Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Xenopus laevis

ABSTRACT: Genome-wide binding pattern of β-catenin during Xenopus gastrulation

PROVIDER: PRJNA310141 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR3133151.fastq.gz	Fastqsanger.gz
	SRR3133152.fastq.gz	Fastqsanger.gz
	SRR3133153.fastq.gz	Fastqsanger.gz
	SRR3133154.fastq.gz	Fastqsanger.gz
	SRR3133155.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Transcriptome analysis of Wnt knockdown embryos reveals candidate canonical Wnt/β-catenin target genes during Xenopus laevis gastrulation

Project description:The canonical Wnt/β-catenin signaling pathway plays multiple roles during Xenopus gastrulation, including posteriorization of the neural plate, patterning of the mesoderm, and induction of the neural crest. Wnt signaling stabilizes β-catenin, which then activates target genes. However, few targets of this signaling pathway that mediate early developmental processes are known. Here we sought to identify transcriptional targets of the Wnt/β-catenin signaling pathway using a genome-wide approach.

2016-04-25 | GSE77364 | GEO

Wnt/β-catenin in Xenopus laevis gastrulation

Project description:Wnt/β-catenin in Xenopus laevis gastrulation

| PRJNA310142 | ENA

Xenopus laevis

Project description:Transcriptome analysis of Wnt knockdown embryos reveals candidate canonical Wnt/β-catenin target genes during Xenopus laevis gastrulation

| PRJNA310139 | ENA

Genome-wide binding pattern of β-catenin during Xenopus gastrulation

2016-04-25 | GSE77363 | GEO

Spemann organizer transcriptome induction by early β-Catenin, Wnt, Nodal and Siamois signals in Xenopus laevis

Project description:During Xenopus gastrulation, dorsal stabilization of β-Catenin at the earliest stage and subsequent target genes expression are critical for dorsal-ventral axis determination. However, many β-Catenin targets that mediate this process are still unkown. Here through RNA-seq analysis of β-Catenin knockdown embryos and self-regulating dorsal and ventral half embryos at early gastrula, we define an early β-Catenin gene signature that is downregulated by β-Catenin MO and enriched in dorsal gastrula tissues. This gene signature includes classic Spemann organizer genes, as well as other novel genes. Further analyses revealed that the early β-Catenin gene signature is positively correlated with LiCl treated, Wnt8 and Siamois mRNA-induced genes, consistent with their early role in dorsal-ventral axis formation. Our results also show that St 10.5 is the appropriate stage to uncover β-Catenin target genes that regulate dorsal-ventral patterning than St 9. Meanwhile, the multi-growth factor antagonist Cerberus inhibits part of the early β-Catenin gene signature and also controls the expression of a unique set of genes. Our findings provide new insight into the pivotal role of β-catenin in dorsal-ventral axis determination and can serve a fruitful resource for this field.

2017-03-15 | GSE93195 | GEO

Xenopus laevis

Project description:Spemann organizer transcriptome induction by early β-Catenin, Wnt, Nodal and Siamois signals in Xenopus laevis

| PRJNA360282 | ENA

Xenopus laevis

Project description:The polycomb repressive complex PRC2 regulates proliferation and neurogenesis in the Xenopus retina, and is governed by Wnt/beta-catenin signaling

| PRJNA205635 | ENA

Identification of specific xWNT5A and xWNT11specific target genes in dorsal marginal zone explants of Xenopus laevis

Project description:The non-canonical signaling branches of the WNT signaling network realize different movements during Xenopus laevis gastrulation movements. The WNT5A branch is responsible for the constriction whereas the WNT11 branch triggers the elongation of the dorsal mesoderm. Therefore we used dorsal marginal zone explants which undergo convergent extension movements as readout system to identify differences in gene expression pattern between the WNT5A and WNT11 signaling branch via microarray analysis.We identified pbk as specific WNT5A target gene and rab11fip5 as specific WNT11 target gene. Therefore the non-canonical branches of the WNT signaling network do not only regulate cell behavior but also the expression of different target genes.

2016-06-21 | GSE81924 | GEO

Xenopus laevis

Project description:Zygotic expression of Exostosin1 (Ext1) is required for establishment of dorsal-ventral pattern in Xenopus

| PRJNA223418 | ENA

Genome-wide analysis of dorsal and ventral transcriptomes of the Xenopus laevis gastrula

Project description:RNA sequencing has allowed high-throughput screening of differential gene expression in many tissues and organisms. Xenopus laevis is a classical embryological and cell-free extract model system, but its genomic sequence had been lacking due to difficulties arising from allotetraploidy. There is currently much excitement surrounding the release of the completed X. laevis genome (version 9.1) by the Joint Genome Institute (JGI), which provides a platform for genome-wide studies. Here we present a deep RNA-seq dataset of transcripts expressed in dorsal and ventral lips of the early Xenopus gastrula embryo using the new genomic information, which was further annotated by blast searches against the human proteome. Overall, our findings confirm previous results from differential screenings using other methods that uncovered classical dorsal genes such as Chordin, Noggin and Cerberus, as well as ventral genes such as Sizzled, Ventx, Wnt8 and BAMBI. Complete transcriptome-wide Excel files of mRNAs suitable for data mining are presented, which include many novel dorsal- and ventral-specific genes. RNA-seq was very quantitative and reproducible, and allowed us to define dorsal and ventral signatures useful for gene set expression analyses (GSEA). As an example of a new gene, we present here data on an organizer-specific secreted protein tyrosine kinase known as Pkdcc (protein kinase domain containing, cytoplasmic) or Vlk (vertebrate lonesome kinase). Overexpression experiments indicate that Pkdcc can act as a negative regulator of Wnt/ β-catenin signaling independently of its kinase activity. We conclude that RNA-seq in combination with the Xenopus laevis complete genome now available provides a powerful tool for unraveling cell-cell signaling pathways during embryonic induction.

2016-06-20 | GSE75278 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data