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Interaction between microglia and endothelial cell facilitates inflammatory BBB disruption in bacterial meningitis

GSE301612 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 18 samples Submitted 2026/06/16 Platform GPL19057Platform GPL34328
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 18 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
18 samples: 8 conditions, mostly in duplicateGroups 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)
The blood-brain barrier (BBB) serves as a physiological and functional protective barrier between the brain parenchyma and the peripheral circulatory system, which protects the brain from bloodborne agents, including pathogens and toxins. Bacterial meningitis, a devastating disease occurring worldwide, remains a major cause of high mortality and morbidity, which can trigger BBB disruption and intense intracerebral inflammatory responses.
Read the full summary ↓
Using single-cell RNA sequencing (scRNA-seq), we show that during neonatal meningitis Escherichia coli (NMEC) challenges, brain endothelial cells undergo pyroptosis and trigger the pyroptotic cascade through intercellular interactions, leading to inflammatory disruption of BBB and strong immune response within the brain. Analyses of the scRNA-seq dataset demonstrate that brian endothelial cells and microglia display the most sensitive to bacterial responses, and the crosstalk between brain vascular cells and immune cells remodels the central nervous system immune microenvironment. We employed a single-cell sequencing approach using 10x Genomics scRNAseq to study neonatal meningitis caused by Escherichia coli (NMEC) infection in mice. This study reveals that NMEC triggers pyroptosis in cerebral cortex cells, leading to inflammatory disruption of the BBB, activation of the apoptotic cascade, and triggering a strong immune response within the brain, disrupting the central nervous system's immune microenvironment. It helps us understand the immunopathological mechanisms of NMEC-induced meningitis and provides a theoretical basis for developing innovative therapeutic strategies targeting the function regulation of cortical cells or microglia and the apoptotic process, thus opening up new avenues for the prevention and treatment of neonatal meningitis.
This dataset
Open GSE301612 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 GSE301612_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1285790 and SRA study SRP598072. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
8 conditions, mostly in duplicate
Isocortex, Hippocampus, 6h, PBS, ×3 Isocortex, Hippocampus, 6h, NMEC, ×3 Isocortex, 6h, PBS, ×2 Hippocampus, 6h, PBS, ×2 Isocortex, 3h, NMEC, ×2 Hippocampus, 3h, NMEC, ×2 Isocortex, 6h, NMEC, ×2 Hippocampus, 6h, NMEC, ×2

Supports a between-group comparison across 18 samples.

How we read this: 8 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
Datasets on a similar topic

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