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 I
GSE283556
Mus musculus (mouse)
RNA-seq (gene expression)
35 samples
Submitted 2025/08/06
Platform GPL30172
At a glance
RNA-seq (gene expression) · mouse · 35 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
- 35 samples: 12 × Microglia,TBI,8months, vs 12 × Microglia,SHAM,8months, vs 11 × Macrophages,TBI,8months,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.
- 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
Paladini MS, Yang BA, Torkenczy KA et al.
· Nature communications 2025
· PMID 41057304
· doi:10.1038/s41467-025-63952-8
This dataset
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.
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 GSE283556_RAW.tar (it can run to tens of gigabytes).
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.
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.
Study design
12 × Microglia,TBI,8months, vs 12 × Microglia,SHAM,8months, vs 11 × Macrophages,TBI,8months,
Supports a between-group comparison across 35 samples.
How we read this: 3 replicated groups read from 35 sample titles; they account for 35 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
- GSM8666220 Microglia,TBI,8months,Rep1 Microglia,TBI,8months,
- GSM8666221 Macrophages,TBI,8months,Rep1 Macrophages,TBI,8months,
- GSM8666222 Microglia,TBI,8months,Rep2 Microglia,TBI,8months,
- GSM8666223 Macrophages,TBI,8months,Rep2 Macrophages,TBI,8months,
- GSM8666224 Microglia,TBI,8months,Rep3 Microglia,TBI,8months,
- GSM8666225 Macrophages,TBI,8months,Rep3 Macrophages,TBI,8months,
- GSM8666226 Microglia,SHAM,8months,Rep1 Microglia,SHAM,8months,
- GSM8666227 Microglia,SHAM,8months,Rep2 Microglia,SHAM,8months,
- GSM8666228 Microglia,SHAM,8months,Rep3 Microglia,SHAM,8months,
- GSM8666229 Microglia,TBI,8months,Rep4 Microglia,TBI,8months,
- GSM8666230 Macrophages,TBI,8months,Rep4 Macrophages,TBI,8months,
- GSM8666231 Microglia,TBI,8months,Rep5 Microglia,TBI,8months,
- GSM8666232 Macrophages,TBI,8months,Rep5 Macrophages,TBI,8months,
- GSM8666233 Microglia,TBI,8months,Rep6 Microglia,TBI,8months,
- GSM8666234 Macrophages,TBI,8months,Rep6 Macrophages,TBI,8months,
- GSM8666235 Microglia,SHAM,8months,Rep4 Microglia,SHAM,8months,
- GSM8666236 Microglia,SHAM,8months,Rep5 Microglia,SHAM,8months,
- GSM8666237 Microglia,SHAM,8months,Rep6 Microglia,SHAM,8months,
- GSM8666238 Microglia,TBI,8months,Rep7 Microglia,TBI,8months,
- GSM8666239 Macrophages,TBI,8months,Rep7 Macrophages,TBI,8months,
- GSM8666240 Microglia,TBI,8months,Rep8 Microglia,TBI,8months,
- GSM8666241 Macrophages,TBI,8months,Rep8 Macrophages,TBI,8months,
- GSM8666242 Microglia,TBI,8months,Rep9 Microglia,TBI,8months,
- GSM8666243 Macrophages,TBI,8months,Rep9 Macrophages,TBI,8months,
- GSM8666244 Microglia,SHAM,8months,Rep7 Microglia,SHAM,8months,
- GSM8666245 Microglia,SHAM,8months,Rep8 Microglia,SHAM,8months,
- GSM8666246 Microglia,SHAM,8months,Rep9 Microglia,SHAM,8months,
- GSM8666247 Microglia,TBI,8months,Rep10 Microglia,TBI,8months,
- GSM8666248 Macrophages,TBI,8months,Rep10 Macrophages,TBI,8months,
- GSM8666249 Microglia,TBI,8months,Rep11 Microglia,TBI,8months,
- GSM8666250 Microglia,TBI,8months,Rep12 Microglia,TBI,8months,
- GSM8666251 Macrophages,TBI,8months,Rep11 Macrophages,TBI,8months,
- GSM8666252 Microglia,SHAM,8months,Rep10 Microglia,SHAM,8months,
- GSM8666253 Microglia,SHAM,8months,Rep11 Microglia,SHAM,8months,
- GSM8666254 Microglia,SHAM,8months,Rep12 Microglia,SHAM,8months,
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Share this dataset
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