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Multimodal characterization of the effects of stimulation on the human brain ex vivo and in vivo.

GSE288939 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 60 samples Submitted 2026/06/06 Platform GPL34284
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 60 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
60 samples: 8 conditions, mostly with about 9 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)
The underlying mechanisms of therapeutics using brain stimulation in humans are not understood. In particular, it is unknown how brain stimulation impacts gene expression in acute and chronic temporal periods. Although therapeutic approaches like deep brain stimulation are becoming more widely used, it is impossible to study stimulation-induced genetic changes without tissue samples which at best could be collected post-mortem.
Read the full summary ↓
To overcome these extremely limiting circumstances, we have implemented a multi-part experimental design involving single cell resolution RNA and ATAC sequencing of human cortex that has been stimulated in several paradigms. In the first, acute human cortex slices are stimulated with a high-density microelectrode array, which allows us to track how neural activity changes after stimulation together with genomic changes. In the second, tissue is collected from neurosurgery patients immediately after direct cortical stimulation in vivo. We have uncovered differentially expressed genes and differentially accessible chromatin regions in both paradigms. We have also determined the impact of stimulation on cell assembly plasticity and celltype-specific changes in firing patterns. Our integrated approach of applying stimulation paradigms in human brain tissue both in vivo and ex vivo has not been completed before. These results represent a key first step in our quest to understand exactly how brain stimulation supports neural function at the cellular level.
This dataset
Open GSE288939 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 GSE288939_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 PRJNA1220064 and SRA study SRP562051. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
8 conditions, mostly with about 9 replicates each
snRNAseq, In vivo control, donor IVS ×9 snATACseq, In vivo control, donor IVS ×9 snRNAseq, In vivo stimulation, donor IVS ×9 snATACseq, In vivo stimulation, donor IVS ×9 snRNAseq, MEA control, donor MEA ×6 snATACseq, MEA control, donor MEA ×6 snRNAseq, MEA stimulation, donor MEA ×6 snATACseq, MEA stimulation, donor MEA ×6

Supports a between-group comparison across 60 samples.

How we read this: 8 replicated groups read from 60 sample titles; they account for 60 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

+ 20 more — browse all 60 samples with per-sample file links →

Datasets on a similar topic

Search all human ChIP / ATAC / CUT&Tag datasets in GEO →

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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.