GEO DataSets

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

Organism:

Xenopus tropicalis

Type:

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

Platforms:

GPL23182 GPL30018

21 Samples

Download data: NARROWPEAK, TAB

(Submitter supplied) Evolutionary novelties entail the origin of morphologies that enable new functions. These features can arise through changes to gene function and regulation. One important noveltyis the fused rod at the end of the vertebral column in anurans, the urostyle. This feature is composed of a coccyx and an ossifying hypochord, and both structures ossify during metamorphosis. These experiments reveal that the coccyx and hypochord have two different molecular signatures. more...

Organism:

Xenopus tropicalis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30018

3 Samples

Download data: NARROWPEAK

(Submitter supplied) Evolutionary novelties entail the origin of morphologies that enable new functions. These features can arise through changes to gene function and regulation. One important noveltyis the fused rod at the end of the vertebral column in anurans, the urostyle. This feature is composed of a coccyx and an ossifying hypochord, and both structures ossify during metamorphosis. These experiments reveal that the coccyx and hypochord have two different molecular signatures. more...

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23182

18 Samples

Download data: TAB

(Submitter supplied) 5-methylcytosine (5mC) is an established epigenetic mark in vertebrate genomic DNA, but whether its oxidation intermediates formed during TET-mediated DNA demethylation possess an instructive role of their own that is also physiologically relevant remains unresolved. Here, we reveal a 5-formylcytosine (5fC) nuclear chromocenter, which transiently forms during zygotic genome activation (ZGA) in Xenopus and mouse embryos. more...

Organism:

Xenopus tropicalis

Type:

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

Platforms:

GPL24884 GPL21875

32 Samples

Download data: BW, TSV

(Submitter supplied) To analyze the role of Tet proteins on global gene expression, we profiled the transcriptome of Xenopus tropicalis blastula embryos upon knockdown of Tet2 and Tet3 using Morpholino antisense oligonucleotides.

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24884

6 Samples

Download data: TSV

(Submitter supplied) The oxC-marks 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) are iterative oxidation products of 5-methylcytosine (5mC) which might also function as epigenetic marks on their own to regulate gene expression. To characterize the genomic profiles of oxC-marks in Xenopus tropicalis blastula embryos, we carried out DIP-seq using 5mC, 5hmC, 5fC and 5caC antibodies.

Organism:

Xenopus tropicalis

Type:

Methylation profiling by high throughput sequencing; Other

Platform:

GPL21875

18 Samples

Download data: BW

(Submitter supplied) To correlate 5fC clusters with RNA polymerase III occupancy genome-wide, we carried out Pol III ChIP-seq profiling in Xenopus tropicalis blastula embryos.

Organism:

Xenopus tropicalis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24884

8 Samples

Download data: BW

(Submitter supplied) ChIP-seq and RNA-seq analyses to understand the establishment of the cis-regulatory mark H3K4me1 during early embryogenesis.

Organism:

Xenopus tropicalis

Type:

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

Platforms:

GPL23182 GPL30018

26 Samples

Download data: NARROWPEAK, TXT

(Submitter supplied) The regulatory system of erythropoiesis through erythropoietin (EPO) and its receptor (EPOR) is essential for vertebrates' life. In humans, EPO affects the erythroid progenitors and stimulates proliferation and differentiation. The EPO-EPOR axis is mainly mediated by the JAK2-STAT5 pathway. After terminal maturation, erythrocytes lost EPOR expression; however, erythrocytes of amphibian Xenopus tropicalis maintain EPOR expression even after their terminal maturation. more...

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30213

15 Samples

Download data: CSV

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

Organism:

Xenopus laevis; Xenopus tropicalis

Type:

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

Platforms:

GPL30018 GPL21875 GPL18936

35 Samples

Download data

(Submitter supplied) Neural crest cells exemplify cellular diversification from a multipotent progenitor population. However, the full sequence of molecular choices governing the emergence of neural crest heterogeneity from the ectoderm remains elusive. Gene regulatory networks govern these steps of embryonic development and cell specification towards definitive neural crest. Here, we combine ultra-dense single cell transcriptomes with machine-learning strategies and experimental validation to provide a comprehensive gene regulatory network driving vertebrate neural crest fate diversification, from induction to early migration stages. more...

Organism:

Xenopus laevis; Xenopus tropicalis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21875 GPL18936

23 Samples

Download data: CSV

(Submitter supplied) Neural crest cells exemplify cellular diversification from a multipotent progenitor population. However, the full sequence of molecular choices governing the emergence of neural crest heterogeneity from the ectoderm remains elusive. Gene regulatory networks govern these steps of embryonic development and cell specification towards definitive neural crest. Here, we combine ultra-dense single cell transcriptomes with machine-learning strategies and experimental validation to provide a comprehensive gene regulatory network driving vertebrate neural crest fate diversification, from induction to early migration stages. more...

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30018

2 Samples

Download data: PKL, TSV

(Submitter supplied) Nager syndrome is a rare craniofacial and limb disorder characterized by midface retrusion, micrognathia, absent thumbs, and radial hypoplasia. This disorder results from haploinsufficiency of SF3B4 (splicing factor 3b, subunit 4) a component of the pre-mRNA spliceosomal machinery. The spliceosome is a complex of RNA and proteins that function together to remove introns and join exons from transcribed pre-mRNA. more...

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30018

17 Samples

Download data: TXT

(Submitter supplied) Cancer is often caused by mutations in many genes. Although genomic studies have identified many oncogenes and tumor suppressor genes, gene sets involved in tumorigenesis remain poorly understood. Xenopus, a genus of aquatic frogs, is a useful model to identify gene sets because it can be genetically and experimentally analyzed. So we analyzed gene expression in tumor tissues of three individuals in Xenopus tropicalis and compared with that in normal tissues.

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30018

12 Samples

Download data: CSV

(Submitter supplied) Activation of Map kinase/Erk signalling downstream of fibroblast growth factor (Fgf) tyrosine kinase receptors regulates gene expression required for mesoderm induction and patterning of the anteroposterior axis during Xenopus development. We have proposed that a subset of Fgf target genes are activated in the embyo in response to inhibition of a transcriptional repressor. Here we investigate the hypothesis that Cic (Capicua), which was originally identified as a transcriptional repressor negatively regulated by receptor tyrosine kinase/Erk signalling in Drosophila, is involved in regulating Fgf target gene expression in Xenopus. more...

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33301

9 Samples

Download data: TXT

(Submitter supplied) LCM-RNA-Seq data obtained from Xenopus tropicalis chondrocytes and osteoblasts at different stages of differentiation -immature chondrocytes and mature (hypertrophic) chondrocytes- isolated from the ceratohyal. Osteoblasts isolated from the mandible (dentary bone).

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21875

9 Samples

Download data: TXT

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

Organism:

Xenopus tropicalis

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL30018

25 Samples

Download data

(Submitter supplied) Here we present clear patterns of age-associated changes in DNA methylation in the aquatic vertebrate species Xenopus tropicalis. We selected approximately 3500 sites highly correlated with age from WGBS data from 9 frogs of 3 different age groups (young, approx. 1 year old; mature, approx. 5 years old; old, approx. 9 years old - GSE221656) and designed probes for the development of cost effective targeted bisulfite sequencing (TBSeq) assay. more...

Organism:

Xenopus tropicalis

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL30018

16 Samples

Download data: TXT

(Submitter supplied) Here we present clear patterns of age-associated changes in DNA methylation in the aquatic vetebrate species Xenopus tropicalis. We generated nine whole-genome bisulfite sequencing (WGBS) datasets from three distinct age groups (young, approx. 1 year old; mature, approx. 5 years old; old, approx. 9 years old) to characterize the gene- and chromosome-scale changes.

Organism:

Xenopus tropicalis

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL30018

9 Samples

Download data: TXT

(Submitter supplied) Histone acetylation is a pivotal epigenetic modification that controls chromatin structures and regulates gene expression. It plays an essential role in modulating zygotic transcription and cell lineage specification of developing embryos. While the outcomes of many inductive signals have been described to require enzymatic activities of histone acetyltransferases and deacetylases (HDACs), the mechanisms by which HDACs confines the utilization of the zygotic genome are not well-characterized. more...

Organism:

Xenopus tropicalis

Type:

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

Platforms:

GPL23182 GPL30018

45 Samples

Download data: NARROWPEAK, RESULTS