GEO DataSets

(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:

Xenopus laevis; Drosophila melanogaster; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19951 GPL21046 GPL18480

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:

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

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:

GPL21248 GPL28901

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:

GPL21248 GPL28901

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

(Submitter supplied) Here we examine the role that epigenetic readers of the BET (Bromodomain and Extra Terminal) family play in controlling the potential of pluripotent blastula and neural crest cells. We find that inhibiting BET activity leads to loss of pluripotency and inability to respond to lineage instructing cues at blastula stages, and a loss of neural crest at neurula stages.

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21248

46 Samples

Download data: XLSX

(Submitter supplied) The Wnt signaling pathway is one of the most ancient and pivotal signaling cascades, governing diverse processes in development and cancer regulation. Within the realm of cancer treatment, genistein emerges as a promising candidate due to its multifaceted modulation of various signaling pathways, including the Wnt pathway. Despite promising preclinical studies, the precise mechanisms underlying genistein's therapeutic effects via Wnt modulation remain elusive. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34551

12 Samples

Download data: TXT

(Submitter supplied) This study was conducted to investigate the temporal expression of patterning genes in the Xenopus mucociliary epidermis.

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22393

6 Samples

Download data: TABULAR, TXT

(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 GPL21875 GPL18936

35 Samples

Download data

(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 laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18936

10 Samples

Download data: CSV

(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 laevis; Xenopus tropicalis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21875 GPL18936

23 Samples

Download data: CSV

(Submitter supplied) Multiciliated cells (MCCs) form when progenitors massively expand centriole number, yielding the hundreds of basal bodies required to extend multiple motile cilia. This organelle biogenesis is promoted transcriptionally by Multicilin acting in a complex with the E2F transcription factors, which activates the expression of genes known to be involved required to form centrioles during the cell cycle, but also requires a cell cycle state required for the centrosome cycle. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18936

12 Samples

Download data: XLSX

(Submitter supplied) During oocyte maturation and early embryonic development, poly(A)-tail lengths strongly influence mRNA translation. However, how tail lengths are controlled at different developmental stages has been unclear. Here, we performed tail-length and translational profiling of mRNA reporter libraries (each with > 10 million 3ʹ-UTR sequence variants) in frog oocytes and embryos, and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5-mer. more...

Organism:

synthetic construct; Xenopus laevis; Danio rerio; Mus musculus

Type:

Other

4 related Platforms

83 Samples

Download data: TXT