Vascular endothelial cells differentiation from mouse embryonic stem cells
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ABSTRACT:
PROVIDER: PRJNA374535 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5249580.fastq.gz | Fastqsanger.gz | |||
| SRR5249590.fastq.gz | Fastqsanger.gz | |||
| SRR5249581.fastq.gz | Fastqsanger.gz | |||
| SRR5249591.fastq.gz | Fastqsanger.gz | |||
| SRR5249572.fastq.gz | Fastqsanger.gz |
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Project description:Although differentiation of mice embryonic stem cells into vascular endothelial cells (ECs) gives a model for investigating molecular mechanisms of vascular development in vivo, temporal dynamics of gene expressions and chromatin modifications have not been studied until now. Here, we interrogated transcriptome and two histone modifications, H3K4me3 and H3K27me3, with a genome-wide scale during ECs differentiation and elucidated epigenetic switch peculiar to ECs. We find Gata2, Fli1, Sox7, and Sox18 are master regulators from genetic and epigenetic data, these genes were induced after Etv2 activation. These genes have specific histone modification pattern which is repressed by H3K27me3 modification at Flk-sorted mesoderm and changed to the bivalent (H3K4me3 and H3K27me3 both positive) state rapidly after vascular endothelial cells growth factor (VEGF) stimuli. Using a previously reported ECs differentiation model, we demonstrate that four transcription factors are critical for ECs specific gene expressions and efficient differentiation. Moreover, from knockdown experiments using si-RNA, we discovered these factors inhibited not only TGFβ signaling pathway, that is endothelial mesenchymal transition pathway, but also other near lineage commitment, including blood cells, skeletal muscle cells, vascular smooth muscle cells, and cardiomyocytes. We further identify each factor specific target genes during ECs differentiation by microarray, including both activating and repressing genes. Together, our findings from a detailed epigenetic approach provide a basic understanding temporal regulated chromatin signatures and resulting gene expression profile during ECs commitment, which is applicable to other models of differentiation and production of mature and long lasting ECs for regenerative medicine. Total 17 samples were derived from [1] ES cells, Flk-sorted mesoderm cells, and in the absense or presence of VEGF (6, 12, 24, and 48h) to determine VEGF activated genes during endothelial cells differentiation, [2] control si-RNA, si-Gata2, si-Fli1, si-Sox7, or si-Sox18 transfected cells under VEGF stimuli, [3] control si-RNA or si-Mix (si-Gata2, si-Fli1, si-Sox7, and si-Sox18) transfected cells under VEGF stimuli for the identification of each transcription factor dependent genes during endothelial cells differentiation.
2016-07-18 | E-GEOD-76964 | biostudies-arrayexpress
Project description:Although differentiation of mice embryonic stem cells into vascular endothelial cells (ECs) gives a model for investigating molecular mechanisms of vascular development in vivo, temporal dynamics of gene expressions and chromatin modifications have not been studied until now. Here, we interrogated transcriptome and two histone modifications, H3K4me3 and H3K27me3, with a genome-wide scale during ECs differentiation and elucidated epigenetic switch peculiar to ECs. We find Gata2, Fli1, Sox7, and Sox18 are master regulators from genetic and epigenetic data, these genes were induced after Etv2 activation. These genes have specific histone modification pattern which is repressed by H3K27me3 modification at Flk-sorted mesoderm and changed to the bivalent (H3K4me3 and H3K27me3 both positive) state rapidly after vascular endothelial cells growth factor (VEGF) stimuli. Using a previously reported ECs differentiation model, we demonstrate that four transcription factors are critical for ECs specific gene expressions and efficient differentiation. Moreover, from knockdown experiments using si-RNA, we discovered these factors inhibited not only TGFβ signaling pathway, that is endothelial mesenchymal transition pathway, but also other near lineage commitment, including blood cells, skeletal muscle cells, vascular smooth muscle cells, and cardiomyocytes. We further identify each factor specific target genes during ECs differentiation by microarray, including both activating and repressing genes. Together, our findings from a detailed epigenetic approach provide a basic understanding temporal regulated chromatin signatures and resulting gene expression profile during ECs commitment, which is applicable to other models of differentiation and production of mature and long lasting ECs for regenerative medicine.
2016-07-18 | GSE76964 | GEO
Project description:To investigate gene regulatory dynamics of normal endothelial cell (EC) differentiation at high resolution, an in vitro differentiation system was employed to derive functional vascular ECs from human embryonic stem cells. Human embryonic stem cells, mesodermal cells, and differentiating cells following VEGF-A stimulation at eight time points (1–48 hours), along with internal controls without VEGF-A treatment (referred to as non-ECs), were collected to profile global RNA expression and H3K27ac signals. In addition, in situ Hi-C data were generated for ECs and non-ECs at 24 hours after VEGF-A treatment to characterize global chromatin contact profiles associated with the EC progenitor state.
2026-05-30 | GSE201709 | GEO
Project description:To investigate gene regulatory dynamics of normal endothelial cell (EC) differentiation at high resolution, an in vitro differentiation system was employed to derive functional vascular ECs from human embryonic stem cells. Human embryonic stem cells, mesodermal cells, and differentiating cells following VEGF-A stimulation at eight time points (1–48 hours), along with internal controls without VEGF-A treatment (referred to as non-ECs), were collected to profile global RNA expression and H3K27ac signals. In addition, in situ Hi-C data were generated for ECs and non-ECs at 24 hours after VEGF-A treatment to characterize global chromatin contact profiles associated with the EC progenitor state.
2026-06-01 | GSE328192 | GEO
Project description:To investigate gene regulatory dynamics of normal endothelial cell (EC) differentiation at high resolution, an in vitro differentiation system was employed to derive functional vascular ECs from human embryonic stem cells. Human embryonic stem cells, mesodermal cells, and differentiating cells following VEGF-A stimulation at eight time points (1–48 hours), along with internal controls without VEGF-A treatment (referred to as non-ECs), were collected to profile global RNA expression and H3K27ac signals. In addition, in situ Hi-C data were generated for ECs and non-ECs at 24 hours after VEGF-A treatment to characterize global chromatin contact profiles associated with the EC progenitor state.
2026-06-01 | GSE328191 | GEO
Project description:Although studies of the differentiation from mouse embryonic stem (ES) cells to vascular endothelial cells (ECs) provide an excellent model for investigating the molecular mechanisms underlying vascular development, temporal dynamics of gene expression and chromatin modifications have not been well studied. Herein, using transcriptomic and epigenomic analyses based on the H3K4me3 and H3K27me3 modifications at a genome-wide scale, we analyzed the EC differentiation steps from ES cells and crucial epigenetic modifications unique to ECs. We determined that Gata2, Fli1, Sox7, and Sox18 are master regulators of EC induced following expression of the hemangioblast commitment pioneer factor, Etv2. These master regulator gene loci were repressed by H3K27me3 under the mesoderm period, but rapidly transitioned to the histone modification switching from H3K27me3 to H3K4me3 after treatment with vascular endothelial growth factor (VEGF). SiRNA knockdown experiments indicated that these regulators are indispensable not only for proper EC differentiation but also for blocking the commitment to other closely aligned lineages. Collectively, our detailed epigenetic analysis might provide an advanced model for understanding temporal regulation of chromatin signature and resulting gene expression profiles during EC commitment. These studies would lead the future development of methods to amplify the vascular endothelium for regenerative medicine.
2017-02-13 | GSE94828 | GEO
Project description:To investigate gene regulatory dynamics of normal endothelial cell (EC) differentiation at high resolution, an in vitro differentiation system was employed to derive functional vascular ECs from human embryonic stem cells. Human embryonic stem cells, mesodermal cells, and differentiating cells following VEGF-A stimulation at eight time points (1–48 hours), along with internal controls without VEGF-A treatment (referred to as non-ECs), were collected to profile global RNA expression and H3K27ac signals. In addition, in situ Hi-C data were generated for ECs and non-ECs at 24 hours after VEGF-A treatment to characterize global chromatin contact profiles associated with the EC progenitor state.
2026-06-01 | GSE328193 | GEO
Project description:To investigate gene regulatory dynamics of normal endothelial cell (EC) differentiation at high resolution, an in vitro differentiation system was employed to derive functional vascular ECs from human embryonic stem cells. Human embryonic stem cells, mesodermal cells, and differentiating cells following VEGF-A stimulation at eight time points (1–48 hours), along with internal controls without VEGF-A treatment (referred to as non-ECs), were collected to profile global RNA expression and H3K27ac signals. In addition, in situ Hi-C data were generated for ECs and non-ECs at 24 hours after VEGF-A treatment to characterize global chromatin contact profiles associated with the EC progenitor state.
2026-06-01 | GSE328189 | GEO
Project description:Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish
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Project description:Endothelial differentiation occurs during normal vascular development in the developing embryo. Mouse embryonic stem (ES) cells were used to further define the molecular mechanisms of endothelial differentiation. By flow cytometry a population of VEGF-R2 positive cells was identified as early as 2.5 days after differentiation of ES cells, and a subset of VEGF-R2 + cells, that were CD41+ positive at 3.5 days. A separate population of VEGF-R2+ stem cells expressing the endothelial-specific marker CD144 (VE-cadherin) was also identified at this same time point. Microarray analysis of >45,000 transcripts was performed on RNA obtained from cells expressing VEGF-R2, CD41, and CD144. Keywords: expression analysis
2008-07-14 | GSE10210 | GEO