GEO series

Shielding Retinal Ganglion Cells: Suppression of the PAX6-JNK3 Axis Protects Against NMDA-Induced Excitotoxicity in a Glaucoma Model [RNA-seq]

GSE275656 Mus musculus (mouse) Single-cell RNA-seq 12 samples Submitted 2026/02/11 Platform GPL32159

At a glance

Single-cell RNA-seq · mouse · 12 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
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: Aberrant maintenance of developmental transcription factor PAX6 promotes neuronal cell death via JNK3 signalingCell death & disease · 2026

Summary (written by the submitters)

Retinal degenerative diseases frequently cause visual impairment due to a lack of regeneration systems and self-renewable cells. Glaucoma is characterized by the progressive degeneration of retinal ganglion cells (RGCs), yet the underlying mechanisms remain poorly understood. Here, our study investigated the role of the transcription factor PAX6 in RGC death during NMDA excitotoxicity, a model for glaucoma.

Read the full summary ↓

Using public single-cell RNA sequencing data, we found that PAX6 is consistently expressed in RGCs across both mouse and human retinas. Notably, we demonstrated that PAX6 phosphorylation was enhanced following NMDA exposure, and JNK3 was identified as a key kinase responsible for PAX6 phosphorylation. Epigenome-wide analysis revealed co-occupancy of PAX6 and JNK3 at key apoptotic gene promoters, with PAX6 acting as a recruitment factor for JNK3. Furthermore, suppressing PAX6 and JNK3 significantly protected against NMDA-induced RGC death, highlighting PAX6-JNK3 contribution to excitotoxicity-mediated apoptosis. Collectively, our findings elucidate a novel mechanism of RGC death in glaucoma, implicating the PAX6-JNK3 signaling axis as a critical mediator of retinal cell fate under excitotoxic conditions, suggesting potential therapeutic targets for preserving RGCs in glaucoma.

Published in

Aberrant maintenance of developmental transcription factor PAX6 promotes neuronal cell death via JNK3 signaling

Kim JY, An MJ, Kim J et al. · Cell death & disease 2026 · PMID 41611657 · doi:10.1038/s41419-026-08417-6

This dataset

Open GSE275656 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 GSE275656_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 PRJNA1152513 and SRA study SRP528625. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41611657) ↗

Study design

6 conditions, mostly in duplicate

Wild type, PBS, ×2 Wild type, NMDA, ×2 shPax6, PBS, ×2 shPax6, NMDA, ×2 JNK3-KO, PBS, ×2 JNK3-KO, NMDA, ×2

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.

Samples in this study

GSM8481975 Wild type, PBS, rep1 Wild type, PBS,
GSM8481976 Wild type, PBS, rep2 Wild type, PBS,
GSM8481977 Wild type, NMDA, rep1 Wild type, NMDA,
GSM8481978 Wild type, NMDA, rep2 Wild type, NMDA,
GSM8481979 shPax6, PBS, rep1 shPax6, PBS,
GSM8481980 shPax6, PBS, rep2 shPax6, PBS,
GSM8481981 shPax6, NMDA, rep1 shPax6, NMDA,
GSM8481982 shPax6, NMDA, rep2 shPax6, NMDA,
GSM8481983 JNK3-KO, PBS, rep1 JNK3-KO, PBS,
GSM8481984 JNK3-KO, PBS, rep2 JNK3-KO, PBS,
GSM8481985 JNK3-KO, NMDA, rep1 JNK3-KO, NMDA,
GSM8481986 JNK3-KO, NMDA, rep2 JNK3-KO, NMDA,

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