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Gene expression of human embryonic stem cells during endoderm differentiation

ABSTRACT: Gene expression of human embryonic stem cells during endoderm differentiation

PROVIDER: PRJNA713297 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13924900_1.fastq.gz	Fastqsanger.gz
	SRR13924900_2.fastq.gz	Fastqsanger.gz
	SRR13924901_1.fastq.gz	Fastqsanger.gz
	SRR13924901_2.fastq.gz	Fastqsanger.gz
	SRR13924902_1.fastq.gz	Fastqsanger.gz

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Dynamic proteomic profiling of extra-embryonic endoderm differentiation in mouse embryonic stem cells

Project description:During mammalian pre-implantation development, the cells of the blastocyst’s inner cell mass differentiate into the epiblast and primitive endoderm lineages, which give rise to the fetus and extra-embryonic tissues, respectively. Extra-embryonic endoderm differentiation can be modeled in vitro by induced expression of GATA transcription factors in mouse embryonic stem cells. Here we use this GATA-inducible system to quantitatively monitor the dynamics of global proteomic changes during the early stages of this differentiation event and also investigate the fully differentiated phenotype, as represented by embryo-derived extra-embryonic endoderm (XEN) cells. Using mass spectrometry-based quantitative proteomic profiling with multivariate data analysis tools, we reproducibly quantified 2,336 proteins across three biological replicates and have identified clusters of proteins characterized by distinct, dynamic temporal abundance profiles. We first used this approach to highlight novel marker candidates of the pluripotent state and extra-embryonic endoderm differentiation. Through functional annotation enrichment analysis, we have shown that the downregulation of chromatin-modifying enzymes, the re-organization of membrane trafficking machinery and the breakdown of cell-cell adhesion are successive steps of the extra-embryonic differentiation process. Thus, applying a range of sophisticated clustering approaches to a time-resolved proteomic dataset has allowed the elucidation of complex biological processes which characterize stem cell differentiation and could establish a general paradigm for the investigation of these processes.

2015-06-13 | PXD001901 | Pride

Gene expression of human embryonic stem cells during endoderm differentiation

Project description:Using a well-established human definitive endoderm differentiation system, we can analyze the gene expression dynamic of human embryonic stem cells (hESCs) during endoderm differentiation. Samples from hESCs, D2 cells and definitive endoderm cells (DE) were collected for deep sequencing with two replicates for each sample. Differentially expressed genes analysis showed that endodermal genes were induced during endoderm differentiation.

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microRNA Profiling during endoderm differentiation from mouse embryonic stem cells

Project description:microRNA Profiling during endoderm differentiation from mouse embryonic stem cells

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microRNA Profiling during endoderm differentiation from mouse embryonic stem cells

Project description:The role of microRNAs (miRNAs) during mouse early development, especially in endoderm germ layer formation, is largely unknown. Here, using miRNA profiling, we discovered that miR-124a negatively regulates endoderm lineage commitment in mouse embryonic stem cells (mESCs). We showed that miR-124a inhibits endoderm differentiation in vitro through targeting the 3’ untranslated region (UTR) of Sox17 and Gata6, revealing the existence of an interplay between miR-124a and Sox17/Gata6 transcription factors in hepato-specific gene regulation. Besides, we proposed an in vivo system that utilizes teratoma to evaluate the functional role of miRNA in lineage specification. We demonstrated that ectopic expression of miR-124a in teratomas suppressed endoderm and mesoderm lineage differentiation while augmented the differentiation of ectoderm lineage. Collectively, our findings suggested that miR-124a plays a significant role in mESCs lineage commitment.

2019-12-31 | GSE131337 | GEO

Arginine methylation of METTL14 promotes RNA N6-methyladenosine modification and endoderm differentiation of mouse embryonic stem cells

Project description:m6A is the most abundant modification of mRNA in mammals and plays an important role in human development and disease. METTL14 is a key component of m6A methyltransferase complex. The project showed that its post-translational arginine methylation can regulate the generation of m6A and the endoderm differentiation of mouse embryonic stem cells, indicating its essential function in the normal development of embryos.

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Endoderm differentiation of human embryonic stem cells (hESCs) [RNA-Seq]

Project description:Purpose: The goal of this study is to identify the whole-genome transcriptome profiling of differentially expressed genes during human embryonic stem cell differentiation. Methods: Triplicate RNA profiles were generated from hESCs and induced endoderm cells, by deep sequencing with Illumina NextSeq 500. Results: We identified 6320 genes differentially expressed between hESCs and induced endoderm cells, with foldchange  1.5 and P < 0.05. Conclusion: Our study confirms that endodermal gene were dramatically induced during endoderm differentiation.

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Embryonic stem sell differentiation time course

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A proteomic roadmap of ribosome heterogeneity during human embryonic stem cell differentiation

Project description:Recent findings suggest that the ribosome itself modulates gene expression. However, whether ribosomes change composition across cell types to control cell fate remains unknown. To determine the magnitude of ribosome heterogeneity and its functional contribution to cell fate specification, we measured ribosomal protein abundance in actively translating ribosomes by quantitative mass spectrometry on a day-by-day basis as human embryonic stem cells differentiate in a step-wise fashion down endoderm and mesoderm lineages. We identified numerous core ribosomal proteins (RPs) as changing significantly in abundance in actively translating ribosomes during cell fate specification, including progressive decreases in ribosome incorporation for several ribosomal proteins during mesoderm differentiation. We further traced ribosome composition changes at the cytoplasmic, whole-cell, and mRNA transcript levels and identified multiple mechanisms regulating actively translating ribosome composition. These findings reveal extensive ribosomal remodeling during differentiation, suggesting that individual ribosomal components may have cell type-specific specialized translation functions.

2022-09-19 | PXD032904 | Pride

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