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Series GSE55611 Query DataSets for GSE55611
Status Public on Mar 06, 2014
Title Cell type-specific epigenomic analysis in the developing heart
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The molecular mechanisms governing heart development provide an important framework to understand congenital heart disease. The embryonic vertebrate heart tube develops an atrioventricular canal that divides the atrial and ventricular chambers, forms atrioventricular conduction tissue and organizes valve development. To better understand the molecular mechanism underlying atrioventricular canal versus chamber myocardium expression, a double-reporter transgenic mouse line was generated in which the expression of EGFP (green fluorescent protein) and Katushka (red fluorescent protein) are selectively expressed in the atrioventricular canal and in the chamber myocardium, respectively. We assessed the genome-wide H3K27ac pattern in isolated embryonic AV canal and in chamber cardiomyocytes, respectively.
 
Overall design EGFP and Katushka-positive cells were purified by FACS and fixed. ChIP was performed with the truemicro ChIP (Diagenode) according to the manufacturer’s protocol using the H3K27ac antibody (abcam ab4729). Chipped DNA were subjected to library preparation using the 5500 Series SOLiD™ Systems ample preparation kit (Applied Biosystems) according to manufactures recommendations and sequenced using the 5500 wildfire system (SOLiD).
 
Contributor(s) Stefanovic S, van Duijvenboden K, Barnett P, Christoffels VM
Citation(s) 24770533
Submission date Mar 05, 2014
Last update date Jul 10, 2017
Contact name Vincent M. Christoffels
E-mail v.m.christoffels@amc.nl
Phone +31205667821
Organization name Academic Medical Center Amsterdam
Department Anatomy, Embryology & Physiology
Street address Meibergdreef 15
City Amsterdam
State/province Noord-Holland
ZIP/Postal code 1105 AZ
Country Netherlands
 
Platforms (1)
GPL16790 AB 5500 Genetic Analyzer (Mus musculus)
Samples (2)
GSM1340163 H3K27ac_chambers_ChIP-seq
GSM1340164 H3K27ac_avc_ChIP-seq
Relations
BioProject PRJNA240217
SRA SRP039436

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE55611_RAW.tar 543.7 Mb (http)(custom) TAR (of BIGWIG, TXT)
Raw data are available in SRA
Processed data provided as supplementary file

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