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Transcriptional profiles of mouse retinal ganglion cells after optic nerve crush [RGC_injury_2019-9205_He]

GSE233822 Mus musculus (mouse) RNA-seq (gene expression) 30 samples Submitted 2025/05/16 Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 30 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
30 samples: 10 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
Repeat-element RNAs integrate a neuronal growth circuitCell · 2025
Summary (written by the submitters)
The removal of the Structure Specific Recognition Protein 1 (Ssrp1) gene from retinal ganglion cells has been shown to improve their survival after acute optic nerve injury in mice. To investigate the transcriptional mechanisms underlying the negative regulation of neuronal survival by Ssrp1, we obtained the bulk transcriptome of pooled RGCs at several time points (1, 2, 3, and 4 days) after optic nerve injury.
Published in
Repeat-element RNAs integrate a neuronal growth circuit
Zahavi EE, Koppel I, Kawaguchi R et al. · Cell 2025 · PMID 40381624 · doi:10.1016/j.cell.2025.04.030
This dataset
Open GSE233822 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 GSE233822_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA978051 and SRA study SRP440494. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40381624) ↗
Study design
10 conditions, mostly in triplicate
NT 1dpc ×3 NT 2dpc ×3 NT 3dpc ×3 NT 4dpc ×3 NT no crush ×3 SSRP1KO 1dpc ×3 SSRP1KO 2dpc ×3 SSRP1KO 3dpc ×3 +2 more

Supports a between-group comparison across 30 samples.

How we read this: 10 replicated groups read from 30 sample titles; they account for 30 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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