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RNA sequencing transcriptome analysis of lesional to perilesional cortex at 5 days after traumatic brain injury

GSE228309 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/12/21 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 24 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
24 samples: 21 distinct titles, 1 of them repeatedGroups 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
CSF1R and IL1R1 inhibitors synergistically attenuate the early pathogenesis of traumatic brain injury in miceNeurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics · 2026
Summary (written by the submitters)
C57BL6/N male mice (14-week-old) were subjected to a controlled cortical impact (CCI) to induce a unilateral traumatic brain injury (TBI). After surgery, mice were treated and monitored for 5 days after TBI (5 dpi). There were four treatment groups, each consisting in five male mice (n = 5 per group). Group-1 received the CSF1R antagonist, PLX3397 (pexidartinib) via food pellets (290 mg per kilogram of pellets, feeding at libitum).
Read the full summary ↓
Group-2 received the interleukin-1 receptor antagonist (IL1RA), anakinra (100 mg/kg body weight subcutaneously at 5 min, 24h, 48h, and 72h after CCI). Group-3 received both PLX3397 and anakinra (PLX3397+anakinra), and Group-4 got vehicle p.o. and s.c.. A control group was subjected to sham-surgy (n = 4)which included anesthesia, skin incision and suture but no skull penetration. PLX3397 leads to a depletion of microglial cells which was confirmed by immunohistochemistry. Lesional to perilesional cortical tissue was obtained 5 dpi (Brgema: +0.64 mm to -2.86 mm) to assess differential gene and transcript expression, microglia depletion and cortical reorganization. Behavioral scores for well-being and motor functions were obatined repeatedly during the observation time. Histology of brain lesion size, indices of neuronal damage and neuroinflammation were obtained at 5 days after TBI. Neuroinflammatory markers tended to be lower in PLX3397 treated mice, there was almost no effects of anakinra alone but inflammation and lesion volume were strongly reduced in the PLX3397+anakinra group, which was associated with better neurological outcome suggesting synergistic effects of PLX3997 and anakinra after TBI.
Published in
CSF1R and IL1R1 inhibitors synergistically attenuate the early pathogenesis of traumatic brain injury in mice
Wang S, Wang Y, Strehle J et al. · Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics 2026 · PMID 41206313 · doi:10.1016/j.neurot.2025.e00787
This dataset
Open GSE228309 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 GSE228309_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 PRJNA949236 and SRA study SRP429582. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41206313) ↗
Study design
21 distinct titles, 1 of them repeated
Sham - J ×4

How we read this: Read from 24 sample titles: 21 distinct titles with little repetition. 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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