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Series GSE85330 Query DataSets for GSE85330
Status Public on Jul 10, 2017
Title Genome-wide chromatin accessibility profiling of cardiomyocyte differentiation from human embryonic stem cells and iPS cells (ATAC-seq)
Organism Homo sapiens
Experiment type Other
Summary In this study, time-course genome-wide chromatin accessibility of caidiomyocyte differentiation derived from human hESCs and hiPSCs was profiled. Two hiPSC lines (C15 and C20) and two hESC lines (H1 and H9) were differentiated to caidiomyocytes by ATAC-seq. The cells were collected for ATAC-seq at day 0(undifferentiated cells) day 2 (mesoderm), day 4 (cardiac mesoderm) and day 30 (cardiomyocytes).
 
Overall design Two hiPSC lines (C15 and C20) and two hESC lines (H1 and H9) were grown in 12-well plates with Essential 8 medium (Thermo Fisher Scientific). The cardiomyocyte differentiation was initiated using a monolayer differentiation method with PSC Cardiomyocyte Differentiation kit (Thermo Fisher Scientific). At day 0, 2, 4 and 30 during the differentiation period (before the medium-change on that day), about 50,000 cells were collected for ATAC-seq. For each cell line and each time-point, cells from two independent differentiation wells were used as two biological replicates.
 
Contributor(s) Liu Q, Snyder M
Citation(s) 28663367
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 HL113006 Human Induced Pluripotent Stem Cells for Cardiovascular Disease Modeling STANFORD UNIVERSITY Joseph C. Wu
R01 HL128170 A Systems Biology Approach to Study Cardiac Arrhythmias: iPS Cells and In Silico Modeling STANFORD UNIVERSITY Joseph C. Wu
R24 HL117756 Biorepository of Human iPSCs for Studying Dilated and Hypertrophic Cardiomyopathy STANFORD UNIVERSITY Joseph C. Wu
P50 HG007735 Project 3 STANFORD UNIVERSITY MICHAEL P SNYDER
Submission date Aug 08, 2016
Last update date Oct 11, 2022
Contact name Qing Liu
E-mail(s) liuqingcell@gmail.com
Organization name Clemson University
Department Biological Sciences
Lab Qing Liu
Street address Jordan Hall
City Clemson
State/province SC
ZIP/Postal code 29634
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (32)
GSM2264802 C15_0_1_ATAC-seq
GSM2264803 C15_0_2_ATAC-seq
GSM2264804 C15_2_1_ATAC-seq
This SubSeries is part of SuperSeries:
GSE85332 Genome-wide transcriptomic analysis and chromatin accessibility profiling of cardiomyocyte differentiation from human embryonic stem cells and iPS cells
Relations
BioProject PRJNA338180
SRA SRP081105

Download family Format
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Supplementary file Size Download File type/resource
GSE85330_RAW.tar 29.3 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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