 Optic cup, rd10, P30, biol replicate 1
GSM8974161 Optic cup, P347S, P30, biol replicate 1
GSM8974162 Optic cup, WT, P60, biol replicate 1
GSM8974163 Optic cup, WT, P60, biol replicate 2
GSM8974164 Optic cup, P347S, P60, biol replicate 1

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