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Treatment of neurologic disorders by brain-wide microglia replacement using a non-conditioning strategy

GSE272257 Mus musculus (mouse) RNA-seq (gene expression) 11 samples Submitted 2025/03/06 Platform GPL30215
At a glance

RNA-seq (gene expression) · mouse · 11 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
11 samples: 4 × Resident microglia, fluorescence-activated cell sorting, vs 4 × Transplantation microglia, fluorescence-activated cell sorting, vs 3 × Primary microglial, cell culture,Groups 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)
Genetic evidence indicates that microglial dysfunctions contribute to the development and progression of various neurologic diseases, emphasizing microglia replacement as a promising therapeutic strategy. However, traditional bone marrow transplantation (BMT) aimed at replenishing brain microglia faces challenges due to low efficiency and potential brain injury from preconditioning with irradiation or chemotherapy.
Read the full summary ↓
Moreover, the BM-derived cells that migrate to the brain fail to replicate the characteristics of resident microglia. Here, we present a simple yet highly effective microglia transplantation strategy devoid of any conditioning, termed "Tri-Cyclic Microglial Depletion for Transplantation" (TCMDT). This approach leverages three cycles of microglial depletion using the CSF1R inhibitor PLX3397, creating a critical window for the efficient engraftment of exogenous microglia. Notably, transplanting primary cultured microglia via the TCMDT strategy achieves their full restoration to the identity and functions of native microglia. To evaluate the therapeutic potential, we applied our strategy to a Sandhoff disease mouse model, a form of neurodegenerative lysosomal storage disorder (LSD) caused by Hexb deficiency. The results revealed that our strategy facilitated the efficient replacement of deficient microglia, leading to a notable decrease in neurodegeneration and an enhancement in motor performance. Similarly, in an Alzheimer's disease (AD) mouse model carrying the Trem2 R47H mutation, our transplantation strategy corrected microglial dysfunction and alleviated AD-related pathology. Overall, our study presents a practical approach for microglia replacement that is simple, efficient, and safe, offering significant therapeutic potential for treating microglia-associated disorders.
This dataset
Open GSE272257 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 GSE272257_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 PRJNA1135958 and SRA study SRP519924. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
4 × Resident microglia, fluorescence-activated cell sorting, vs 4 × Transplantation microglia, fluorescence-activated cell sorting, vs 3 × Primary microglial, cell culture,

Supports a between-group comparison across 11 samples.

How we read this: 3 replicated groups read from 11 sample titles; they account for 11 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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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.