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Brain-Engrafted Monocyte-derived Macrophages from Blood and Skull-Bone Marrow Exhibit Distinct Properties [bulkRNA_isolatedBrainParenchymalMacrophages]

GSE313387 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2026/03/11 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 18 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
18 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
Brain-engrafted monocyte-derived macrophages from blood and skull-bone marrow exhibit distinct propertiesNeuron · 2026
Summary (written by the submitters)
Microglia arise from yolk sac (YS) progenitors and are thought to persist throughout life with minimal input from adult hematopoiesis. However, whether brain-engrafted monocyte-derived macrophages (MDM) exist at homeostasis and during turnover, and how they function relative to yolk sac-derived microglia (YSM) remain unsettled. Here, we combine lineage tracing, pharmacological microglia depletion, and multi-omics profiling to define the ontogeny, identity, and function of MDM in the mouse brain.
Read the full summary ↓
Despite sharing the parenchymal milieu, MDM display unique transcriptional and epigenetic landscapes distinct from YSM. Fate-mapping reveals that newly engrafted MDM transiently express CD206, echoing a developmental stage of embryonic microglial precursors. The engraftment and polarization of MDM are modulated by the CSF1R ligand IL 34 and the chemokine receptor CCR2. Furthermore, parabiosis and skull‑flap transplantation reveal that both blood and skull marrow supply the niche via distinct routes, yielding origin‑biased MDM states. Functionally, engraftment of MDM exacerbates cuprizone-mediated demyelination. Together, our study reveals the cellular dynamics of brain parenchymal macrophages at homeostasis and during turnover. We define the core molecular features and heterogeneous origins of MDM and imply their context-dependent roles in CNS pathology.
Published in
Brain-engrafted monocyte-derived macrophages from blood and skull-bone marrow exhibit distinct properties
Du S, Ou F, Drieu A et al. · Neuron 2026 · PMID 41819099 · doi:10.1016/j.neuron.2026.01.032
This dataset
Open GSE313387 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 GSE313387_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 PRJNA1379431 and SRA study SRP654337. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41819099) ↗
Study design
6 conditions, mostly with about 4 replicates each
GFP- BMT-treated mouse ×4 Old tdTomato+ mouse ×4 Young tdTomato+ mouse ×3 Old tdTomato- mouse ×3 GFP+ BMT-treated mouse ×2 Young tdTomato- mouse ×2 1_td.pos, MDM ×1 2_td.pos, MDM ×1 +4 more

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 24 sample titles; they account for 18 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
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