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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of Xenopus animal cap cardiogenesis model to examine immediate early targets of Gata4 and Gata5.

ABSTRACT: Gata factors are amongst the genes expressed early on in the process of cardiogenesis. We used microarrays to examine the immediate early targets of Gata4 and Gata5 in the Xenopus leavis animal cap cardiogenesis model. We hope to use these data to examine the roles of Gata4 and Gata5 in cardiogenesis and also to begin to dissect out the common and distinct targets of Gata4 and Gata5. Experiment Overall Design: Xenopus leavis embryos were injected at the one cell stage with dexamethasone-inducible Gata4 or Gata5 mRNA constructs (to examine endodermal and mesodermal targets) or with Gata4 in the presence of Dkk1 (to examine mesodermal targets.) Embryos were cultured to stage 9, whereupon animal caps were excised and cultured for 2.5 hours in media containing dexamethasone to induce the constructs and cycloheximide to block de novo protein synthesis and thus give only immediate early targets.

ORGANISM(S): Xenopus laevis

SUBMITTER: Kathryn Maddison

PROVIDER: E-GEOD-8496 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Examining the immediate early targets of Gata4 and Gata5.

Project description:Gata factors are amongst the genes expressed early on in the process of cardiogenesis. We used microarrays to examine the immediate early targets of Gata4 and Gata5 in the Xenopus leavis animal cap cardiogenesis model. We hope to use these data to examine the roles of Gata4 and Gata5 in cardiogenesis and also to begin to dissect out the common and distinct targets of Gata4 and Gata5. Keywords: genetic modification, gene overexpresison.

2008-07-15 | GSE8496 | GEO

Xenopus laevis

Project description:Examining the immediate early targets of Gata4 and Gata5.

| PRJNA101597 | ENA

GATA factors efficiently direct cardiac fate from ESCs

Project description:Gata5 efficiently promotes cardiomyocyte fate from murine ESCs.By removing serum from the culture conditions, GATA4 and GATA6 are each also able to efficiently promote cardiogenesis in ESC derivatives, with some distinctions. Thus, GATA factors can function in ESC derivatives upstream of other cardiac transcription factors to direct specification of progenitors with cardiac potential. We used microarray to compared the global gene expression of Gata5-induced cardiac cells with other growth factor directed ESC-derived cardiac cells iGata5 ESCs were induced with doxycycline at day 4 and harvested at day16 for RNA extraction and hybridization on Affymetrix microarrays.

2013-02-02 | E-GEOD-43831 | biostudies-arrayexpress

GATA factors efficiently direct cardiac fate from ESCs

2013-02-02 | GSE43831 | GEO

Gene expression profiles in in vitro cardiogenesis.

Project description:We performed time-dependent, genome-wide analysis to explore gene expression profiles during in vitro cardiogenesis from embryonic stem cells to cardiac progenitor cells. Total RNA was extracted from undifferentiated stem cells, early mesodermal cells, cardiac mesodermal cells and cardiac progenitor cells. As a result of cluster analysis, Cited gene family was considered as candidate genes in cardiogenesis. Cited4 gene expression was specific for early cardiogenesis and Cited4 functioned as a cell cycle controling factor for early cardiac progenitor cells. Embryoid body was formed as in vitro cardiogenesis. Total RNA was extracted from Rex1-positive undifferentiated stem cells at day 0, Bra-positive early mesodermal cells at day 4.5, Flk1-positive cardiac mesodermal cells at day 4.5 and Nkx2.5-positive cardiac progenitor cells at day 7.5.

2016-03-31 | E-GEOD-63069 | biostudies-arrayexpress

Transcription profiling of Xenopus laevis early embryos to investigate the roles of Nodal, Mixer and Sox17 in endoderm formation

Project description:A conserved molecular pathway has emerged controlling endoderm formation in Xenopus zebrafish and mice. Key genes in this pathway include Nodal ligands and transcription factors of the Mix-like paired homeodomain class, Gata4-6 zinc finger factors and Sox17 HMG domain proteins. While a linear epistatic pathway has been proposed, the precise hierarchical relationships between these factors and their downstream targets are largely unresolved. Here we used a combination of microarray analysis and loss-of-function experiments to examine the global regulatory network controlling Xenopus endoderm formation. We identified over 300 transcripts enriched in the gastrula endoderm, including most of the known endoderm regulators as well as over a hundred uncharacterized genes. Surprisingly only 10% of the endoderm transcriptome is regulated as predicted by the current linear model. We find that Nodals, Mixer and Sox17 have both shared and distinct sets of downstream targets and that a number of unexpected autoregulatory loops exist between Sox17 and Gata4-6, Sox17 and Bix1, 2, 4 and between Sox17 and Xnr4. We find that Mixer does not function primarily via Sox17 as previously proposed. This data provides a new insight into the complexity of endoderm formation and will serve as valuable resource for establishing a complete endoderm gene regulatory network. Experiment Overall Design: Define a set of transcripts with enriched expression in the gastrula endoderm of the Xenopus laevis embryo and determine how these are regulated by nodal signaling, Mixer and Sox17 using loss-of-function experiments. For more specific details see Sinner et al., (2006) Global analysis of the transcriptional network controlling Xenopus endoderm formation.

2007-10-05 | E-GEOD-4448 | biostudies-arrayexpress

MicroRNA expression signatures for gata4/5/6 knocking down in zebrafish

Project description:Previous works showed that gata4/5/6 lie at the hierarchical apex of the regulatory network of the hemangioblast formation and primitive myelopoiesis in zebrafish. To explore the roles of miRNAs in zebrafish primitive myelopoiesis, we employed deep sequencing to analyze the difference of miRNA expression profiles between gata4/5/6 knockdown embryos (gata5/6 morphants) and control embryos.

2021-08-14 | GSE118850 | GEO

Gene expression profiles in in vitro cardiogenesis.

2016-03-31 | GSE63069 | GEO

Global analysis of the transcriptional network controlling Xenopus endoderm formation

Project description:A conserved molecular pathway has emerged controlling endoderm formation in Xenopus zebrafish and mice. Key genes in this pathway include Nodal ligands and transcription factors of the Mix-like paired homeodomain class, Gata4-6 zinc finger factors and Sox17 HMG domain proteins. While a linear epistatic pathway has been proposed, the precise hierarchical relationships between these factors and their downstream targets are largely unresolved. Here we used a combination of microarray analysis and loss-of-function experiments to examine the global regulatory network controlling Xenopus endoderm formation. We identified over 300 transcripts enriched in the gastrula endoderm, including most of the known endoderm regulators as well as over a hundred uncharacterized genes. Surprisingly only 10% of the endoderm transcriptome is regulated as predicted by the current linear model. We find that Nodals, Mixer and Sox17 have both shared and distinct sets of downstream targets and that a number of unexpected autoregulatory loops exist between Sox17 and Gata4-6, Sox17 and Bix1, 2, 4 and between Sox17 and Xnr4. We find that Mixer does not function primarily via Sox17 as previously proposed. This data provides a new insight into the complexity of endoderm formation and will serve as valuable resource for establishing a complete endoderm gene regulatory network. Keywords: Embryonic, Development. Endoderm, Xenopus, nodal, Sox17, Mixer, microarray, gene regulatory network

2006-03-11 | GSE4448 | GEO

Essential and unexpected role of YY1 to promote mesodermal cardiac differentiation

Project description:Rationale: Cardiogenesis is regulated by a complex interplay between transcription factors and chromatin-modifying enzymes. However, little is known about how these interactions regulate the transition from mesodermal precursors to cardiac progenitor cells (CPCs). Objective: To identify novel regulators of mesodermal cardiac lineage commitment. Methods and Results: We performed a bioinformatic-based transcription factor-binding site analysis on upstream promoter regions of genes that are enriched in ES cell-derived CPCs. From 32 candidate transcription factors screened, we found that YY1, a repressor of sarcomeric gene expression, is present in CPCs in vivo. Interestingly, we uncovered the ability of YY1 to transcriptionally activate Nkx2.5, a key marker of early cardiogenic commitment. YY1 regulates Nkx2.5 expression via a 2.1 kb cardiac-specific enhancer as demonstrated by in vitro luciferase-based assays and in vivo chromatin immunoprecipitation (ChIP) and genome-wide sequencing analysis. Furthermore, the ability of YY1 to activate Nkx2.5 expression depends on its cooperative interaction with GATA4 at a nearby chromatin. Cardiac mesoderm-specific loss-of-function of YY1 resulted in early embryonic lethality. This was corroborated in vitro by ES cell-based assays where we show that the over-expression of YY1 enhanced the cardiogenic differentiation ES cells into CPCs in a cell autonomous manner. Conclusion: These results demonstrate an essential and unexpected role for YY1 to promote cardiogenesis as a transcriptional activator of Nkx2.5 and other CPC-enriched genes. We report the identification of putative YY1 target genes in cardiac progenitor cells (CPCs). Two samples of independently FACS-purified eGFP+ CPCs were examined against the input.

2013-06-01 | E-GEOD-35370 | biostudies-arrayexpress

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