GEO series

CSF1R-inhibitor resistant model for CNS-wide microglia replacement strategies

GSE311140 Mus musculus (mouse) RNA-seq (gene expression) 23 samples Submitted 2025/11/25 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.
Paper: CSF1R inhibitor-resistant model for CNS-wide microglia replacement strategiesMolecular therapy : the journal of the American Society of Gene Therapy · 2026

Summary (written by the submitters)

Recent advances in cell-based therapies have demonstrated therapeutic safety and efficacy for a variety of diseases. However, significant challenges remain in their development for the treatment of neurological disorders. Preclinical studies have explored microglial replacement strategies utilizing bone marrow transplantation and CSF1R-inhibitor (CSF1Ri) treatment.

Read the full summary ↓

However, these approaches often require highly invasive strategies and result in engrafted cells that remain transcriptionally and functionally distinct from microglia. To assess less invasive microglia replacement strategies capable of preserving microglial ontogeny, we developed a Csf1r-G793A knockin mouse. We found G793A mice develop typical microglial densities and peripheral hematopoietic populations which exhibit broad CSF1Ri resistance enabling widespread microglia replacement following direct intraparenchymal injection or bone marrow transplantation. Furthermore, we demonstrate that widespread microglia replacement can be achieved via less invasive intracisternal delivery of CSF1Ri-resistant murine and iPSC-derived human microglia. Together with the accompanying study by Lombroso and colleagues, our findings demonstrate that G793A mice provide a robust and broadly applicable source of engraftable donor microglia and peripheral macrophages for the preclinical investigation of microglia replacement strategies.

Published in

CSF1R inhibitor-resistant model for CNS-wide microglia replacement strategies

Chadarevian JP, Nguyen J, Le L et al. · Molecular therapy : the journal of the American Society of Gene Therapy 2026 · PMID 41232524 · doi:10.1016/j.ymthe.2025.10.051

This dataset

Open GSE311140 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 GSE311140_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 PRJNA1368731 and SRA study SRP648428. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41232524) ↗

Study design

6 conditions, mostly with about 4 replicates each

G793A, control, ×4 WT, PLX3397, ×4 G793A, PLX3397, ×4 WT, PLX5622, ×4 G793A, PLX5622, ×4 WT, control, ×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

GSM9317632 WT, control, rep1 WT, control,
GSM9317633 WT, control, rep2 WT, control,
GSM9317634 WT, control, rep3 WT, control,
GSM9317635 G793A, control, rep1 G793A, control,
GSM9317636 G793A, control, rep2 G793A, control,
GSM9317637 G793A, control, rep3 G793A, control,
GSM9317638 G793A, control, rep4 G793A, control,
GSM9317639 WT, PLX3397, rep1 WT, PLX3397,
GSM9317640 WT, PLX3397, rep2 WT, PLX3397,
GSM9317641 WT, PLX3397, rep3 WT, PLX3397,
GSM9317642 WT, PLX3397, rep4 WT, PLX3397,
GSM9317643 G793A, PLX3397, rep1 G793A, PLX3397,
GSM9317644 G793A, PLX3397, rep2 G793A, PLX3397,
GSM9317645 G793A, PLX3397, rep3 G793A, PLX3397,
GSM9317646 G793A, PLX3397, rep4 G793A, PLX3397,
GSM9317647 WT, PLX5622, rep1 WT, PLX5622,
GSM9317648 WT, PLX5622, rep2 WT, PLX5622,
GSM9317649 WT, PLX5622, rep3 WT, PLX5622,
GSM9317650 WT, PLX5622, rep4 WT, PLX5622,
GSM9317651 G793A, PLX5622, rep1 G793A, PLX5622,
GSM9317652 G793A, PLX5622, rep2 G793A, PLX5622,
GSM9317653 G793A, PLX5622, rep3 G793A, PLX5622,
GSM9317654 G793A, PLX5622, rep4 G793A, PLX5622,

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