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Histone H3 lysine 9 tri-methylation is associated with pterygium

GSE272511 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 24 samples Submitted 2025/01/19 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 24 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
24 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.
Paper
Histone H3 lysine 9 tri-methylation is associated with pterygiumBMC ophthalmology · 2025
Summary (written by the submitters)
Pterygium, abnormal growths of conjunctival tissue onto the cornea, are common ocular surface conditions with a high risk of recurrence after surgery and potential ophthalmic complications. The exact cause of pterygium remains unclear, and the triggers are still unknown. In this study, we investigate the epigenetic profiles of patients with pterygium, focusing on histone H3 lysine 4 (H3K4) and lysine 9 (H3K9) trimethylation (me3).
Read the full summary ↓
While H3K4me3 levels showed no significant genome-wide change, they were significantly altered in genes related to development and ocular diseases. Conversely, H3K9me3 levels were markedly elevated genome-wide, particularly at the promoters of 82 genes involved in developmental pathways. Furthermore, we identify six genes, ANK2, AOAH, CBLN2, CDH8, CNTNAP4, and DPP6, with decreased gene expression correlated with substantially increased H3K9me3, suggesting their potential as biomarkers for pterygium. This study represents the first report linking histone modification to pterygium progression, providing valuable insights into therapeutic strategies and potential drug targets.
Published in
Histone H3 lysine 9 tri-methylation is associated with pterygium
Choi D, Na AY, Jeoung SW et al. · BMC ophthalmology 2025 · PMID 40033254 · doi:10.1186/s12886-025-03939-7
This dataset
Open GSE272511 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 GSE272511_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 PRJNA1137234 and SRA study SRP520690. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40033254) ↗
Study design
8 conditions, mostly in duplicate
60-F-Ct-K ×2 60-F-Pt-K ×2 60-M-Ct-K ×2 60-M-Pt-K ×2 70-F-Ct-K ×2 70-F-Pt-K ×2 70-M-Ct-K ×2 70-M-Pt-K ×2 +8 more

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 24 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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