GEO series

Astrocyte-microglia signaling controls developmental thalamocortical synapse refinement

GSE259420 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/12/31 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 12 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: 12 samples: 4 × Ms_Microglia_Hevin vs 4 × Ms_Microglia_LPS vs 4 × Ms_Microglia_MediaGroups 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: Astrocyte-microglia crosstalk through Hevin and Toll-like receptor signaling controls developmental thalamocortical synapse refinementNeuron · 2026

Summary (written by the submitters)

Synapse formation and elimination are two crucial processes that concurrently take place in the developing brain. Astrocytes and microglia have been shown to control both processes. However, it is largely unknown how these two major glial cell types of the central nervous system (CNS) communicate to balance synapse formation and elimination.

Read the full summary ↓

Astrocytes secrete a synaptogenic protein called Hevin/SPARCL1, which induces the formation and plasticity of thalamocortical synapses in the mouse visual cortex. Hevin does so by physically localizing to synaptic clefts and bridging the thalamic axon/cortical dendrite via its interactions with presynaptic Neurexin1a and postsynaptic Neuroligin1b. Here, we found that in addition to this synaptogenic function, Hevin directly signals to microglia cells by interacting with Toll-like Receptors (TLRs) TLR4 and TLR2. This signaling occurs when Hevin is proteolytically cleaved producing an active C-terminal fragment. This fragment is sufficient to upregulate TLR2 expression in microglia and increase microglia phagocytic activity in vivo. This signaling is required for proper refinement of thalamocortical synapses in early postnatal development and for early life ocular dominance plasticity.

Published in

Astrocyte-microglia crosstalk through Hevin and Toll-like receptor signaling controls developmental thalamocortical synapse refinement

Ramirez JJ, Hardin EJ, Sakers K et al. · Neuron 2026 · PMID 41720089 · doi:10.1016/j.neuron.2025.12.028

This dataset

Open GSE259420 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 GSE259420_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 PRJNA1081450 and SRA study SRP492163. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41720089) ↗

Study design

4 × Ms_Microglia_Hevin vs 4 × Ms_Microglia_LPS vs 4 × Ms_Microglia_Media

Supports a between-group comparison across 12 samples.

How we read this: 3 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

GSM8115880 Ms_Microglia_Hevin_rep1 Ms_Microglia_Hevin
GSM8115881 Ms_Microglia_LPS_rep1 Ms_Microglia_LPS
GSM8115882 Ms_Microglia_Media_rep1 Ms_Microglia_Media
GSM8115883 Ms_Microglia_Hevin_rep2 Ms_Microglia_Hevin
GSM8115884 Ms_Microglia_LPS_rep2 Ms_Microglia_LPS
GSM8115885 Ms_Microglia_Media_rep2 Ms_Microglia_Media
GSM8115886 Ms_Microglia_Hevin_rep3 Ms_Microglia_Hevin
GSM8115887 Ms_Microglia_LPS_rep3 Ms_Microglia_LPS
GSM8115888 Ms_Microglia_Media_rep3 Ms_Microglia_Media
GSM8115889 Ms_Microglia_Hevin_rep4 Ms_Microglia_Hevin
GSM8115890 Ms_Microglia_LPS_rep4 Ms_Microglia_LPS
GSM8115891 Ms_Microglia_Media_rep4 Ms_Microglia_Media

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