GEO DataSets

(Submitter supplied) Studies of the Xenopus organizer have laid the foundation for our understanding of the conserved signaling pathways that pattern vertebrate embryos during gastrulation. Here, we use this wealth of knowledge as leverage in the design and analysis of a genomic visualization of organizer-related gene transcription. Using ectopic expression of the two major activities of the organizer, BMP and Wnt inhibition, as well as endogenous tissues, we generate a focused set of samples that represent different aspects of organizer signaling. more...

Organism:

Xenopus laevis

Type:

Expression profiling by array

Dataset:

GDS2301

Platform:

GPL1318

20 Samples

Download data: CEL

Analysis of stage 10 early and stage 11.5 late gastrula embryos ectopically expressing Noggin, Dkk-1, or both to induce different aspects of organizer activity. The organizer patterns vertebrate embryos during gastrulation. Results provide insight into organizer function during gastrulation.

Organism:

Xenopus laevis

Type:

Expression profiling by array, count, 4 agent, 2 development stage, 4 other, 2 tissue sets

Platform:

GPL1318

Series:

GSE3368

20 Samples

Download data: CEL

(Submitter supplied) 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. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

7 Samples

Download data: TXT, XLSX

(Submitter supplied) Exostosin 1 (Ext1) is a glycosyltransferase involved in the biosynthesis of the extracellular matrix Heparan Sulfate Proteoglycan (HSPG). Knockdown of Ext1 caused gastrulation defects and formation of an abnormal body axis. Since ext1 has been implicated as an indirect contributor to multiple signaling pathways in vertebrate development, microarray was used to identify genes expressed in gastrulae that would be affected by a reduction in ext1 expression. more...

Organism:

Xenopus laevis

Type:

Expression profiling by array

Platform:

GPL10756

6 Samples

Download data: CEL

(Submitter supplied) Embryos were injected with either control or Activin antisense morpholino oligonucleotides and harvested at Stage 10.5 for RNA analysis. Keywords: Knock-down analysis

Organism:

Xenopus laevis; Xenopus tropicalis

Type:

Expression profiling by array

Platform:

GPL3728

6 Samples

Download data: GPR

(Submitter supplied) 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. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

46 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17682

12 Samples

Download data: BED, TXT

(Submitter supplied) 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.

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

6 Samples

Download data: TXT

(Submitter supplied) 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.

Organism:

Xenopus laevis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17682

6 Samples

Download data: BED

(Submitter supplied) The transcription factors Mixer and Sox17beta have well characterized roles in endoderm specification during Xenopus embryogenesis. In order to more thoroughly understand the mechanisms by which these endodermal regulators act, we expressed Mixer and Sox17beta in naïve ectodermal tissue and, using oligonucleotide-based microarrays, compared their genomic transcriptional profile to that of unaffected tissue. more...

Organism:

Xenopus laevis

Type:

Expression profiling by array

Dataset:

GDS1715

Platform:

GPL1318

6 Samples

Download data: CEL

Analysis of naïve ectodermal tissue excised from embryos injected with Mixer or Sox17beta mRNA. Mixer and Sox17beta are important in endoderm specification during embryogenesis. Results provide insight into the molecular mechanisms underlying the regulation of endoderm development.

Organism:

Xenopus laevis

Type:

Expression profiling by array, transformed count, 3 genotype/variation sets

Platform:

GPL1318

Series:

GSE3334

6 Samples

Download data: CEL

(Submitter supplied) To identify genes with different expression levels in Xenopus laevis embryos of different sizes, RNAseq of middle gastrula RNA of the wild-size and artificially prepared half-size embryos was done. As a result, several genes with drastically different expression between these two types of embryos were found.

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18936

6 Samples

Download data: CSV, TXT

(Submitter supplied) We studied the transcriptomic differences between ventralised and dorsalised Xenopus tropicalisembryos as a result of UV irradiation and LiCl treatment, respectvely. Both manipulations have been used by researchers to perturb the establishment of the dorso-ventral axis, however the whole transcriptomes of the resulting embryos have never been fully characterised or compared. We show that ventralized embryos are transcriptionally closer related to untreated embryos than dorsalized embryos. more...

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21875

15 Samples

Download data: GTF, TXT

(Submitter supplied) Animal embryos have the remarkable property of self-organization. Over 125 years ago Hans Driesch separated the two blastomeres of sea urchin embryos and obtained twins, in what was the foundational experiment of experimental embryology. Since then, embryonic twinning has been obtained experimentally in many animals by diverse methods. In a recent study, we developed bisection methods that generate identical twins reliably from Xenopus blastula embryos. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

30 Samples

Download data: XLSX

(Submitter supplied) To determine if Xnr2 induces mesodermal genes expression in ectodermal tissues

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18936

2 Samples

Download data: TXT

(Submitter supplied) We applied chromatin accessibility and single cell transcriptome analyses to explore the emergence of heterogeneity and underlying gene-regulatory mechanisms during early gastrulation in Xenopus. TF activity was inferred by integrating chromatin accessibility and single cell transcriptomics. Our results show that combinatorial activity of zygotically expressed transcription factors acts on maternally-regulated accessible chromatin to induce organizer gene expression.

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21875 GPL24884

132 Samples

Download data: BED, TAB, TBI, TSV

(Submitter supplied) During the maternal-to-zygotic transition (MZT), maternal RNAs are actively degraded and replaced by newly-synthesized zygotic transcripts in a highly coordinated manner. However, it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here, through genome-wide profiling of RNA abundance and 3′ modification, we show that uridylation is induced at the onset of maternal mRNA clearance. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

20 Samples

Download data: CSV

(Submitter supplied) To adapt to its changing dietary environment, the digestive tract is extensively remodeled from the embryo to the adult during vertebrate development. Xenopus laevis metamorphosis is an excellent model system for studying mammalian gastrointestinal development and is used to determine the genes and signaling programs essential for intestinal development and maturation. The metamorphosing intestine can be divided into four distinct developmental time points and these were analyzed with X. more...

Organism:

Xenopus laevis

Type:

Expression profiling by array

Platform:

GPL10302

11 Samples

Download data: TXT

(Submitter supplied) Dorsal-ventral (DV) patterning of the Drosophila embryo is initiated by Dorsal, a sequence specific transcription factor distributed in a broad nuclear gradient in the precellular embryo.Previous studies have identified as many as 70 protein-coding genes and one microRNA gene that are directly or indirectly regulated by this gradient. A gene regulation network, or circuit diagram, including the functional interconnections among 40 Dorsal target genes and 20 associated tissue-specific enhancers, has been determined for the initial stages of gastrulation. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by genome tiling array

Platform:

GPL3923

6 Samples

Download data: CEL, TXT

(Submitter supplied) Identification of genes enriched in the presumptive primary mouth. Dissected tissues from the primary mouth anlage and two other anterior regions for comparison, the anterior dorsal and ventral plus cement gland.

Organism:

Xenopus laevis

Type:

Expression profiling by array

Platform:

GPL1318

9 Samples

Download data: CEL, CHP