GEO series
Characterizing the metabolomes of microglia, astrocytes, and neurons in the brain across states of health, aging, and disease
GSE316928
Mus musculus (mouse)
RNA-seq (gene expression)
35 samples
Submitted 2026/02/04
Platform GPL24247Platform GPL30215
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: 7 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.
Summary (written by the submitters)
Neurons and glia are distinct in their morphology, development, and function. They have unique transcriptomes and proteomes, but little is known about their metabolomes. The challenge of brain cell metabolic profiling is to obtain a large number of pure cells for reliable analysis. Here, we purify microglia, astrocytes, and neurons from the genetically labeled-brain.
Read the full summary ↓
We identified >70 metabolites in them with targeted metabolomics and 9,854 metabolite features with untargeted metabolomics. We systematically characterized cell type–enriched metabolites and metabolic pathways. The enrichment of glutathione (GSH) metabolism in microglia was further validated in vivo. A significant decrease in GSH levels and GSH metabolism observed in microglia in aging and Alzheimer's disease (AD) models. Disrupting GSH metabolism in microglia results in aberrant morphogenesis, upregulation of mitophagy-related genes, and the deposition of β-Amyloid. Our results provide a valuable resource for metabolic studies related to aging, AD and other neurological diseases.
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 GSE316928_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 PRJNA1405558 and SRA study SRP664706. Searching any of these in the dataset finder brings you back here.
Study design
7 conditions, mostly with about 4 replicates each
mouse brain cortex, Neuron_40 ×11
mouse brain cortex, Astrocyte_40 ×5
mouse brain cortex, Microglia_40 ×4
mouse brain cortex, Microglia_1y ×4
mouse brain cortex, mg_gpx1 ×4
mouse brain cortex,mg_fad ×3
mouse brain cortex,Ast_12month_AD60 ×2
mouse brain cortex, Ast_12month_AD ×1
+1 more
Supports a between-group comparison across 33 samples.
How we read this: 7 replicated groups read from 35 sample titles; they account for 33 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
- GSM9462704 RNA-seq of mus musculus: mouse brain cortex, Microglia_40_1 mouse brain cortex, Mic…
- GSM9462705 RNA-seq of mus musculus: mouse brain cortex, Microglia_40_2 mouse brain cortex, Mic…
- GSM9462706 RNA-seq of mus musculus: mouse brain cortex, Microglia_40_3 mouse brain cortex, Mic…
- GSM9462707 RNA-seq of mus musculus: mouse brain cortex, Microglia_40_4 mouse brain cortex, Mic…
- GSM9462708 RNA-seq of mus musculus: mouse brain cortex, Astrocyte_40_1 mouse brain cortex, Ast…
- GSM9462709 RNA-seq of mus musculus: mouse brain cortex, Astrocyte_40_2 mouse brain cortex, Ast…
- GSM9462710 RNA-seq of mus musculus: mouse brain cortex, Astrocyte_40_3 mouse brain cortex, Ast…
- GSM9462711 RNA-seq of mus musculus: mouse brain cortex, Astrocyte_40_4 mouse brain cortex, Ast…
- GSM9462712 RNA-seq of mus musculus: mouse brain cortex, Astrocyte_40_5 mouse brain cortex, Ast…
- GSM9462713 RNA-seq of mus musculus: mouse brain cortex, Neuron_40_1 mouse brain cortex, Neu…
- GSM9462714 RNA-seq of mus musculus: mouse brain cortex, Neuron_40_2 mouse brain cortex, Neu…
- GSM9462715 RNA-seq of mus musculus: mouse brain cortex, Neuron_40_3 mouse brain cortex, Neu…
- GSM9462716 RNA-seq of mus musculus: mouse brain cortex, Neuron_40_4 mouse brain cortex, Neu…
- GSM9462717 RNA-seq of mus musculus: mouse brain cortex, Neuron_40_5 mouse brain cortex, Neu…
- GSM9462718 RNA-seq of mus musculus: mouse brain cortex, Neuron_40_6 mouse brain cortex, Neu…
- GSM9462719 RNA-seq of mus musculus: mouse brain cortex, Neuron_40_7 mouse brain cortex, Neu…
- GSM9462720 RNA-seq of mus musculus: mouse brain cortex, Neuron_40_8 mouse brain cortex, Neu…
- GSM9462721 RNA-seq of mus musculus: mouse brain cortex, Neuron_40_9 mouse brain cortex, Neu…
- GSM9462722 RNA-seq of mus musculus: mouse brain cortex, Neuron_40_10 mouse brain cortex, Neu…
- GSM9462723 RNA-seq of mus musculus: mouse brain cortex, Neuron_40_11 mouse brain cortex, Neu…
- GSM9462724 RNA-seq of mus musculus: mouse brain cortex, Microglia_1y_1 mouse brain cortex, Mic…
- GSM9462725 RNA-seq of mus musculus: mouse brain cortex, Microglia_1y_2 mouse brain cortex, Mic…
- GSM9462726 RNA-seq of mus musculus: mouse brain cortex, Microglia_1y_3 mouse brain cortex, Mic…
- GSM9462727 RNA-seq of mus musculus: mouse brain cortex, Microglia_1y_4 mouse brain cortex, Mic…
- GSM9462728 RNA-seq of mus musculus: mouse brain cortex, mg_gpx1_1 mouse brain cortex, mg_…
- GSM9462729 RNA-seq of mus musculus: mouse brain cortex, mg_gpx1_2 mouse brain cortex, mg_…
- GSM9462730 RNA-seq of mus musculus: mouse brain cortex, mg_gpx1_3 mouse brain cortex, mg_…
- GSM9462731 RNA-seq of mus musculus: mouse brain cortex, mg_gpx1_4 mouse brain cortex, mg_…
- GSM9462732 RNA-seq of mus musculus: mouse brain cortex,mg_fad_1 mouse brain cortex,mg_f…
- GSM9462733 RNA-seq of mus musculus: mouse brain cortex,mg_fad_2 mouse brain cortex,mg_f…
- GSM9462734 RNA-seq of mus musculus: mouse brain cortex,mg_fad_3 mouse brain cortex,mg_f…
- GSM9462735 RNA-seq of mus musculus: mouse brain cortex, Ast_12month_AD58
- GSM9462736 RNA-seq of mus musculus: mouse brain cortex,Ast_12month_AD59
- GSM9462737 RNA-seq of mus musculus: mouse brain cortex,Ast_12month_AD60_1 mouse brain cortex,Ast_…
- GSM9462738 RNA-seq of mus musculus: mouse brain cortex,Ast_12month_AD60_2 mouse brain cortex,Ast_…
Datasets on a similar topic
- GSE267592 Microglia are not necessary for maintenance of blood-brain barrier properties in health, but PLX5622 alters brain endothelial cholesterol metabolism (Brain Endo Bulk Seq) 10 samples shares microglia, health, brain
- GSE327428 GPR34 regulation of disease-associated microglial states in mice 96 samples shares microglia, states
- GSE302808 Depletion of Peripheral Monocytes Alters Long-Term Gene Expression in Microglia in a Murine Model of Traumatic Brain Injury 84 samples shares microglia, brain
- GSE304010 A transcriptomic microglia taxonomy across mouse and human pathologies 74 samples shares microglia, across
- GSE300113 Heterogenous microglial reactivity contrasts with stable vascular transcriptional programs in mouse models of Alzheimer’s, CADASIL, and Traumatic Brain Injury (Main dataset) 59 samples shares microglia, brain
- GSE296508 Transcriptional Regulation of Microglial Metabolic and Activation States by P2RY12 57 samples shares microglia, states
- GSE276647 Gene expression profile of microglia following traumatic brain injury and nasal anti-CD3 treatment at acute and chronic timepoints 54 samples shares microglia, brain
- GSE276182 NF-κB activation in astrocytes critically affects wound regeneration after traumatic brain injury 51 samples shares astrocytes, brain
Share this dataset
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.