GPL30018[Accession] - GEO DataSets

(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

Series

Accession:: GSE240549

ID:: 200240549

Select item 2001723953.

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:: GPL23182 GPL30018
26 Samples

Download data: NARROWPEAK, TXT

Series

Accession:: GSE172395

ID:: 200172395

SRA Run Selector

Select item 2001984944.

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 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]

(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

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 2002221088.

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 2002221079.

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 20022165610.

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 20019837811.

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:: GPL30018 GPL23182
45 Samples

Download data: NARROWPEAK, RESULTS

Series

Accession:: GSE198378

ID:: 200198378

PubMed Full text in PMC Similar studies

Select item 20021045612.

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 20018615813.

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:: Xenopus tropicalis; Mus musculus; Rattus norvegicus; Danio rerio; Macaca mulatta; 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 20018667014.

Membrane potential drives the exit from pluripotency and the ontogeny of cell fate via calcium and mTOR

(Submitter supplied) High temporal resoultion profiling of Xenopus tropicalis transcriptome in control and High K+ conditions.

Organism:: Xenopus tropicalis

Type:: Expression profiling by high throughput sequencing

Platform:: GPL30018
26 Samples

Download data: TSV

Series

Accession:: GSE186670

ID:: 200186670

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20020499015.

Engagement of Foxh1 in chromatin regulation revealed by protein interactome analyses

(Submitter supplied) Precise gene expression patterns, both in time and space, is required for developmental processes to properly progress. Early embryonic cell fates are specified through the coordinated integration of transcription factor activities and epigenetic states of the genome. Foxh1 is a key maternal transcription factor controlling the mesendodermal gene regulatory program. Proteomic interactome analyses using FOXH1 as a bait in mouse embryonic stem cells revealed that FOXH1 interacts with PRC2 subunits and Hdac1. more...