GEO series

Fate mapping of peripherally derived macrophages reveals a long-lasting engrafted population that maintains a distinct transcriptomic profile for up to 8 months after Traumatic Brain Injury III

GSE283560 Mus musculus (mouse) RNA-seq (gene expression) 65 samples Submitted 2025/08/06 Platform GPL30172

At a glance

RNA-seq (gene expression) · mouse · 65 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: 65 samples: 13 conditions, mostly in triplicateGroups 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: Fate mapping of peripherally-derived macrophages after traumatic brain injury in mice reveals a long-lasting population with a distinct transcriptomic signatureNature communications · 2025

Summary (written by the submitters)

Traumatic Brain Injury (TBI) is one of the most established environmental risk factors for the development of dementia and long term neurological deficits representing a critical health problem for our society. It is well-established that TBI-induced neuroinflammation contributes to the long-lasting cognitive deficits and engages brain-resident macrophages (microglia) as well as monocytes-derived macrophages (MDMs) recruited from the periphery.

Read the full summary ↓

While numerous studies have characterized microglia response to TBI, and the critical role of early infiltrated MDMs in the development of cognitive dysfunctions, the fate of MDMs in TBI remains unknown. Microglia and MDMs have distinct embryological origins and it is unclear if MDMs can fully transition to microglia after infiltrating the brain. This gap in knowledge is due to the fact that after brain engraftment, MDMs stop expressing their signature markers, thus making discrimination from resident microglia cells elusive. Here, for the first time, we longitudinally trace the fate of MDMs by taking advantage of two complementary yet distinct fate mapping mouse lines, CCR2-creERT2 and Ms4a3-cre, where inflammatory monocytes are permanently labeled even after in situ reprogramming. We demonstrated that early infiltrated MDMs persist in the brain for up to 8 months after TBI in adult female and male mice. Notably, MDMs retain their phagocytic activity while remaining transcriptomically distinct from microglia, and show a signature associated with aging and disease. Our data significantly advance the understanding of long-lasting MDMs and provide critical knowledge for developing more targeted therapeutic interventions for myeloid cells.

Published in

Fate mapping of peripherally-derived macrophages after traumatic brain injury in mice reveals a long-lasting population with a distinct transcriptomic signature

Paladini MS, Yang BA, Torkenczy KA et al. · Nature communications 2025 · PMID 41057304 · doi:10.1038/s41467-025-63952-8

This dataset

Open GSE283560 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 GSE283560_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 PRJNA1191420 and SRA study SRP547973. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41057304) ↗

Study design

13 conditions, mostly in triplicate

Microglia,TBI,7dpi, ×8 Monocytes,TBI,7dpi, ×8 Macrophages,TBI,7dpi, ×8 Monocytes,Naive,0dpi, ×6 Microglia,Naive,0dpi, ×6 Monocytes,TBI,30dpi, ×6 Macrophages,Naive,0dpi, ×6 Microglia,TBI,30dpi, ×3 +5 more

Supports a between-group comparison across 65 samples.

How we read this: 13 replicated groups read from 65 sample titles; they account for 65 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

GSM8666313 Monocytes,Naive,0dpi,Rep1 Monocytes,Naive,0dpi,
GSM8666314 Microglia,Naive,0dpi,Rep1 Microglia,Naive,0dpi,
GSM8666315 Microglia,TBI,7dpi,Rep1 Microglia,TBI,7dpi,
GSM8666316 Monocytes,TBI,30dpi,Rep1 Monocytes,TBI,30dpi,
GSM8666317 Monocytes,TBI,30dpi,Rep2 Monocytes,TBI,30dpi,
GSM8666318 Microglia,TBI,30dpi,Rep1 Microglia,TBI,30dpi,
GSM8666319 Monocytes,TBI,7dpi,Rep1 Monocytes,TBI,7dpi,
GSM8666320 Monocytes,TBI,7dpi,Rep2 Monocytes,TBI,7dpi,
GSM8666321 Microglia,TBI,7dpi,Rep2 Microglia,TBI,7dpi,
GSM8666322 Microglia,TBI,7dpi,Rep3 Microglia,TBI,7dpi,
GSM8666323 Monocytes,TBI,7dpi,Rep3 Monocytes,TBI,7dpi,
GSM8666324 Macrophages,Naive,0dpi,Rep1 Macrophages,Naive,0dpi,
GSM8666325 Macrophages,TBI,7dpi,Rep1 Macrophages,TBI,7dpi,
GSM8666326 Macrophages,TBI,30dpi,Rep1 Macrophages,TBI,30dpi,
GSM8666327 Macrophages,TBI,7dpi,Rep2 Macrophages,TBI,7dpi,
GSM8666328 Macrophages,TBI,7dpi,Rep3 Macrophages,TBI,7dpi,
GSM8666329 Monocytes,Naive,0dpi,Rep2 Monocytes,Naive,0dpi,
GSM8666330 Microglia,Naive,0dpi,Rep2 Microglia,Naive,0dpi,
GSM8666331 Microglia,TBI,7dpi,Rep4 Microglia,TBI,7dpi,
GSM8666332 Monocytes,TBI,30dpi,Rep3 Monocytes,TBI,30dpi,
GSM8666333 Monocytes,TBI,30dpi,Rep4 Monocytes,TBI,30dpi,
GSM8666334 Microglia,TBI,30dpi,Rep2 Microglia,TBI,30dpi,
GSM8666335 Monocytes,TBI,7dpi,Rep4 Monocytes,TBI,7dpi,
GSM8666336 Monocytes,TBI,7dpi,Rep5 Monocytes,TBI,7dpi,
GSM8666337 Microglia,TBI,7dpi,Rep5 Microglia,TBI,7dpi,
GSM8666338 Microglia,TBI,7dpi,Rep6 Microglia,TBI,7dpi,
GSM8666339 Monocytes,TBI,7dpi,Rep6 Monocytes,TBI,7dpi,
GSM8666340 Macrophages,Naive,0dpi,Rep2 Macrophages,Naive,0dpi,
GSM8666341 Macrophages,TBI,7dpi,Rep4 Macrophages,TBI,7dpi,
GSM8666342 Macrophages,TBI,30dpi,Rep2 Macrophages,TBI,30dpi,
GSM8666343 Macrophages,TBI,7dpi,Rep5 Macrophages,TBI,7dpi,
GSM8666344 Macrophages,TBI,7dpi,Rep6 Macrophages,TBI,7dpi,
GSM8666345 Monocytes,SHAM,7dpi,Rep1 Monocytes,SHAM,7dpi,
GSM8666346 Microglia,SHAM,7dpi,Rep1 Microglia,SHAM,7dpi,
GSM8666347 Monocytes,TBI,30dpi,Rep5 Monocytes,TBI,30dpi,
GSM8666348 Monocytes,TBI,30dpi,Rep6 Monocytes,TBI,30dpi,
GSM8666349 Microglia,TBI,30dpi,Rep3 Microglia,TBI,30dpi,
GSM8666350 Monocytes,SHAM,7dpi,Rep2 Monocytes,SHAM,7dpi,
GSM8666351 Monocytes,TBI,7dpi,Rep7 Monocytes,TBI,7dpi,
GSM8666352 Microglia,TBI,7dpi,Rep7 Microglia,TBI,7dpi,

+ 25 more — browse all 65 samples with per-sample file links →

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