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SRX3009247: GSM2705260: ChIP-seq-Input; Homo sapiens; ChIP-Seq
1 ION_TORRENT (Ion Torrent Proton) run: 14M spots, 2G bases, 1.1Gb downloads

Submitted by: NCBI (GEO)
Study: Dysregulation of PDGFRB contributes to the pathogenesis of LMNA-related dilated cardiomyopathy
show Abstracthide Abstract
Purpose: LMNA-DCM accounts for 5-10% of DCM cases and has an age-related penetrance whose onset typically appears between the ages of 30 and 40. However, the precise mechanisms linking the LMNA mutation to increased arrhythmogenicity are still unknown. Methods: We utilized human iPSC-CMs, hESC-CMs, and cardiac tissues with RNA-seq, ChIP-seq, and ATAC-seq technologies. Results: The electrophysiological studies of iPSC-CMs identify the LMNA mutation as a cause of increased arrhythmogenicity in mutant iPSC-CMs through abnormal calcium homeostasis. We find that the mutations in LMNA disrupt the global chromatin conformation, resulting in hyper-activation of the platelet-derived growth factor (PDGF) signaling pathway in LMNA-mutant iPSC-CMs. Inhibition of the PDGF signaling pathway can rescue the arrhythmic phenotype of mutant iPSC-CMs. Conclusions: These findings were corroborated in cardiac tissues from healthy and LMNA-DCM patients, thus confirming a novel mechanism of LMNA-DCM pathogenesis both in vitro and in vivo. Overall design: RNA-seq, ChIP-seq, and ATAC-seq of iPSC-CMs and hESC-CMs
Sample: ChIP-seq-Input
SAMN07357721 • SRS2359332 • All experiments • All runs
Organism: Homo sapiens
Library:
Instrument: Ion Torrent Proton
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: SINGLE
Construction protocol: (RNA-seq) iPSC-CMs were detached from cell culture plates and RNA was extracted using a microRNeasy kit (QIAGEN). (ChIP-seq) Lysates were clarified from sonicated nuclei and LMNA-DNA complexes were isolated with antibody. (ATAC-seq) The samples were extracted as described in previous protocol (Buenrostro J et al. Nat Methods 10: 1213-1218) (RNA-seq) RNA libraries were prepared for sequencing using standard Illumina protocols. (ChIP-seq) ChIP-seq libraries were prepared for sequencing using The Ion Proton™ System protocols. (ATAC-seq) ATAC-seq libraries were prepared for sequencing using TruSeq Library Prep Kit (illumina).
Experiment attributes:
GEO Accession: GSM2705260
Links:
Runs: 1 run, 14M spots, 2G bases, 1.1Gb
Run# of Spots# of BasesSizePublished
SRR583194114,014,6622G1.1Gb2020-07-18

ID:
4283531

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