GEO DataSets

(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) Numerous studies report active pharmaceutical compounds detected in both wastewater effluent and surface waters. Exposure to statin drugs in general, and atorvastatin in particular, is likely to be a concern. We hypothesized that chronic exposure to low concentrations of atorvastatin in water would result in an adverse effect on production of steroids regulating growth and development of the model amphibian Xenopus laevis. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28901

6 Samples

Download data: XLSX

(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) Hi-C on mitotic chromosomes in Xenopus system to study mitotic chromosome scaling by comparing replicated sperm vs stage 8 embryo chromosomes

Organism:

Xenopus laevis

Type:

Other

Platform:

GPL22393

4 Samples

Download data: MCOOL

(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

(Submitter supplied) To investigate whether X. laevis have a PLCz ortholog or comparable enzyme.

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21248

3 Samples

Download data: TXT

(Submitter supplied) To investigate which genes expression are inhibited in TR double knockout tadpoles under over thyroid hormone condition in each tissue.

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30018

24 Samples

Download data: TXT

(Submitter supplied) Conclusions: Our study represents the first detailed analysis of liver transcriptomes in wild-type tadpoles, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles.

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21875

12 Samples

Download data: TXT

(Submitter supplied) We utilized single-cell RNA sequencing (scRNA-seq) to carry out comparative transcriptome analysis in various immune cells from the spleens across seven vertebrate species.

Organism:

Homo sapiens; Sus scrofa; Danio rerio; Macaca mulatta; Xenopus tropicalis; Mus musculus; Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

7 related Platforms

7 Samples

Download data: TAR

(Submitter supplied) We hypothesized that embryonic exposure to a mixture of chemicals (containing phenols, phthalates, pesticides, heavy metals, and perfluorinated, polychlorinated, and polybrominated compounds) identified as commonly found in the human amniotic fluid (as calculated in Fini et al., ) could lead to altered brain development. We assessed its effect on TH signaling and neuro-development in an amphibian model (Xenopus laevis) highly sensitive to thyroid disruption. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21248

12 Samples

Download data: TXT

(Submitter supplied) Vertebrate sperm genome differs from somatic cells and undergoes dramatic transformation after fertilization. However, the functional implications of the sperm genome structures have not been fully investigated. Here we show, in the sperms of Xenopus tropicalis, tens of genomic regions harbor multi-megabases, super-sized clustered loops (SSCLs) whose anchors are enriched with Helitrons, the only group of rolling-circle transposons. more...

Organism:

Xenopus laevis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL31294

2 Samples

Download data: HIC

(Submitter supplied) Vertebrate sperm genome differs from somatic cells and undergoes dramatic transformation after fertilization. However, the functional implications of the sperm genome structures have not been fully investigated. Here we show, in the sperms of Xenopus tropicalis, tens of genomic regions harbor multi-megabases, super-sized clustered loops (SSCLs) whose anchors are enriched with Helitrons, the only group of rolling-circle transposons. more...

Organism:

Xenopus tropicalis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30213

8 Samples

Download data: BW

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

Organism:

Xenopus laevis; Xenopus tropicalis; Xenopus tropicalis x Xenopus laevis

Type:

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

4 related Platforms

67 Samples

Download data: BW, COOL, HIC, TXT

(Submitter supplied) Vertebrate sperm genome differs from somatic cells and undergoes dramatic transformation after fertilization. However, the functional implications of the sperm genome structures have not been fully investigated. Here we show, in the sperms of Xenopus tropicalis, tens of genomic regions harbor multi-megabases, super-sized clustered loops (SSCLs) whose anchors are enriched with Helitrons, the only group of rolling-circle transposons. more...

Organism:

Xenopus tropicalis x Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32016

26 Samples

Download data: TXT

(Submitter supplied) Vertebrate sperm genome differs from somatic cells and undergoes dramatic transformation after fertilization. However, the functional implications of the sperm genome structures have not been fully investigated. Here we show, in the sperms of Xenopus tropicalis, tens of genomic regions harbor multi-megabases, super-sized clustered loops (SSCLs) whose anchors are enriched with Helitrons, the only group of rolling-circle transposons. more...

Organism:

Xenopus tropicalis; Xenopus tropicalis x Xenopus laevis

Type:

Other

Platforms:

GPL30213 GPL32015

8 Samples

Download data: COOL, HIC

(Submitter supplied) Vertebrate sperm genome differs from somatic cells and undergoes dramatic transformation after fertilization. However, the functional implications of the sperm genome structures have not been fully investigated. Here we show, in the sperms of Xenopus tropicalis, tens of genomic regions harbor multi-megabases, super-sized clustered loops (SSCLs) whose anchors are enriched with Helitrons, the only group of rolling-circle transposons. more...

Organism:

Xenopus tropicalis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30213

3 Samples

Download data: BW