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Chromatin changes after long term vitamin D supplementation

GSE322656 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 42 samples Submitted 2026/03/06 Platform GPL18573
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 42 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
42 samples: 42 × PBMC, Day 84, ATAC-seq, IndividualGroups 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)
In this study, we investigate the long-term in vivo modulation of the human epigenome following vitamin D₃ supplementation. Specifically, we analyse epigenetic changes in peripheral blood mononuclear cells (PBMCs) collected 84 days after administration of a single bolus dose of vitamin D₃ (1,000 IU/kg). Vitamin D is a well-known regulator of gene expression through the vitamin D receptor (VDR), which interacts with chromatin and modulates the epigenetic landscape of immune cells.
Read the full summary ↓
However, the persistence and extent of these epigenomic effects in vivo remain insufficiently characterized.To address this question, we assess genome-wide epigenetic alterations in PBMCs to determine whether a single high dose of vitamin D₃ induces sustained modifications in regulatory regions associated with immune function and cellular signalling pathways. The study focuses on identifying changes in chromatin accessibility and regulatory element activity that may reflect long-lasting transcriptional priming of immune cells. This work represents a continuation of the VitDPAS study, which previously examined the immediate molecular responses to vitamin D₃ supplementation. By extending the analysis to the 84-day time point, the present study aims to determine whether the epigenetic effects of vitamin D₃ persist over the long term and contribute to prolonged immune modulation. Understanding these sustained epigenomic changes may provide new insights into the mechanisms through which vitamin D influences immune regulation and long-term health outcomes.
This dataset
Open GSE322656 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 GSE322656_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 PRJNA1430814 and SRA study SRP680335. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
42 × PBMC, Day 84, ATAC-seq, Individual

Supports a between-group comparison across 42 samples.

How we read this: 1 replicated groups read from 42 sample titles; they account for 42 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

+ 2 more — browse all 42 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.