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Cerebrospinal fluid-linked periventricular gradient pathology in multiple sclerosis associates with ependymal cell reactivity and cell adhesion disruption

GSE283715 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 18 samples Submitted 2026/07/10 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 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
Homo sapiens (human)
Samples
18 samples: 18 samples, each with a distinct title — no replicated groupsGroups 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)
Cerebrospinal fluid (CSF)-adjacent brain surfaces – namely the subpial cortical and ependyma-adjacent periventricular regions – are uniquely vulnerable to diffuse pathology in multiple sclerosis (MS). So-called surface-in gradients, which predict disease relapses independent of white matter lesions, are thought to arise from CSF-borne cytotoxic factors and represent a distinct therapeutic target.
Read the full summary ↓
Yet, how such factors access the brain, particularly at the ventricular border, remains unclear. While ependymal injury in MS has been suggested, a comprehensive assessment of cell health in the disease is lacking. Using ultra-high-field MRI-guided histology, electron microscopy, and single-nucleus multiomics, we deeply profiled human ependymal cells in MS. We found that ependymal pathology correlates with periventricular gradients and involves an immune-reactive state marked by transporter and junctional protein dysregulation. We then further defined the gene regulatory networks underpinning the MS ependymal state, predicted ligands known to be enriched in MS CSF that could drive the emergence of this state, and tested one candidate in vivo. IFNγ increased murine ependymal permeability and conditional knockout of its receptor (Ifngr1) reversed this effect. These findings implicate ependymal dysfunction in periventricular pathology and highlight how CSF ligands modulate ependymal function and regional inflammation.
This dataset
Open GSE283715 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE283715_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 PRJNA1195083. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
18 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 18 sample titles: 18 distinct titles with little repetition. 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.