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Mechanistic and Epigenetic Partitioning of Lamina-Associated Chromatin Revealed by a Genome-Wide Imaging Screen

GSE303855 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 45 samples Submitted 2025/08/27 Platform GPL24676Platform GPL30882Platform GPL18573Platform GPL34284
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 45 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
45 samples: 38 distinct titles, 3 of them repeatedGroups 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
Mechanistic and Epigenetic Partitioning of Lamina-Associated Chromatin Revealed by a Genome-Wide Imaging ScreenbioRxiv : the preprint server for biology · 2025
Summary (written by the submitters)
The nuclear periphery is a key site for heterochromatin organization in eukaryotic cells, where lamina-associated domains (LADs) promote transcriptional repression and genome stability. Despite their importance, the mechanisms governing LAD positioning in human cells remain poorly understood. To this end, we performed a genome-wide imaging-based screen and identified 101 genes critical for perinuclear LAD localization, with a significant enrichment for RNA-binding proteins.
Read the full summary ↓
Among these, hnRNPK emerged as a key regulator, required for the perinuclear positioning of approximately 70% of LADs genome-wide. Loss of hnRNPK led to their repositioning away from the nuclear periphery without altering global heterochromatin state, yet resulted in misexpression of genes within these domains. Notably, hnRNPK-sensitive LADs are uniquely enriched for H3K27me3, distinguishing them from hnRNPK-insensitive LADs that are predominantly marked by H3K9me3. These findings reveal mechanistically distinct classes of LADs and suggest that specialized pathways underlie their spatial organization. Our results uncover a pivotal role for hnRNPK in regulating chromatin architecture and highlight the broader diversity of LAD tethering mechanisms.
Published in
Mechanistic and Epigenetic Partitioning of Lamina-Associated Chromatin Revealed by a Genome-Wide Imaging Screen
Walsh PJ, Kraeutler EB, Linares-Saldana R et al. · bioRxiv : the preprint server for biology 2025 · PMID 40832213 · doi:10.1101/2025.08.13.670143
This dataset
Open GSE303855 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 GSE303855_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 PRJNA1297768 and SRA study SRP604067. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40832213) ↗
Study design
38 distinct titles, 3 of them repeated
RNA, siControl, ×4 RNA, siHNRNPK, ×4 siControl, ×2

How we read this: Read from 45 sample titles: 38 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

+ 5 more — browse all 45 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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