GEO DataSets

(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) 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:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17682

6 Samples

Download data: BED

(Submitter supplied) In the embryo, inductive cues are interpreted by competent tissues in a spatially and temporally restricted manner, and the mechanisms for the loss of responsiveness are not well understood. To test the hypothesis that loss of competence is associated with changes in chromatin accessibility, we adapted the assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) for use in Xenopus laevis to evaluate genome-wide changes in chromatin accessibility in early and late gastrula stages. more...

Organism:

Xenopus laevis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22393

6 Samples

Download data: BED

(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) The aim of our study is to identify direct target genes of Wnt/β-catenin signaling operating in gastrula-stage X. tropicalis embryos. We characterized the genomic loci bound by the Wnt signaling downstream component β-catenin in intact X. tropicalis gastrulae using ChIP-seq. We also determined the normal mRNA expression profile in control (uninjected and control-MO-injected) embryos and altered mRNA expression profiles in two experimental samples: embryos where endogenous wnt8a function was knocked down with wnt8a MO, and where we experimentally re-instated Wnt8a expression with a DNA construct (pCSKA-wnt8a) in the same wnt8a knock down.

Organism:

Xenopus tropicalis

Type:

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

Platforms:

GPL15472 GPL18470

14 Samples

Download data: BW, TXT

(Submitter supplied) We examined the location of ETS2 biding in gastrula stage Xenopus embryos to identify direct transcriptional targets of the FGF signaling pathway.

Organism:

Xenopus laevis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22393

4 Samples

Download data: BED, BW

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

Organism:

Xenopus laevis

Type:

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

Platform:

GPL18936

57 Samples

Download data

(Submitter supplied) Digestive system development is orchestrated by combinatorial signaling interactions between endoderm and mesoderm, but how they are integrated in the genome is poorly understood. Here we identified the Xenopus foregut and hindgut progenitor transcriptomes, which are largely conserved with mammals. Using RNA-seq and ChIP-seq we show that BMP/Smad1 regulates dorsal-ventral gene expression in both the endoderm and mesoderm, whereas Wnt/b-catenin acts as a genome-wide toggle between foregut and hindgut programs. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18936

37 Samples

Download data: XLSX

(Submitter supplied) Digestive system development is orchestrated by combinatorial signaling interactions between endoderm and mesoderm, but how they are integrated in the genome is poorly understood. Here we identified the Xenopus foregut and hindgut progenitor transcriptomes, which are largely conserved with mammals. Using RNA-seq and ChIP-seq we show that BMP/Smad1 regulates dorsal-ventral gene expression in both the endoderm and mesoderm, whereas Wnt/b-catenin acts as a genome-wide toggle between foregut and hindgut programs. more...

Organism:

Xenopus laevis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18936

20 Samples

Download data: BED

(Submitter supplied) The process that partitions the nascent vertebrate central nervous system into forebrain, midbrain, hindbrain, and spinal cord after neural induction is of fundamental interest in developmental biology, and is known to be dependent on Wnt/beta-catenin signaling at multiple steps. Neural induction specifies neural ectoderm with forebrain character that is subsequently posteriorized by graded Wnt signaling: embryological and mutant analyses have shown that progressively higher levels of Wnt signaling induce progressively more posterior fates. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

23 Samples

Download data: TXT

(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) 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) In Xenopus, establishment of the anterior-posterior axis involves two key signalling pathways, canonical Wnt and Nodal-related TGF-β. There are also a number of transcription factors that feedback upon these pathways. The homeodomain protein Hex, an early marker of anterior positional information, acts as a transcriptional repressor suppressing induction and propagation of the Spemman organiser while specifying anterior identity. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL81

44 Samples

Download data

(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) Single-cell technology was used to investigate dynamic transcriptional changes in the blastula and gastrula of Drosophila embryos. Cells from embryo of stages 5 to 9 were isolated and subjected to library construction. Mesoderm cells were labeled with mCD8-GFP utilizing the GAL/UAS system. PCA identified 12 unique cell clusters that represent the blastoderm, mesoderm, endoderm and ectoderm anlage, primordia, and a sampling of differentiating cell types. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21306 GPL25244

3 Samples

Download data: H5

(Submitter supplied) Leptin binding to the leptin receptor (LepR) causes rapid signaling to the nucleus. We investigated the early (2 hr) transcriptional response to acute leptin injection (intracerebroventricular) in the preoptic area/hypothalamus/pituitary of Xenopus tadpoles.

Organism:

Xenopus laevis

Type:

Expression profiling by array

Platform:

GPL10756

6 Samples

Download data: CEL