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Items: 1 to 20 of 6010

1.

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
2.

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
3.

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
4.

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
5.

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
6.

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
7.

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
8.

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
9.

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
10.

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
11.

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

(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
40 Samples
Download data: CEL
Series
Accession:
GSE196422
ID:
200196422
12.

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
13.

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
14.

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
15.

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
16.

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
17.

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
18.

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
19.

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.
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17682
9 Samples
Download data: TXT
Series
Accession:
GSE180269
ID:
200180269
20.

Whole transcriptome bisufilte sequencing for multiple species

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Danio rerio; Xenopus laevis; Drosophila melanogaster; Xenopus tropicalis; Mus musculus; Homo sapiens
Type:
Methylation profiling by high throughput sequencing
6 related Platforms
67 Samples
Download data: CSV
Series
Accession:
GSE127780
ID:
200127780
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