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Histone modification clocks for robust cross-species biological age prediction and elucidating senescence regulation

GSE296812 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 46 samples Submitted 2026/02/24 Platform GPL34281Platform GPL34815
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 46 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
46 samples: 13 conditions, mostly in triplicateGroups 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 modification clocks for robust cross-species biological age prediction and elucidating senescence regulationProceedings of the National Academy of Sciences of the United States of America · 2026
Summary (written by the submitters)
By analyzing ChIP-seq data across six tissues and six histone marks, we developed 36 tissue-specific histone modification-based epigenetic clocks that detect age acceleration in leukemia and reversal following treatment. Many age-associated loci showed nonlinear trajectories peaking at midlife, and super-enhancer fragmentation was observed with age.
Read the full summary ↓
Functional validation of an H3K27ac peak near IGF2BP3 confirmed its role in senescence via TRA2A regulation. These clocks also generalized to Drosophila melanogaster, highlighting the evolutionary conservation and utility of histone modifications as aging biomarkers.
Published in
Histone modification clocks for robust cross-species biological age prediction and elucidating senescence regulation
Niu Z, Liu C, Fan Y et al. · Proceedings of the National Academy of Sciences of the United States of America 2026 · PMID 41805570 · doi:10.1073/pnas.2533687123
This dataset
Open GSE296812 in finder → Find more 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 GSE296812_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 PRJNA1261086 and SRA study SRP584264. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41805570) ↗
Study design
13 conditions, mostly in triplicate
Input ChIP-seq, fly adult, day ×10 mRNA-seq, HL60 cells, control, ×3 mRNA-seq, HL60 cells, dCas9-HDAC, ×3 H3K27ac ChIP-seq, fly adult, day1, ×3 H3K27ac ChIP-seq, fly adult, day3, ×3 H3K27ac ChIP-seq, fly adult, day5, ×3 H3K27ac ChIP-seq, fly adult, day13, ×3 H3K27ac ChIP-seq, fly adult, day20, ×3 +5 more

Supports a between-group comparison across 46 samples.

How we read this: 13 replicated groups read from 46 sample titles; they account for 46 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

+ 6 more — browse all 46 samples with per-sample file links →

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