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The cytoskeleton drives abnormal chromatin-lamina interactions in LMNA-deficient cardiomyocytes.

GSE300197 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 30 samples Submitted 2026/03/26 Platform GPL18573Platform GPL30882
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 30 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
30 samples: 11 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
The cytoskeleton contributes to abnormal genome-lamina interactions in LMNA-deficient cardiomyocytesThe Journal of cell biology · 2026
Summary (written by the submitters)
Spatial organization of chromatin at the nuclear lamina is critical for cellular identity, but mechanisms governing genome-lamina interactions remain unresolved. In particular, it remains unclear if and how mechanical inputs impact genome-lamina interactions. We modeled aspects of laminopathies via siRNA-mediated lamin A/C (LMNA) knockdown to examine how the nuclear lamina and cytoskeleton contribute to loss of lamina-associated domain (LAD) organization.
Read the full summary ↓
Genomics and imaging analyses reveal spatial positioning of LADs with a specific molecular signature are particularly vulnerable to LMNA reduction. Further, a subset of these LADs retain their lamina-association with either concomitant disruption of the Linker of Nucleoskeleton and Cytoskeleton complex or microtubule depolymerization. Conversely, microtubule stabilization phenocopies spatial positioning changes observed in LMNA-knockdown cells. These data suggest peripheral chromatin organization is regulated by the balance of nuclear lamina and cytoskeletal interactions across the nuclear membrane. In the context of a compromised nuclear lamina, such as LMNA reduction, the cytoskeleton contributes to loss of peripheral chromatin organization.
Published in
The cytoskeleton contributes to abnormal genome-lamina interactions in LMNA-deficient cardiomyocytes
Shen KM, Shields EJ, Barka V et al. · The Journal of cell biology 2026 · PMID 41891953 · doi:10.1083/jcb.202506137
This dataset
Open GSE300197 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 GSE300197_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 PRJNA1279218 and SRA study SRP593002. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41891953) ↗
Study design
11 conditions, mostly in duplicate
hiPSC, siScr mCh, LMNB1, ×3 hiPSC, siLMNA mCh, LMNB1, ×3 hiPSC, siLMNA DNKASH, LMNB1, ×3 hiPSC, siScr DNKASH, LMNB1 ×3 hiPSC, siScr mCh, rep1, tech ×2 hiPSC, siScr mCh, rep2, tech ×2 hiPSC, siScr mCh, rep3, tech ×2 hiPSC, siLMNA mCh, rep1, tech ×2 +7 more

Supports a between-group comparison across 26 samples.

How we read this: 11 replicated groups read from 30 sample titles; they account for 26 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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