GEO series

Retinoid X Receptor as a Mediator of Post Stroke Recovery by Reversing Age-Associated Phenotypes of Microglia/Hematogenous Macrophages

GSE287142 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2025/09/17 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 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: Retinoid-X-Receptor as a Mediator of Poststroke Recovery by Reversing Age-Associated Phenotypes of Microglia/Hematogenous MacrophagesThe Journal of neuroscience : the official journal of the Society for Neuroscience · 2025

Summary (written by the submitters)

After stroke, microglia/blood-derived macrophages, together MF, clear dead cells and cellular debris in the infarcted brain through phagocytosis as an essential part of the repair/recovery process. However, the phagocytic capability of MF declines with age. Furthermore, aged MF become overactivated in response to stroke, enhancing secondary brain injury.

Read the full summary ↓

Now, demonstrate that by reversing the age-related dysfunctions in MF through activating the retinoid x receptor (RXR), the recovery after stroke in the aged brain could be improved. Using RNA sequencing, we compared the transcriptomes between MF isolated from the brains of young and aged mice. We observed higher levels of pro-inflammatory genes and lower levels of phagocytosis-facilitating genes (Cd206, Cd36) expressed by aged MF. Meanwhile, the treatment with RXR agonist bexarotene (BEX) reversed the signature genes of microglia aging in the aged MF. With the in vivo phagocytosis model, we showed that BEX enhanced the phagocytic ability of aged MF. Using mouse MCAo stroke model, we established that BEX improved sensorimotor and cognitive recovery after MCAo in a myeloid-RXRa-specific and -dependent manner. In conclusion, we showed that activating RXRa partially restores age-related MF dysfunctions and that RXRa deficiency in MF limits the therapeutic effect of RXR in improving post-stroke recovery in the aged brain

Published in

Retinoid-X-Receptor as a Mediator of Poststroke Recovery by Reversing Age-Associated Phenotypes of Microglia/Hematogenous Macrophages

Ting SM, Zhao X, Sun G et al. · The Journal of neuroscience : the official journal of the Society for Neuroscience 2025 · PMID 40803891 · doi:10.1523/JNEUROSCI.0248-25.2025

This dataset

Open GSE287142 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 GSE287142_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 PRJNA1211183 and SRA study SRP557668. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40803891) ↗

Study design

6 conditions, mostly in triplicate

MF, young, vehicle, biol ×3 MF, young, BEX, biol ×3 MF, aged, vehicle, biol ×3 MF, aged, BEX, biol ×3 MF, aged, stroked, vehicle, biol ×3 MF, aged, stroked, BEX, biol ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 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

GSM8739593 MF, young, vehicle, biol rep 1 MF, young, vehicle, biol
GSM8739594 MF, young, vehicle, biol rep 2 MF, young, vehicle, biol
GSM8739595 MF, young, vehicle, biol rep 3 MF, young, vehicle, biol
GSM8739596 MF, young, BEX, biol rep 1 MF, young, BEX, biol
GSM8739597 MF, young, BEX, biol rep 2 MF, young, BEX, biol
GSM8739598 MF, young, BEX, biol rep 3 MF, young, BEX, biol
GSM8739599 MF, aged, vehicle, biol rep 1 MF, aged, vehicle, biol
GSM8739600 MF, aged, vehicle, biol rep 2 MF, aged, vehicle, biol
GSM8739601 MF, aged, vehicle, biol rep 3 MF, aged, vehicle, biol
GSM8739602 MF, aged, BEX, biol rep 1 MF, aged, BEX, biol
GSM8739603 MF, aged, BEX, biol rep 2 MF, aged, BEX, biol
GSM8739604 MF, aged, BEX, biol rep 3 MF, aged, BEX, biol
GSM8739605 MF, aged, stroked, vehicle, biol rep 1 MF, aged, stroked, vehi…
GSM8739606 MF, aged, stroked, vehicle, biol rep 2 MF, aged, stroked, vehi…
GSM8739607 MF, aged, stroked, vehicle, biol rep 3 MF, aged, stroked, vehi…
GSM8739608 MF, aged, stroked, BEX, biol rep 1 MF, aged, stroked, BEX,…
GSM8739609 MF, aged, stroked, BEX, biol rep 2 MF, aged, stroked, BEX,…
GSM8739610 MF, aged, stroked, BEX, biol rep 3 MF, aged, stroked, BEX,…

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