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Alpha retinal ganglion cell-derived SPP1 instructs microglia to limit neurodegeneration

GSE304931 Mus musculus (mouse) RNA-seq (gene expression) 23 samples Submitted 2026/07/17 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 23 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
23 samples: 6 conditions, mostly with about 4 replicates eachGroups 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)
Communication between neurons and microglia is essential for microglial functions and neuronal survival. Here we report that alpha retinal ganglion cells (αRGCs) respond to glaucomatous or traumatic axonal injury by increasing the expression and secretion of secreted phosphoprotein 1 (SPP1), which in turn instructs retinal microglia to assume a neuroprotective phenotype.
Read the full summary ↓
Alpha RGCs increase the secretion of SPP1, which acts on its specific receptor, ItgαV, on microglia and elicits transcriptional and morphological changes. SPP1 functionally increases the capacity of microglia to clear protein aggregates and inhibits neuroinflammation. SPP1 positively regulates microglial debris clearance through an upregulation of autophagy-selective receptors. This shifts microglia towards the expression of neuroprotective mediators, such as interleukin-10, protecting ganglion cells and limiting vision decline. Our findings identify SPP1 as a key mediator of αRGC-microglia crosstalk in autophagy and debris clearance, and a promising candidate for therapy in neurodegeneration.
This dataset
Open GSE304931 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 GSE304931_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 PRJNA1303445 and SRA study SRP607568. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly with about 4 replicates each
CX3CR1-GFP microglia, control, ×4 CX3CR1-GFP microglia, high IOP, ×4 Spp1KO/CX3CR1-GFP microglia, control, ×4 Spp1KO/CX3CR1-GFP microglia, high IOP, ×4 Spp1KO/CX3CR1-GFP microglia, ONC, ×4 CX3CR1-GFP microglia, ONC, ×3

Supports a between-group comparison across 23 samples.

How we read this: 6 replicated groups read from 23 sample titles; they account for 23 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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