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Series GSE79882 Query DataSets for GSE79882
Status Public on Jun 21, 2016
Title Genome-wide map of DNA 5-Hydroxymethylcytosine in cardiomyocytes isolated from E14.5, Neonatal, Adult, pressure-overload (TAC), sh-control and sh-TET2 isolated cardiomyocytes
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary Methylation at 5-cytosine (5-mC) is a fundamental epigenetic DNA modification associated recently with cardiac disease. In contrast, the role of 5-hydroxymethylcytosine (5-hmC) – 5-mC’s oxidation product – is unknown in the context of the heart. Here, we assess the hydroxymethylome in embryonic, neonatal, adult and hypertrophic mouse cardiomyocytes, showing that dynamic modulation of hydroxymethylated DNA is associated with specific transcriptional networks during heart development and failure. DNA hydroxymethylation marks gene bodies of highly expressed genes and distal regulatory regions with enhanced activity. Pathological hypertrophy is characterized by a partial shift towards a fetal-like distribution pattern.
We further demonstrate a regulatory function of TET2 and provide evidence that the expression of key cardiac genes, such as Myh7 is modulated by TET2-mediated 5-hmC deposition on the gene body and at enhancers in cardiac cells.
We thus provide the first genome-wide analysis of 5-hmC in the cardiomyocyte, and establish the role of this epigenetic modification in heart development and disease
Overall design Profiling of 5hmC in E14.5, Neonatal, Adult, pressure-overload (TAC), sh-control and sh-TET2 isolated cardiomyocytes
Contributor(s) Kunderfranco P, Greco CM, Condorelli G
Citation(s) 27489048
Submission date Apr 04, 2016
Last update date May 15, 2019
Contact name Paolo Kunderfranco
Organization name Humanitas Research Hospital
Department Research
Lab Bioinformatic Unit
Street address Via Rita Levi Montalcini 4
City Pieve Emanuele
State/province Milano
ZIP/Postal code 20090
Country Italy
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (22)
GSM2107805 5hmC_E14.5_rep1_hMeDIPSeq
GSM2107806 5hmC_E14.5_rep2_hMeDIPSeq
GSM2107807 5hmC_Neonatal_rep1_hMeDIPSeq
This SubSeries is part of SuperSeries:
GSE66847 Dynamics of 5-hmC in cardiac maturation and hypertrophy
BioProject PRJNA317319
SRA SRP072831

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Supplementary file Size Download File type/resource
GSE79882_5hmC_Adult.bigWig 39.9 Mb (ftp)(http) BIGWIG
GSE79882_5hmC_E14.5.bigWig 37.2 Mb (ftp)(http) BIGWIG
GSE79882_5hmC_Neonatal.bigWig 40.5 Mb (ftp)(http) BIGWIG
GSE79882_5hmC_TAC.bigWig 41.0 Mb (ftp)(http) BIGWIG
GSE79882_5hmC_sh-TET2.bigWig 37.5 Mb (ftp)(http) BIGWIG
GSE79882_5hmC_sh-control.bigWig 37.9 Mb (ftp)(http) BIGWIG
GSE79882_Differential_Analysis-1.xlsx 2.4 Mb (ftp)(http) XLSX
GSE79882_Differential_Analysis-2.xlsx 11.3 Mb (ftp)(http) XLSX
GSE79882_INPUT_DNA_Adult.bigWig 37.0 Mb (ftp)(http) BIGWIG
GSE79882_INPUT_DNA_E14.5.bigWig 37.1 Mb (ftp)(http) BIGWIG
GSE79882_INPUT_DNA_Neonatal.bigWig 37.1 Mb (ftp)(http) BIGWIG
GSE79882_INPUT_DNA_TAC.bigWig 36.7 Mb (ftp)(http) BIGWIG
GSE79882_INPUT_DNA_sh-TET2.bigWig 31.4 Mb (ftp)(http) BIGWIG
GSE79882_INPUT_DNA_sh-control.bigWig 32.0 Mb (ftp)(http) BIGWIG
GSE79882_RAW.tar 12.3 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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