GEO DataSets

(Submitter supplied) We examined the role of Taf15 in in gastrula and neurula stage Xenopus tropicalis embryos.

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21874

13 Samples

Download data: CSV

(Submitter supplied) Here, we use scRNA-seq to expand our understanding of the vertebrate corneal epithelium in an amphibian model, having undertaken a comprehensive characterization of cellular and transcriptional heterogeneity to identify novel corneal marker genes.

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28901

1 Sample

Download data: MTX, TSV

(Submitter supplied) In animal oocytes and early embryos, mRNA poly(A)-tail length strongly influences translational efficiency (TE), but later in development this coupling between tail length and TE disappears. Here, we elucidate how this coupling is first established and why it disappears. Overexpressing cytoplasmic poly(A)-binding protein (PABPC) in frog oocytes specifically improved translation of short-tailed mRNAs, thereby diminishing coupling between tail length and TE. more...

Organism:

Xenopus laevis; Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL16791 GPL17021 GPL18936

79 Samples

Download data: TXT

(Submitter supplied) Hi-C on reconstituted mitotic chromosomes in Xenopus system in IGG or specific depleted egg extracts to study to role of condensin and linker histone in chromosome condensation

Organism:

Xenopus laevis

Type:

Other

Platform:

GPL22393

25 Samples

Download data: MCOOL

(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) Limb regeneration, while observed lifelong in salamanders, is restricted to pre-metamorphic stages in Xenopus laevis frogs. After amputation, post-metamorphic frogs form a blastema that grows only an unsegmented cartilage rod. Whether this loss is due to systemic factors such as the immune system or due to an intrinsic incapability of cells to form competent stem cells has been unclear. Here, we use genetic fate mapping to establish that, as in axolotl, connective tissue (CT) cells form the post-metamorphic frog blastema. more...

Organism:

Ambystoma mexicanum; Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27159 GPL22800 GPL28901

18 Samples

Download data: MTX, TSV

(Submitter supplied) This study was designed to identify Xenopus laevis genes that respond to stimulation with an immune agonist, poly(I:C).

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28901

12 Samples

Download data: TXT

(Submitter supplied) We investigated genome folding across the eukaryotic tree of life. We find four general manifestations of genome organization at chromosome-scale that each emerge and disappear repeatedly over the course of evolution. The submission represents chromosome-length Hi-C contact maps, architecture type and homolog separation analyses for 26 species across the tree of life, representing all subphyla of chordates, all 7 extant vertebrate classes, and 7 out of 9 major animal phyla, as well as plants and fungi.

Organism:

Arachis hypogaea; Agaricus bisporus; Branchiostoma lanceolatum; Xenopus laevis; Notamacropus eugenii; Pygocentrus nattereri; Cristatella mucedo; Clonorchis sinensis; Chiloscyllium punctatum; Triticum aestivum; Caenorhabditis elegans; Aplysia californica; Aedes aegypti; Culex quinquefasciatus; Homo sapiens; Muntiacus reevesi; Muntiacus muntjak; Strongylocentrotus purpuratus; Ciona intestinalis; Pleurobrachia bachei; Acropora millepora; Python bivittatus; Saccharomyces cerevisiae; Drosophila melanogaster; Gallus gallus; Hypsibius dujardini; Lethenteron camtschaticum

Type:

Other

30 related Platforms

32 Samples

Download data: BEDPE, FASTA, HIC, VCF, WIG

(Submitter supplied) Xenopus embryonic ectodermal cells are responsive to various inducing factors. Mesoderm is specified and patterned by extracellular factors including FGF, Nodal, BMP and Wnt families. Pinhead is another secreted protein implicated in mesoderm formation. We found that Pinhead physically interacts with and antagonizes ADMP (anti-dorsalizing morphogenetic protein) that acts as BMP-like protein to promote ventral mesoderm formation. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

8 Samples

Download data: XLSX

(Submitter supplied) Spemann-Mangold organizer-specific transcription factors (TFs), Otx2, Lim1/Lhx1, and Gsc, are essential for embryonic head specification. However, the molecular mechanisms by which those TFs interact with the genome to direct head formation are largely unknown. Here we employed ChIP-seq and RNA-seq approaches in Xenopus tropicalis gastrulae and found that occupancy of the corepressor, TLE/Groucho, is a better indicator of tissue-specific cis-regulatory modules (CRMs) than the coactivator p300, during early embryonic stages. more...

Organism:

Xenopus tropicalis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24898

11 Samples

Download data: BROADPEAK, BW, NARROWPEAK

(Submitter supplied) Sequencing of cDNAs derived from RNA transcripts from nine adult Xenopus tropicalis tissues

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29986

9 Samples

Download data: XLSX

(Submitter supplied) Our experiment revealed that TR double knockout completely blocks intestinal length shortening, larval cell death, and adult stem cell development, demonstrating a requirement for TR in adult intestinal development.

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21875

12 Samples

Download data: TXT

(Submitter supplied) Adenosine N6-methylation (m6A) is one of the most pervasive mRNA modifications, and yet the physiological significance of m6A removal (demethylation) remains elusive. Here we report the m6A demethylase FTO functions as a conserved regulator of motile ciliogenesis. Mechanistically, FTO demethylates and thereby stabilizes the mRNA encoding the master ciliary transcription factor FOXJ1. Depletion of Fto in Xenopus laevis embryos caused widespread motile cilia defects, and Foxj1 was identified as one of the major phenocritical targets. more...

Organism:

Xenopus laevis

Type:

Other

Platform:

GPL22426

4 Samples

Download data: TXT

(Submitter supplied) To analyze the limits of embryo robustness, several different types of surgeries were performed on the anterior-posterior neural axis of Xenopus laevis embryos. Our RNA-Seq data suggests a model in which aspects of early neural plasticity are associated with unique pathways and their associated genes. The transcriptome analysis reveals several combinations of pathways and genes that incorporate and heal foreign tissue, but also re-pattern the anterior-posterior axis. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29672

74 Samples

Download data: TXT

(Submitter supplied) Background: Variation in locomotor capacity among animals often reflects adaptations to different environments. Despite evidence that physical performance is heritable, the molecular basis of locomotor performance and performance trade-offs remains poorly understood. In this study we identify the genes, signaling pathways, and regulatory processes responsible for the trade-off between burst performance and endurance observed in Xenopus allofraseri, using a transcriptomic approach. more...

Organism:

Xenopus allofraseri

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29147

8 Samples

Download data: TXT

(Submitter supplied) Gene Ontology analyses of autism spectrum disorders (ASD) risk genes have repeatedly highlighted synaptic function and transcriptional regulation as key points of convergence. However, these analyses rely on incomplete knowledge of gene function across brain development. Here we leverage Xenopus tropicalis to study in vivo ten genes with the strongest statistical evidence for association with ASD. All genes are expressed in developing telencephalon at time points mapping to human mid-prenatal development, and mutations lead to an increase in the ratio of neural progenitor cells to maturing neurons, supporting previous in silico systems biological findings implicating cortical neurons in ASD vulnerability, but expanding the range of convergent functions to include neurogenesis. more...

Organism:

Xenopus tropicalis; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23182 GPL23934

39 Samples

Download data

(Submitter supplied) Gene Ontology analyses of autism spectrum disorders (ASD) risk genes have repeatedly highlighted synaptic function and transcriptional regulation as key points of convergence. However, these analyses rely on incomplete knowledge of gene function across brain development. Here we leverage Xenopus tropicalis to study in vivo ten genes with the strongest statistical evidence for association with ASD. All genes are expressed in developing telencephalon at time points mapping to human mid-prenatal development, and mutations lead to an increase in the ratio of neural progenitor cells to maturing neurons, supporting previous in silico systems biological findings implicating cortical neurons in ASD vulnerability, but expanding the range of convergent functions to include neurogenesis. more...

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23182

27 Samples

Download data: CSV

(Submitter supplied) Background: The efficient regenerative abilities at larvae stages followed by a non-regenerative response after metamorphosis in froglets makes Xenopus an ideal model organism to understand the cellular responses leading to spinal cord regeneration. Methods: We compared the cellular response to spinal cord injury between the regenerative and non-regenerative stages of Xenopus laevis. For this analysis, we used electron microscopy, immunofluorescence and histological staining of the extracellular matrix. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22393

2 Samples

Download data: TXT

(Submitter supplied) We investigated the multi- and transgenerational impact of BaP on Xenopus females following F0 generation exposure from the tadpole to the mature adult stage at a concentration (50 ng.L-1). 5 females from F1 and F2 generations by parentale xposure conditions (control vs BaP) were used for studying liver transcriptome by RNAseq. RNA-seq libraries were sequenced on an illumina GAIIx sequencer as 75bp single reads

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24898

21 Samples

Download data: TAB

(Submitter supplied) Purpose: Study the developing neural cell fate of the D1 blastomere in the 8-cell embryo. Determine what transcripts are dependant on cell/cell signaling and which are inherit to the single cell and do not depend on the rest of the embryo. Methods: D1 blastomere was either injected with fluorescent dye or explanted away from the developing embryo. Transcript profile was taken at 7 time points: 8-cell, 16-cell, 32-cell, blastula, gastrula, early neurula, and mid/late neurula. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21248

42 Samples

Download data: TXT