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Depletion of Peripheral Monocytes Alters Long-Term Gene Expression in Microglia in a Murine Model of Traumatic Brain Injury

GSE302808 Mus musculus (mouse) RNA-seq (gene expression) 84 samples Submitted 2026/02/18 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 84 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
84 samples: 22 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
Depletion of Peripheral Monocytes Alters Long-Term Gene Expression in Microglia in a Murine Model of Traumatic Brain InjuryShock (Augusta, Ga.) · 2026
Summary (written by the submitters)
Background: Traumatic brain injury (TBI) is a growing and under-recognized public health threat with significant long-term complications suffered by its survivors. Monocytes are amongst the first immune cells to infiltrate the injured brain and have the ability to both foster wound repair and promote inflammation. Microglia, the resident innate immune cells in the brain, drive the long-term direction of the inflammatory response within the injured brain.
Read the full summary ↓
Previously published data from our laboratory has shown that a brief course of peri-injury monocyte depletion attenuates long-term neurocognitive deficits and preserves white matter connectivity post-injury. Nonetheless, the role that monocytes play in directing the local inflammatory response to injury via crosstalk with microglia remains unknown. To this end, we hypothesized that infiltrating monocytes shape the long-term transcriptional response of microglia to TBI. Methods: We employed a 2x2 study design consisting of four experimental groups—TBI, sham, TBI with monocyte depletion, and TBI with sham monocyte depletion. Male C57BL/6 mice were randomly assigned to groups. Monocyte depletion and sham depletion were induced via intravenous injection of liposome-encapsulated clodronate versus naked liposomes 24 hour prior to TBI. Depletion was maintained via repeat injections on days 2 and 5. Monocyte depletion was confirmed via flow cytometry. TBI was induced using our established model of controlled cortical impact. BMice were euthanized on post-injury days 1, 7, 14, 30, and 60. Brains were harvested and microglia sorted via flow cytometry. The transcriptional response of microglia across groups and timepoints was assess via bulk RNA sequencing. Conclusion:These data shows that short-course of peri-injury depletion of peripheral monocytes may have a neuroprotective effect after TBI. While the mechanisms of this protection are multifactorial, alteration of the long-term transcriptional profile of microglia may, in part, be responsible for the observed improvements in motor coordination, learning, and memory. Identified pathways include inflammation, neuroplasticity and regeneration, and a neuroprotective heat shock response. These data warrant further investigation into possible therapeutic benefits of peri-injury immune modulation.Results:Monocyte-depleted mice demonstrated improvement in motor coordination, contextual and associative learning, and memory. These neurocognitive differences were associated with distinctly different microglial transcriptional profiles evident within the first 1-2 weeks post injury. In particular, microglia within the monocyte-depleted group showed distinct upregulation of pathways including synaptic signaling, regulation of neuron differentiation, and myeloid leukocyte activation as compared to those from Vehicle TBI groups. By 60 days post injury, microglia from the monocyte-depleted TBI group had upregulation of the heat shock protein transcripts as compared to microglia from the Vehicle TBI group.
Published in
Depletion of Peripheral Monocytes Alters Long-Term Gene Expression in Microglia in a Murine Model of Traumatic Brain Injury
Islam MBAR, Chen Z, Just T et al. · Shock (Augusta, Ga.) 2026 · PMID 40961400 · doi:10.1097/SHK.0000000000002695
This dataset
Open GSE302808 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 GSE302808_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 PRJNA1292202 and SRA study SRP601247. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40961400) ↗
Study design
22 conditions, mostly with about 4 replicates each
1day post TBI microglia only TBI ×5 1day post TBI microglia Sham ×5 7day post TBI microglia only TBI ×5 7day post TBI microglia Clodroante TBI ×5 14day post TBI microglia Clodroante TBI ×5 14day post TBI microglia Vehicle TBI ×5 7day post TBI microglia Sham ×4 7day post TBI microglia Vehicle TBI ×4 +15 more

Supports a between-group comparison across 83 samples.

How we read this: 22 replicated groups read from 84 sample titles; they account for 83 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

+ 44 more — browse all 84 samples with per-sample file links →

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.