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Microglia drive diurnal variation in susceptibility to inflammatory blood-brain barrier breakdown

GSE263794 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2024/12/06 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 16 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
16 samples: 5 × AM_LPS vs 5 × PM_LPS vs 3 × AM_PBS vs 3 × PM_PBSGroups 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
Microglia drive diurnal variation in susceptibility to inflammatory blood-brain barrier breakdownJCI insight · 2024
Summary (written by the submitters)
The blood brain barrier (BBB) is critical for maintaining brain homeostasis but is susceptible to inflammatory breakdown. Permeability of the BBB to polar molecules shows circadian variation due to rhythmic transporter expression, while basal permeability to polar molecules in non-rhythmic. Whether daily timing influences BBB permeability in response to inflammation is unknown.
Read the full summary ↓
Here, we induced systemic inflammation through repeated lipopolysaccharide (LPS) injections either in the morning (ZT1) or evening (ZT13) under standard lighting conditions, then examined BBB permeability to a polar molecule. We observed clear diurnal variation in inflammatory BBB permeability, with a striking increase in BBB breakdown specifically following evening LPS injection. Evening LPS led to persisting glia activation and inflammation in the brain that was not observed in the periphery. The exaggerated evening neuroinflammation and BBB disruption were suppressed by microglial depletion, were associated with enhanced expression of the Nos2 gene, and could be prevented in vivo by treatment with an iNOS inhibitor. Our data show that diurnal rhythms in microglial inflammatory responses to LPS drive daily variability in BBB breakdown, and reveals time-of-day as a key regulator of inflammatory BBB disruption.
Published in
Microglia drive diurnal variation in susceptibility to inflammatory blood-brain barrier breakdown
Lawrence JH, Patel A, King MW et al. · JCI insight 2024 · PMID 39513366 · doi:10.1172/jci.insight.180081
This dataset
Open GSE263794 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 GSE263794_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 PRJNA1099251 and SRA study SRP501313. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39513366) ↗
Study design
5 × AM_LPS vs 5 × PM_LPS vs 3 × AM_PBS vs 3 × PM_PBS

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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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