xenopus[Organism] - GEO DataSets

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Select item 2001866701.

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

SRA Run Selector

Select item 2002049902.

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...

Organism:: Xenopus tropicalis

Type:: Expression profiling by high throughput sequencing

Platform:: GPL30018
4 Samples

Download data: TXT

Series

Accession:: GSE204990

ID:: 200204990

PubMed Similar studies

Select item 2001895503.

CPEB1-4 RIP-Seq in S.VI Xenopus laevis oocytes [RIP-seq]

(Submitter supplied) The aim of this experiment was to investigate the binding profiles of the CPEB-family of RNA-binding proteins. To attain comparable results, all IPs were performed against the HA-tagged CPEBs.

Organism:: Xenopus laevis

Type:: Other

Platform:: GPL18936
20 Samples

Download data: XLSX

Series

Accession:: GSE189550

ID:: 200189550

Analyze with GEO2R SRA Run Selector

Select item 2001933644.

RNA sequencing of wild-type and TRα (-/-) hindlimb with and without T3 Treatment

(Submitter supplied) Conclusions: Our study represents the first detailed analysis of hindlimb transcriptomes in wild-type and TRα (-/-) 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:: GSE193364

ID:: 200193364

PubMed Full text in PMC Similar studies

Select item 2001933635.

ChIP sequencing of wild-type and TRα (-/-) hindlimb with and without T3 Treatment

(Submitter supplied) Our study represents the first detailed analysis of thyroid hormone binding to the genome in the hindlimb of wild-type and TRα (-/-) tadpoles, with biological replicates, generated by ChIP-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of TR binding profiles.

Organism:: Xenopus tropicalis

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL21875
12 Samples

Download data: TXT

Series

Accession:: GSE193363

ID:: 200193363

PubMed Full text in PMC Similar studies

Select item 2001617186.

Thyroid hormone receptor α controls larval intestinal epithelial cell death by regulating the CDK1 pathway

(Submitter supplied) Our study represents the first detailed analysis of thyroid hormone binding to the genome in the intestine of wild-type and TRα (-/-) tadpoles, with biological replicates, generated by ChIP-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of TR binding profiles.

Organism:: Xenopus tropicalis

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL21875
12 Samples

Download data: TXT

Series

Accession:: GSE161718

ID:: 200161718

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001957907.

Cell landscape of Xenopus laevis at single-cell resolution

(Submitter supplied) Single-cell mRNA sequencing (scRNA-seq) technologies are reshaping the current cell-type classification system. In previous studies, we built the mouse cell atlas (MCA) and human cell landscape (HCL) to catalog all cell types by collecting scRNA-seq data. However, systematically study for Xenopus laevis is still lacking. Here, we construct the Xenopus cell landscape with Microwell-seq protocols, which provides valuable resources for characterization of diverse cell populations of Xenopus laevis, and studying difference between vertebrates at single cell level.

Organism:: Xenopus laevis

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL32324 GPL31294
56 Samples

Download data: TXT

Series

Accession:: GSE195790

ID:: 200195790

PubMed Full text in PMC Similar studies

Select item 2001791588.

RNA-Seq analysis of the stage 51 hind limb bud of Xenopus laevis

(Submitter supplied) Reporting data obtained from dividing the stage 51 Xenopus laevis hind limb bud into thirds along the proximal distal axis (proximal, medial, distal) and sequencing the extracted RNA to investigate differences in gene expression

Organism:: Xenopus laevis

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17682
6 Samples

Download data: CSV, TXT

Series

Accession:: GSE179158

ID:: 200179158

SRA Run Selector

Select item 2001964259.

Enhancers of host immune tolerance to bacterial infection discovered using linked computational and experimental approaches

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

Organism:: Xenopus laevis

Type:: Expression profiling by array

Platform:: GPL10756
67 Samples

Download data: CEL

Series

Accession:: GSE196425

ID:: 200196425

Select item 20019642410.

Enhancers of host immune tolerance to bacterial infection discovered using linked computational and experimental approaches II

(Submitter supplied) Current therapeutic strategies against bacterial infections focus on reduction of pathogen load using antibiotics; however, stimulation of host tolerance to infection in the presence of pathogens might offer an alternative approach. We used computational transcriptomics and Xenopus laevis embryos to discover infection response pathways, identify potential tolerance inducer drugs, and validate their ability to induce broad tolerance. more...

Organism:: Xenopus laevis

Type:: Expression profiling by array

Platform:: GPL10756
27 Samples

Download data: CEL

Series

Accession:: GSE196424

ID:: 200196424

Select item 20019642211.

Enhancers of host immune tolerance to bacterial infection discovered using linked computational and experimental approaches I

Organism:: Xenopus laevis

Type:: Expression profiling by array

Platform:: GPL10756
40 Samples

Download data: CEL

Series

Accession:: GSE196422

ID:: 200196422

Select item 20013322012.

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type Xenopus tropicalis Tail and Notochord During Metamorphosis

(Submitter supplied) Our experiment revealed the notochord specific metamorphosis-induced genes to clarify the molecular mechanisms of tail regression.

Organism:: Xenopus tropicalis

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21875
9 Samples

Download data: TXT, XLSX

Series

Accession:: GSE133220

ID:: 200133220

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20020582713.

Expression profiling of retinoic acid targets in lateral mesoderm from Xenopus laevis embryos

(Submitter supplied) Renal precusors of the Xenopus pronephros arise from dorso-lateral mesoderm at the early neurula stage. This process is under the control of retinoic acid (RA). We have used microarrays to identify RA targets in dorso-latearl mesoderm by performing differential expression analysis between control and RA-depleted situations

Organism:: Xenopus laevis

Type:: Expression profiling by array

Platform:: GPL10756
18 Samples

Download data: CEL

Series

Accession:: GSE205827

ID:: 200205827

Analyze with GEO2R

Select item 20019580614.

Role of maternal Wnt11b in cortical rotation and axis formation

(Submitter supplied) Asymmetric signalling centres in the early embryo are essential for axis formation in vertebrates. These regions, namely the dorsal morula, yolk syncytial layer, and distal hypoblast/anterior visceral endoderm (in amphibians, teleosts and mammals, respectively), require the localised stabilisation of nuclear Beta-catenin (Ctnnb1), implying that localised Wnt/Beta-catenin signalling activity is critical in their establishment. more...

Organism:: Xenopus laevis

Type:: Expression profiling by high throughput sequencing

Platform:: GPL28901
8 Samples

Download data: BW, TXT

Series

Accession:: GSE195806

ID:: 200195806

Select item 20017566215.

Chromatin Accessibility Analysis Reveals Distinct Functions for HDAC and EZH2 Activities in Early Regeneration

(Submitter supplied) Xenopus tropicalis tadpoles have the capability to scarlessly regenerate appendages including the limb and tail. Following injury, complex genetic processes must be activated and inactivated with high spatial and temporal resolution to result in a properly patterned appendage. Functional studies have established that histone modifying enzymes that act to close chromatin are required for regeneration, but the genomic regions sensitive to these activities are not established. more...

Organism:: Xenopus tropicalis

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL24884
35 Samples

Download data: BED, TXT

Series

Accession:: GSE175662

ID:: 200175662

SRA Run Selector

Select item 20019967116.

Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

(Submitter supplied) Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus and Hymenochirus boettgeri. more...

Organism:: Xenopus tropicalis

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL23182
11 Samples

Download data: BED, TAB

Series

Accession:: GSE199671

ID:: 200199671

Select item 20016160017.

Uncovering the mesendoderm gene regulatory network through multi-omic data integration

(Submitter supplied) We report the ChIP-seq analysis of multiple Xenopus transcription factors binding. Also, we report loss-of-function transcriptomic analysis of Tcf7l1 by RNA-seq at different developmental stages. These newly generated datasets are analyzed using self-organizing maps, along with previously published Xenopus genomic data.

Organism:: Xenopus tropicalis

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

Platforms:: GPL21875 GPL24898
19 Samples

Download data: NARROWPEAK, TXT

Series

Accession:: GSE161600

ID:: 200161600

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20019904918.

Target-agnostic discovery of Rett Syndrome therapeutics by coupling computational network analysis and CRISPR-enabled in vivo disease modeling

(Submitter supplied) It is difficult to develop effective treatments for neurodevelopmental genetic disorders, such as Rett syndrome, which are caused by a single gene mutation but trigger changes in numerous other genes, and thereby also severely impair functions of organs beyond the central nervous system (CNS). This challenge is further complicated by the lack of sufficiently broad and biologically relevant drug screens, and the inherent complexity in identifying clinically relevant targets responsible for diverse phenotypes. more...

Organism:: Xenopus laevis

Type:: Expression profiling by array

Platform:: GPL10756
13 Samples

Download data: CEL

Series

Accession:: GSE199049

ID:: 200199049

Analyze with GEO2R

Select item 20018026919.

Analysis of RA vs 4-oxo-RA gene expression regulation in Xenopus laevis

(Submitter supplied) We analyzed anterior halves of NF stage 15 embryos that were treated with 10uM DMSO (control), or 1uM RA and 10uM 4-oxo-RA (experimental) for changes in gene expression induced by the two mophogens. RNA-sequencing revealed significant overlap in genes upregulated by both RA and 4-oxo-RA, and to a lesser extent, those downregulated by them. We report all Zic-1 targets described in accompanying manuscript to be regulated by both RA and 4-oxo-RA.