GEO series
The cytoskeleton drives abnormal chromatin-lamina interactions in LMNA-deficient cardiomyocytes.
GSE300197
Homo sapiens
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
30 samples
Submitted 2026/03/26
Platform GPL18573Platform GPL30882
Summary
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. 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
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Direct links to NCBI, no account and no request form: the whole study as GSE300197_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 30 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1279218 and SRA study SRP593002. Searching any of these in the dataset finder brings you back here.
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.
11 replicated groups read from 30 sample titles; they account for 26 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9055526 hiPSC, siScr mCh, rep1, tech rep 1
- GSM9055527 hiPSC, siScr mCh, rep2, tech rep 1
- GSM9055528 hiPSC, siScr mCh, rep3, tech rep 1
- GSM9055529 hiPSC, siLMNA mCh, rep1, tech rep 1
- GSM9055530 hiPSC, siLMNA mCh, rep2, tech rep 1
- GSM9055531 hiPSC, siLMNA mCh, rep3, tech rep 1
- GSM9055532 hiPSC, siLMNA mCh, rep4, tech rep 1
- GSM9055533 hiPSC, siScr mCh, rep1, tech rep 2
- GSM9055534 hiPSC, siScr mCh, rep2, tech rep 2
- GSM9055535 hiPSC, siScr mCh, rep3, tech rep 2
- GSM9055536 hiPSC, siLMNA mCh, rep1, tech rep 2
- GSM9055537 hiPSC, siLMNA mCh, rep2, tech rep 2
- GSM9055538 hiPSC, siLMNA mCh, rep3, tech rep 2
- GSM9055539 hiPSC, siLMNA mCh, rep4, tech rep 2
- GSM9055540 hiPSC, siScr mCh, IgG
- GSM9055541 hiPSC, siScr mCh, LMNB1, rep1
- GSM9055542 hiPSC, siScr mCh, LMNB1, rep2
- GSM9055543 hiPSC, siScr mCh, LMNB1, rep3
- GSM9055544 hiPSC, siLMNA mCh, IgG
- GSM9055545 hiPSC, siLMNA mCh, LMNB1, rep1
- GSM9055546 hiPSC, siLMNA mCh, LMNB1, rep2
- GSM9055547 hiPSC, siLMNA mCh, LMNB1, rep3
- GSM9055548 hiPSC, siLMNA DNKASH, IgG
- GSM9055549 hiPSC, siLMNA DNKASH, LMNB1, rep1
- GSM9055550 hiPSC, siLMNA DNKASH, LMNB1, rep2
- GSM9055551 hiPSC, siLMNA DNKASH, LMNB1, rep3
- GSM9437246 hiPSC, siScr DNKASH, IgG
- GSM9437247 hiPSC, siScr DNKASH, LMNB1 rep1
- GSM9437248 hiPSC, siScr DNKASH, LMNB1 rep2
- GSM9437249 hiPSC, siScr DNKASH, LMNB1 rep3
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