GEO DataSets

(Submitter supplied) The fate of differentiated cells in our body can be reverted and changed by nuclear reprogramming. In this way, cells valuable for therapeutic purposes and disease modeling are produced. However, the efficiency of this process is low, partly due to the properties of the somatic donor which stabilize its differentiated fate and compromise reprogramming-associated cell fate changes. The identity of these reprogramming barriers is not fully understood.Here, we developed an artificial intelligence-based approach that models reprogramming and identifies the chromatin modification H3K27ac as a novel epigenetic barrier to reprogramming-induced cell fate changes. more...

Organism:

Xenopus laevis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21046

94 Samples

Download data: BW

(Submitter supplied) The fate of differentiated cells in our body can be reverted and changed by nuclear reprogramming. In this way, cells valuable for therapeutic purposes and disease modeling are produced. However, the efficiency of this process is low, partly due to the properties of the somatic donor which stabilize its differentiated fate and compromise reprogramming-associated cell fate changes. The identity of these reprogramming barriers is not fully understood.Here, we developed an artificial intelligence-based approach that models reprogramming and identifies the chromatin modification H3K27ac as a novel epigenetic barrier to reprogramming-induced cell fate changes. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28901 GPL21046

115 Samples

Download data: TSV

(Submitter supplied) The fate of differentiated cells in our body can be reverted and changed by nuclear reprogramming. In this way, cells valuable for therapeutic purposes and disease modeling are produced. However, the efficiency of this process is low, partly due to the properties of the somatic donor which stabilize its differentiated fate and compromise reprogramming-associated cell fate changes. The identity of these reprogramming barriers is not fully understood.Here, we developed an artificial intelligence-based approach that models reprogramming and identifies the chromatin modification H3K27ac as a novel epigenetic barrier to reprogramming-induced cell fate changes. more...

Organism:

Xenopus laevis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL35244

16 Samples

Download data: BW

(Submitter supplied) Accurately established transcriptional programs are paramount for successful embryonic development. At zygotic genome activation, gene expression is initiated for the first time in the life of an embryo. Pioneer transcription factors present in the embryo are essential for this process, however, the role of active chromatin modifications is less clear. It is unknown if active chromatin modifications established in the gamete are propagated in the embryo as epigenetic memory to support zygotic genome activation and development. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL35244

90 Samples

Download data: CSV

(Submitter supplied) Accurately established transcriptional programs are paramount for successful embryonic development. At zygotic genome activation, gene expression is initiated for the first time in the life of an embryo. Pioneer transcription factors present in the embryo are essential for this process, however, the role of active chromatin modifications is less clear. It is unknown if active chromatin modifications established in the gamete are propagated in the embryo as epigenetic memory to support zygotic genome activation and development. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL35244

72 Samples

Download data: CSV

(Submitter supplied) Accurately established transcriptional programs are paramount for successful embryonic development. At zygotic genome activation, gene expression is initiated for the first time in the life of an embryo. Pioneer transcription factors present in the embryo are essential for this process, however, the role of active chromatin modifications is less clear. It is unknown if active chromatin modifications established in the gamete are propagated in the embryo as epigenetic memory to support zygotic genome activation and development. more...

Organism:

Xenopus laevis

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL34812

4 Samples

Download data: BROADPEAK, BW

(Submitter supplied) Accurately established transcriptional programs are paramount for successful embryonic development. At zygotic genome activation, gene expression is initiated for the first time in the life of an embryo. Pioneer transcription factors present in the embryo are essential for this process, however, the role of active chromatin modifications is less clear. It is unknown if active chromatin modifications established in the gamete are propagated in the embryo as epigenetic memory to support zygotic genome activation and development. more...

Organism:

Xenopus laevis

Type:

Other

Platform:

GPL28901

2 Samples

Download data: BROADPEAK, BW

(Submitter supplied) Our study represents the first detailed analysis of thyroid hormone binding to the genome in the tail 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

(Submitter supplied) High temporal resolution profiling of Xenopus tropicalis transcriptome during early development in control and nup107 MO conditions.

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30018

84 Samples

Download data: TSV

(Submitter supplied) Conclusions: Our study represents the first detailed comparative analysis of TR binding between wild-type,TRαLKO, TRβKO intestine, with biologic replicates, generated by ChIP-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles.

Organism:

Xenopus tropicalis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21875

18 Samples

Download data: TSV, TXT

(Submitter supplied) To investigate what genes/pathways that specific induced by T3/TRs which inhibited tail regeneration. In addition, to detect the gene regulation program that important for regeneration were altered by T3 through TRs during the initiation period of tail regeneration

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30018

24 Samples

Download data: TXT

(Submitter supplied) To investigate the genes involved in the compensatory behavior observed in Xenopus Borealis following a genetic perturbation on the Notch signaling pathway, we analyzed the gene expression of the embryos using RNA-Seq for three developmental stages and three treatments

Organism:

Xenopus borealis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34010

18 Samples

Download data: TXT

(Submitter supplied) To investigate the genes involved in the compensatory behavior observed in Xenopus laevis following a genetic perturbation on the Notch signaling pathway, we analyzed the gene expression of the embryos using RNA-Seq for three developmental stages and three treatments

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17682 GPL28901

36 Samples

Download data: TXT

(Submitter supplied) Foxi1 is a master regulator of ionocytes (ISCs) across species and organs. Two subtypes of ISCs exist, and both a- and b-ISCs regulate pH- and ion-homeostasis in epithelia. Gain and loss of Foxi1 function are associated with human diseases, including Pendred syndrome, male infertility, kidney malfunction and cancers. Foxi1 functions were predominantly studied in the context of ISC specification, however, reports indicate additional functions in early and ectodermal development. more...

Organism:

Xenopus laevis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL28901

6 Samples

Download data: BED, BEDGRAPH, BIGWIG

(Submitter supplied) Histone modifications play a key role in regulating gene expression and cell fate during development and disease. Current methods for cell-type specific genome-wide profiling of histone modifications require dissociation and isolation of cells and are not compatible with all tissue types. Here we adapt Targeted DamID to recognise specific histone marks, by fusing chromatin binding proteins or single-chain antibodies to Dam, an E. more...

Organism:

Drosophila melanogaster; Mus musculus; Xenopus laevis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21046 GPL19951 GPL18480

47 Samples

Download data: BW

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

Organism:

Xenopus tropicalis

Type:

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

Platforms:

GPL23182 GPL30018

21 Samples

Download data: NARROWPEAK, TAB

(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

(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:

Expression profiling by high throughput sequencing

Platform:

GPL23182

18 Samples

Download data: TAB

(Submitter supplied) The standard paradigm of developmental and synthetic biology focuses on changes in morphology driven by gene expression. Here, we investigated the reverse relationship: would transcriptomes change if cell collectives acquired a novel morphogenetic and behavioral phenotype in the absence of genomic editing, transgenes, heterologous materials, or drugs? We investigated the effects of morphology and nascent emergent life history on gene expression in Xenobots – motile, autonomous constructs that self-assemble from frog embryo epidermal progenitor cells. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18936

6 Samples

Download data: CSV, TSV

(Submitter supplied) Cerebellar granule neuron progenitors (GNPs) originate from the upper rhombic lip (URL), a germinative niche in which developmental defects produce human diseases. T-cell factor (TCF) responsiveness and Notch dependence are hallmarks of self-renewal in neural stem cells. TCF activity, together with transcripts encoding proneural gene repressors hairy and enhancer of split (Hes/Hey), are detected in the URL; however, their functions and regulatory modes are undeciphered. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34884

12 Samples

Download data: TXT