Transcriptomics,Genomics

Dataset Information

145

Genome-wide transcriptomic analysis of cardiomyocyte differentiation from human embryonic stem cells and iPS cells (RNA-seq)


ABSTRACT: In this study, time-course transcriptome profiling of caidiomyocyte differentiation derived from human hESCs and hiPSCs was investigated. Two hiPSC lines (C15 and C20) and two hESC lines (H1 and H9) were differentiated to caidiomyocytes. The cells were collected for RNA-seq analysis at day0(undifferentiated cells) day2 (mesoderm), day4 (cardiac mesoderm) and day30 (cardiomyocytes) using Illumina HiSeq 2000 sequencer. 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), cells were collected using Accutase (Thermo Fisher Scientific), and then store in -80C till RNA isolation. For each cell line and each time-point, cells from two independent differentiation wells were used as two biological replicates. RNA-seq libriries were sequenced by a HiSeq 2000 sequencer (Illumina) with 2 X 101 cycles. RNA-seq fastq data were aligned with Tophat (version 2.0.9) to GRCh39/hg19 Homo sapiens reference genome from the UCSC Genome Browser. Cuffdiff of the Cufflinks software (version 2.2.1) and GRCh39/hg19 Homo sapiens gtf file from UCSC Genome Browser were used to estimate abundances of transcripts and generate their FPKM values. Table of FPKM values of all samples were created using cummeRbund package in R.

INSTRUMENT(S): Illumina HiSeq 2000 (Homo sapiens)

SUBMITTER: Qing Liu  

PROVIDER: GSE85331 | GEO | 2017-07-10

SECONDARY ACCESSION(S): PRJNA338181

REPOSITORIES: GEO

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Publications

Genome-Wide Temporal Profiling of Transcriptome and Open Chromatin of Early Cardiomyocyte Differentiation Derived From hiPSCs and hESCs.

Liu Qing Q   Jiang Chao C   Xu Jin J   Zhao Ming-Tao MT   Van Bortle Kevin K   Cheng Xun X   Wang Guangwen G   Chang Howard Y HY   Wu Joseph C JC   Snyder Michael P MP  

Circulation research 20170629 4


RATIONALE:Recent advances have improved our ability to generate cardiomyocytes from human induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs). However, our understanding of the transcriptional regulatory networks underlying early stages (ie, from mesoderm to cardiac mesoderm) of cardiomyocyte differentiation remains limited. OBJECTIVE:To characterize transcriptome and chromatin accessibility during early cardiomyocyte differentiation from hiPSCs and hESCs. METHODS AND  ...[more]

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