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:

GPL21046 GPL28901

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) 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:

Mus musculus; Xenopus laevis; Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21046 GPL18480 GPL19951

47 Samples

Download data: BW

(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

(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:

GPL25291

6 Samples

Download data: TSV

(Submitter supplied) Lead (Pb) is a widespread environmental toxicant that can elicit a wide variety of adverse effects in aquatic species. In fish, exposure to Pb can induce oxidative stress and reduce antioxidant capacity and there is evidence that Pb-induced developmental abnormalities are the result of dysregulated metabolism pathways but to date, no studies have characterised the molecular mechanisms of lead toxicity in amphibians. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28901

15 Samples

Download data: CSV, TXT

(Submitter supplied) Chemical RNA modifications, collectively referred to as the ‘epitranscriptome’, have been intensively studied during the last years, largely facilitated by the use of next-generation sequencing technologies. Recent efforts have turned towards the nanopore direct RNA sequencing (DRS) platform, as it allows simultaneous detection of diverse RNA modification types in full-length native RNA molecules. While RNA modifications can be identified in the form of systematic basecalling ‘errors’ in DRS datasets, m6A modifications produce very modest ‘errors’, limiting the applicability of this approach to sites that are modified at high stoichiometries. more...

Organism:

Arabidopsis thaliana; Homo sapiens; Mus musculus; Saccharomyces cerevisiae; synthetic construct; Xenopus laevis

Type:

Other

6 related Platforms

70 Samples

Download data: CSV, FA, FASTA, TSV, TXT

(Submitter supplied) Somatic cell nuclear transfer and transcription factor overexpression can induce reprogramming of somatic cells, whereby one cell fate is changed into another cell fate of choice. Yet the efficiency of this process for generating functional cells is low, limiting their therapeutic applications. The persistence of transcriptional memory from the cell's prior identity is thought to be a major hindrance to effective reprogramming and differentiation to functional cell types. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18936

4 Samples

Download data: CSV

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

Organism:

Xenopus laevis

Type:

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

Platforms:

GPL28901 GPL21248

21 Samples

Download data

(Submitter supplied) Here we investigate a functional role for SoxB1 transcription factors, Sox2 and Sox3, on the transient embryonic cell population, the neural plate border. We find through gain/loss-of-function studies necessary for neural plate border cells to become neural crest cells. and genomics experiments (ChIP-seq and RNA-seq) that SoxB1 transcription factors directly promote neural plate border formation. and that down-regulation of SoxB1 expression is

Organism:

Xenopus laevis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL28901 GPL21248

12 Samples

Download data: TXT

(Submitter supplied) Here we investigate a functional role for SoxB1 transcription factors, Sox2 and Sox3, on the transient embryonic cell population, the neural plate border. We find through gain/loss-of-function studies necessary for neural plate border cells to become neural crest cells. and genomics experiments (ChIP-seq and RNA-seq) that SoxB1 transcription factors directly promote neural plate border formation. and that down-regulation of SoxB1 expression is

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21248

9 Samples

Download data: TXT

(Submitter supplied) We address the evolutionary origins of vertebrate pluripotency by comparing the development of neural crest and blastula stem cells using representatives from both jawed (Xenopus) and jawless (lamprey) vertebrates.

Organism:

Petromyzon marinus; Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24750 GPL21248

21 Samples

Download data: CSV