GEO DataSets

(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) 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) 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) In amphibian embryo, the animal cap explants treated with activin A, which is a member of TGF-β family protein, have a potent of Spemann-Mangold organizer-like activities, leading the induction of mesendodermal tissue. We report the temporal RNA expression profile of the mesendodermal cell lineage induced by activin A to Xenopus animal cap explants, which have multipotency. Depending on the duration of activin A treatment to animal cap, dynamic changes of gene expressions were observed. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21248

15 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) To identify asymmetrically localized maternal mRNAs along the animal-vegetal axis in cleavage Xenopus embryos, we isolated animal and vegetal blastomeres at 8-cell stage, extracted the maternal mRNA respectively and analyzed them by RNA-seq technology. We identified 43 maternal transcripts significantly enriched in the vegetal region (FDR<0.05) by R/Bioconductor package DESeq

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14834

4 Samples

Download data: TXT

(Submitter supplied) Transcript abundances were examined in single Capitella teleta embryos at three timepoints: 8-cell, 16-cell, and 32-cell stage. 

Organism:

Capitella teleta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28854

12 Samples

Download data: CSV, 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) The goal of this study is to investigate the molecular mechanism of lhx1 on regulation of pronephros formation during the early embryonic development. In the vertebrate embryo the kidney is derived from the intermediate mesoderm. The LIM-class homeobox transcription factor lhx1 is expressed early in the intermediate mesoderm and is one of the first genes to be expressed in the nephric mesenchyme. The animal cap cells can be induced by treatment of activin and retinoic acid to differentiate into pronephros tissue. more...

Organism:

Xenopus laevis

Type:

Expression profiling by array

Platform:

GPL1318

12 Samples

Download data: CEL, CHP

(Submitter supplied) We report on the implications of genetic KO versus MO-mediated KD of the mesoderm-specifying Brachyury paralogues in the Western clawed frog Xenopus tropicalis. While both KO and KD embryos fail to activate the same core gene regulatory network, resulting in virtually identical morphological defects, embryos injected with control or target MOs also show a systemic GC content dependent immune response and many off-target splicing defects.

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23182

36 Samples

Download data: GFF3, TXT

(Submitter supplied) Geminin cooperates with Polycomb to restrain multi-lineage commitment in the early embryo: Transient maintenance of a pluripotent embryonic cell population followed by the onset of multi-lineage commitment is a fundamental aspect of development. However, molecular regulation of this transition is not well characterized in vivo. Here we demonstrate that the nuclear protein Geminin is required to restrain commitment and spatially restrict mesoderm, endoderm, and non-neural ectoderm to their proper locations in the Xenopus embryo. more...

Organism:

Xenopus laevis

Type:

Expression profiling by array

Platform:

GPL1318

12 Samples

Download data: CEL

(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

(Submitter supplied) Left-right axis determination is a fundamental and conserved developmental process, with consequences for human pathology. At the molecular level, this process requires at least two centers of nodal-type TGFbeta signals: the first center, containing nodal/Xn Microarrays were used to determine differences in gene expression in posterior mesoderm of Xenopus embryos. We compared controls and Derriere depleted embryos. more...

Organism:

Xenopus laevis

Type:

Expression profiling by array

Platform:

GPL1318

2 Samples

Download data

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL24247 GPL13112

32 Samples

Download data: BW

(Submitter supplied) Despite the fundamental roles to cell fates determination in all metazoans, the mechanism by which the TGF-β family signaling is interpreted into spatial and temporal manner and multiple cell fates is still elusive. The cell context dependent function of TGF-β signaling largely relies on the transcriptional regulation centered by SMAD proteins. Here, we discovered that the DNA-repair related protein, HMCES contributes to early development by maintaining the nodal/activin or BMP signaling related transcriptome homeostasis. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

26 Samples

Download data: CSV, TXT

(Submitter supplied) Despite the fundamental roles to cell fates determination in all metazoans, the mechanism by which the TGF-β family signaling is interpreted into spatial and temporal manner and multiple cell fates is still elusive. The cell context dependent function of TGF-β signaling largely relies on the transcriptional regulation centered by SMAD proteins. Here, we discovered that the DNA-repair related protein, HMCES contributes to early development by maintaining the nodal/activin or BMP signaling related transcriptome homeostasis. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: BW

(Submitter supplied) The purpose of this study is to examine transciptome dynamics at high resolution to 4 separate lineages. Here we provide snapshots of the Xenopus laevis transcriptome at Nieuwkoop and Faber stages 9., 10, 10.5, 11, 12 and 13 for the epidmeral, neural, ventral mesoderm and endoderm lineage

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21248 GPL22393

74 Samples

Download data: CSV