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Gene expression profile of microglia and border-associated macrophages carrying hDNMT3A mutation

GSE282223 Mus musculus (mouse) RNA-seq (gene expression) 28 samples Submitted 2024/12/02 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 28 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
28 samples: 8 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
Clonal hematopoiesis-associated motoric deficits caused by monocyte-derived microglia accumulating in aging miceCell reports · 2025
Summary (written by the submitters)
To probe for the impact of a age-related clonal hematopoiesis associated somatic mutation on monocyte-derived microglia and macrophages in the CNS, we took advantage of a mouse model that harbors a replacement of the murin Dnmt3a gene with a cDNA cassette encoding the human DNMT3A R882H variant. To seed the CNS with monocyte-derived cells from hDNMT3A mut hematopoietic stem cells, we engrafted Cx3cr1-gfp mice with bone marrow of 10-month-old Vav-Cre: hDNMT3A fl/fl mice.
Read the full summary ↓
After 4 months following irradiation, endogenous microglia and leptomeningeal macrophages, and engrafted cells were isolated from both mutation and wild type groups for bulk RNAseq analysis.
Published in
Clonal hematopoiesis-associated motoric deficits caused by monocyte-derived microglia accumulating in aging mice
Kim JS, Trzebanski S, Shin SH et al. · Cell reports 2025 · PMID 40279248 · doi:10.1016/j.celrep.2025.115609
This dataset
Open GSE282223 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 GSE282223_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 PRJNA1187610 and SRA study SRP545999. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40279248) ↗
Study design
8 conditions, mostly with about 4 replicates each
Control_MoMg ×4 Control_hostMg ×4 Mutant_MoMg ×4 Mutant_hostMg ×4 Control_leptoMoMac ×4 Mutant_leptoMoMac ×4 Control_leptohostMac ×2 Mutant_leptohostMac ×2

Supports a case/control comparison: 14 samples read as cases, 14 as controls.

How we read this: 8 replicated groups read from 28 sample titles; they account for 28 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
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.