GEO series

Targeted ATAC-see (tATAC-see): A Visual Assay for Target-Specific Chromatin Profiling

GSE338034 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 15 samples Submitted 2026/07/31 Platform GPL30173

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 15 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: 15 samples: 15 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)

We present Targeted ATAC-see (tATAC-see), a visual genomics assay for site-specific chromatin profiling. By integrating the in situ visualization of ATAC-see with antibody-tethered tagmentation, tATAC-see captures chromatin states at defined protein-occupied domains with the simplicity of standard immunofluorescence. Modulating the spatial interaction radius of Tn5 via salt titration enables extended tagmentation of target-proximal chromatin local environments.

Read the full summary ↓

We validated this imaging-based method by capturing the expanded chromatin neighborhoods of active euchromatin (H3K27ac, H3K4me3) alongside the dense structural Lamina-Associated Domains (LADs) of Lamin A/C and Lamin B1. Utilizing an HDAC inhibitor, we test the assay’s sensitivity to detect dynamic structural remodeling. We not only tracked chromatin decompaction, but also demonstrated the robust structural resistance of LADs. As a proof of principle biological application, we applied tATAC-see to models of replicative, chronological, and pathological (Hutchinson-Gilford Progeria Syndrome) aging to assess its ability to detect well-characterized peripheral heterochromatin and LAD remodeling. We observed divergent chromatin trajectories at the nuclear envelope reflective of the Lamin’s distinct roles. Lamin B1 domains exhibited increased local accessibility consistent with age-associated heterochromatin erosion, while Lamin A/C-associated domains physically detach from their scaffold. Ultimately, tATAC-see provides a robust, accessible platform for mechanistic and population-level studies to uncover spatial epigenome dynamics natively in single cells.

This dataset

Open GSE338034 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 GSE338034_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 PRJNA1492147 and SRA study SRP716427. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

15 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 15 sample titles: 15 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

GSM9865082 Human dermal fibroblast, Targeted ATAC-see, IgG, high-salt (300mM NaCl)
GSM9865083 Human dermal fibroblast, Targeted ATAC-see, H3K27ac, low-salt (0mM NaCl)
GSM9865084 Human dermal fibroblast, Targeted ATAC-see, H3K27ac, high-salt (300mM NaCl)
GSM9865085 Human dermal fibroblast, Targeted ATAC-see, H3K4me3, low-salt (0mM NaCl)
GSM9865086 Human dermal fibroblast, Targeted ATAC-see, H3K4me3, high-salt (300mM NaCl)
GSM9865087 BJ fibroblast, Targeted ATAC-see, IgG, low-salt (0mM NaCl)
GSM9865088 BJ fibroblast, Targeted ATAC-see, IgG, high-salt (300mM NaCl)
GSM9865089 BJ fibroblast, Targeted ATAC-see, H3K27ac, low-salt (0mM NaCl)
GSM9865090 BJ fibroblast, Targeted ATAC-see, H3K27ac, high-salt (300mM NaCl)
GSM9865091 BJ fibroblast, Targeted ATAC-see, H3K4me3, low-salt (0mM NaCl)
GSM9865092 BJ fibroblast, Targeted ATAC-see, H3K4me3, high-salt (300mM NaCl)
GSM9865093 BJ fibroblast, Targeted ATAC-see, LaminAC, low-salt (0mM NaCl)
GSM9865094 BJ fibroblast, Targeted ATAC-see, LaminAC, high-salt (300mM NaCl)
GSM9865095 BJ fibroblast, Targeted ATAC-see, LaminB1, low-salt (0mM NaCl)
GSM9865096 BJ fibroblast, Targeted ATAC-see, LaminB1, high-salt (300mM NaCl)

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