TETs during directed differentiation of human embryonic stem cells to cardiomyocyte
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ABSTRACT:
PROVIDER: PRJNA776283 | ENA |
REPOSITORIES: ENA
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Project description:We interrogated the transcriptome using RNA-seq at several stages of an mouse embryonic stem cell to cardiomyocyte directed differentiation protocol. These four stages represent timepoints when differentiating cultures are enriched for embryonic stem cells (ESC), mesodermal cells (MES), cardiac precursors (CP), or cardiomyocytes (CM) respectively. This study revealed many dynamic patterns of mRNAs and long non-coding RNAs (lncRNAs) and identified groups of genes with similar expression patterns during differentiation. RNA-seq analysis of global RNA levels at 4 stages of directed cardiac differentiation of mouse embryonic stem cells. Each stage in biological duplicates
2013-06-15 | E-GEOD-47948 | biostudies-arrayexpress
Project description:We interrogated the genome-wide occupancy of histone modifications and RNA polymerase II at several stages of an mouse embryonic stem cell to cardiomyocyte directed differentiation protocol. These four stages represent timepoints when differentiating cultures are enriched for embryonic stem cells (ESC), mesodermal cells (MES), cardiac precursors (CP), or cardiomyocytes (CM) respectively. This study revealed many dynamic patterns of histone modifications during differentiation that are coordinated with stage-specific gene expression including a novel preactivation chromatin pattern found at genes associated with cardiac function. In addition, this study identified distal enhancer elements and enriched transcription factor motifs within enhancer regions for each stage of differentiation, which were used to predict novel transcription regulatory networks. ChIP-seq analysis of histone modifications and RNA polymerase II at 4 stages of directed cardiac differentiation of mouse embryonic stem cells. Each stage in biological duplicate or triplicate
2013-06-15 | E-GEOD-47949 | biostudies-arrayexpress
Project description:We interrogated the transcriptome using RNA-seq at several stages of an mouse embryonic stem cell to cardiomyocyte directed differentiation protocol. These four stages represent timepoints when differentiating cultures are enriched for embryonic stem cells (ESC), mesodermal cells (MES), cardiac precursors (CP), or cardiomyocytes (CM) respectively. This study revealed many dynamic patterns of mRNAs and long non-coding RNAs (lncRNAs) and identified groups of genes with similar expression patterns during differentiation.
2013-06-15 | GSE47948 | GEO
Project description:miRNA plays a critical role in a wide variety of biological processes Profiling miRNA expression during the differentiation of embryonic stem cells will help us to understand the regulation pathway of differentiation, therefore to explain disease mechanisms and to find possible therapeutical targets. In this study miRNA expressions were profiled during cardiomyocyte-specific differentiation of murine embryonic stem cells with high-throughput microarray platforms.
2011-12-31 | GSE24066 | GEO
Project description:miRNA plays a critical role in a wide variety of biological processes Profiling miRNA expression during the differentiation of embryonic stem cells will help us to understand the regulation pathway of differentiation, therefore to explain disease mechanisms and to find possible therapeutical targets. In this study miRNA expressions were profiled during cardiomyocyte-specific differentiation of murine embryonic stem cells with high-throughput microarray platforms. Two high throughput platforms (Affymetrix and Febit) were involved in miRNA profiling in order to compare the effect of platform on miRNA profiling result as well as to increase the plausibility of target miRNA identification. Four time points (day 0, day 12, day 19, day 26) which correspond to different stages during cardiac-specific differentiation were chosen for the miRNA profiling study.
2011-12-31 | E-GEOD-24066 | biostudies-arrayexpress
Project description:Human embryonic stem cells (hESCs) can be used to generate scalable numbers of cardiomyocytes for studying cardiac biology, disease modeling, drug screens, and potentially for regenerative therapies. Directed differentiation protocols for cardiomyocytes using hESCs are well established, but methods to isolate highly pure population of cardiomyocytes are limited. Reporter cell lines can be valuable for purification and visualization of cells for such applications. We used CRISPR/Cas9 in hESCs to place an mCherry reporter gene into the MYH6 locus, facilitating a simple method to purify cardiomyocytes. MYH6:mCherry positive cells express atrial and ventricular markers and display a range of cardiomyocyte action potential morphologies. At 20 days of differentiation, MYH6:mCherry+ cells show features characteristic of human cardiomyocytes and can be used successfully to monitor drug-induced cardiotoxicity and oleic acid-induced cardiomyocyte arrhythmia. The MYH6:mCherry hESC reporter line should serve as a useful tool for disease modeling and drug development relevant to cardiomyocyte biology.
2019-01-01 | GSE111365 | GEO
Project description:During in vitro differentiation, pluripotent stem cells undergo extensive remodeling of their gene expression profiles. While studied extensively at the transcriptome level, much less is known about protein dynamics, which might differ significantly from their mRNA counterparts. Here, we present deep proteome-wide measurements of protein levels during the differentiation of embryonic stem cells.
2017-01-10 | MSV000080461 | MassIVE
Project description:We interrogated the genome-wide occupancy of histone modifications and RNA polymerase II at several stages of an mouse embryonic stem cell to cardiomyocyte directed differentiation protocol. These four stages represent timepoints when differentiating cultures are enriched for embryonic stem cells (ESC), mesodermal cells (MES), cardiac precursors (CP), or cardiomyocytes (CM) respectively. This study revealed many dynamic patterns of histone modifications during differentiation that are coordinated with stage-specific gene expression including a novel preactivation chromatin pattern found at genes associated with cardiac function. In addition, this study identified distal enhancer elements and enriched transcription factor motifs within enhancer regions for each stage of differentiation, which were used to predict novel transcription regulatory networks.
2013-06-15 | GSE47949 | GEO
Project description:The integration of cell metabolism with signalling pathways, transcription factor networks and epigenetic mediators is critical in coordinating molecular and cellular events during embryogenesis. Induced pluripotent stem cells (IPSCs) are an established model for embryogenesis, germ layer specification and cell lineage differentiation, advancing the study of human embryonic development and the translation of innovations in drug discovery, disease modelling and cell-based therapies. The metabolic regulation of IPSC pluripotency is mediated by balancing glycolysis and oxidative phosphorylation, but there is a paucity of data regarding the influence of individual metabolite changes during cell lineage differentiation. We used <sup>1</sup>H NMR metabolite fingerprinting and footprinting to monitor metabolite levels as IPSCs are directed in a three-stage protocol through primitive streak/mesendoderm, mesoderm and chondrogenic populations. Metabolite changes were associated with central metabolism, with aerobic glycolysis predominant in IPSC, elevated oxidative phosphorylation during differentiation and fatty acid oxidation and ketone body use in chondrogenic cells. Metabolites were also implicated in the epigenetic regulation of pluripotency, cell signalling and biosynthetic pathways. Our results show that <sup>1</sup>H NMR metabolomics is an effective tool for monitoring metabolite changes during the differentiation of pluripotent cells with implications on optimising media and environmental parameters for the study of embryogenesis and translational applications.
2023-05-24 | MTBLS4854 | MetaboLights
Project description:The differentiation to cardiomyocytes is a prerequisite and an important part of heart development. A good understanding of the complicated cardiomyocyte differentiation process benefits cardiogenesis study. Embryonic stem cells (ESCs), cell lines with infinite ability to proliferate and to be differentiated into all cell types of the adult body, are important research tools for investigation of differentiation and meanwhile good models for developmental research. In the current study, genome-wide gene expression of ESCs is profiled through high throughput platform during cardiomyocyte-specific differentiation and maturation. Gene expression patterns of undifferentiated ESCs and ESC-derived cardiomyocytes provide a global overview of genes involved in cardiomyocyte-specific differentiation, whereas marker gene expression profiles of both ESC-related genes and cardiac-specific genes presented the expression pattern shift during differentiation in a pure ESC-derived cardiomyocyte cell culture system. Transgenic mouse ESC clone with M-NM-1-MHCM-bM-^@M-^SPacM-bM-^@M-^SIRESM-bM-^@M-^SEGFP vector containing the EGFP gene and the PuromycinR (Pac) cassette under control of the cardiac M-NM-1-myosin heavy chain (M-NM-1-MHC) promoter was cultured and induced into differentiation. Puromycin was applied after differentiation start to enable cardiomyocyte-specific differentiation. Cells were harvested at 4 time points after differentiation start (day0, day12, day19 and day26). Two biological replicates were taken for every time point.
2014-09-25 | E-GEOD-58300 | biostudies-arrayexpress