txid8364[Organism:noexp] - GEO DataSets

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Select item 2001723951.

Maternal and zygotic factors sequentially shape the tissue regionalization of chromatin landscapes in early vertebrate embryos

(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:: GPL30018 GPL23182
26 Samples

Download data: NARROWPEAK, TXT

Series

Accession:: GSE172395

ID:: 200172395

SRA Run Selector

Select item 2002519012.

Effect of erythropoietin on the gene expression of Xenopus tropicalis peripheral blood cells.

(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

Series

Accession:: GSE251901

ID:: 200251901

Select item 2001984943.

From neural border epithelium to neural crest emigration: A comprehensive single cell roadmap of the timing and regulatory logic underlying cranial and vagal neural crest emergence

(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 GPL18936 GPL21875
35 Samples

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Series

Accession:: GSE198494

ID:: 200198494

Select item 2001984924.

From neural border epithelium to neural crest emigration: A comprehensive single cell roadmap of the timing and regulatory logic underlying cranial and vagal neural crest emergence [ChIPseq]

(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

Series

Accession:: GSE198492

ID:: 200198492

Select item 2001984915.

From neural border epithelium to neural crest emigration: A comprehensive single cell roadmap of the timing and regulatory logic underlying cranial and vagal neural crest emergence [scRNAseq]

Organism:: Xenopus tropicalis

Type:: Expression profiling by high throughput sequencing

Platform:: GPL30018
2 Samples

Download data: PKL

Series

Accession:: GSE198491

ID:: 200198491

Select item 2002490756.

Sf3b4 mutation in Xenopus tropicalis causes RNA splicing defects and gene dysregulation across development and disrupts cranial neural crest cell migration and survival

(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

Series

Accession:: GSE249075

ID:: 200249075

PubMed Full text in PMC Similar studies

Select item 2002332877.

Identification of tumor-related genes via RNA sequencing of tumor tissues in Xenopus tropicalis

(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

Series

Accession:: GSE233287

ID:: 200233287

PubMed Full text in PMC Similar studies

Select item 2002286998.

Regulation of gene expression downstream of a novel Fgf/Erk pathway during Xenopus development

(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

Series

Accession:: GSE228699

ID:: 200228699

PubMed Full text in PMC Similar studies

Select item 2002313259.

LCM-RNA-Seq data obtained from Xenopus tropicalis chondrocytes and osteoblasts

(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

Series

Accession:: GSE231325

ID:: 200231325

Select item 20022210810.

Age-associated DNA methylation changes in Xenopus frogs, and Targeted bisulfite sequencing to profile age-associated DNA methylation changes in Xenopus frogs

(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

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Series

Accession:: GSE222108

ID:: 200222108

PubMed Full text in PMC Similar studies

Select item 20022210711.

Targeted bisulfite sequencing to profile age-associated DNA methylation changes in Xenopus frogs

(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

Series

Accession:: GSE222107

ID:: 200222107

PubMed Full text in PMC Similar studies

Select item 20022165612.

Age-associated DNA methylation changes in Xenopus frogs

(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

Series

Accession:: GSE221656

ID:: 200221656

PubMed Full text in PMC Similar studies

Select item 20019837813.

Histone deacetylase 1 maintains lineage integrity through histone acetylome refinement during early embryogenesis

(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

Series

Accession:: GSE198378

ID:: 200198378

PubMed Full text in PMC Similar studies

Select item 20021045614.

Comparative analysis of transcriptome profiles reveals organ-dependent (Intestine and Tail) genomic and nongenomic actions of thyroid hormone in Xenopus tropicalis tadpoles

(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

Series

Accession:: GSE210456

ID:: 200210456

PubMed Full text in PMC Similar studies

Select item 20020116815.

RNA sequencing of wild-type liver at stage 54, stage 61, stage 66 and T3 treated liver.

(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

Series

Accession:: GSE201168

ID:: 200201168

Select item 20018615816.

Single-cell transcriptomic atlas reveals the evolution of immune cells and molecules across multiple vertebrate species

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

Type:: Expression profiling by high throughput sequencing

7 related Platforms
7 Samples

Download data: TAR

Series

Accession:: GSE186158

ID:: 200186158

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20021851517.

Super-sized clustered loops anchored at transposon Helitrons in Xenopus tropicalis sperm associate with late gene expression during embryogenesis [ChIP-Seq2]

(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...