GEO DataSets

(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:

GPL21875 GPL30018 GPL18936

35 Samples

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(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:

GPL18936 GPL21875

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:

Xenopus laevis; synthetic construct; Danio rerio; Mus musculus

Type:

Other

4 related Platforms

83 Samples

Download data: TXT

(Submitter supplied) Purpose: Identify gene expression changes in whole intestines of Xenopus laevis embryos exposed to atrazine (35 mg/L) compared to DMSO controls Methods: NF 39 embryos were exposed to 35 mg/L ATR or DMSO control for 24 hours. After 24 hours of exposure, intestines from embryos of each treatment group were dissected from anesthetized embryos with sharpened forceps. The anterior portion of the embryo (including the head, heart, and foregut) were removed and discarded, leaving only the mid-and hindgut portion of the intestine. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28901

8 Samples

Download data: CSV

(Submitter supplied) During gastrulation and neurulation, the chordamesoderm and overlying neuroectoderm of vertebrate embryos converge under the control of a specific genetic programme to the dorsal midline, simultaneously extending along it. However, whether mechanical tensions resulting from these morphogenetic movements play a role in long-range feedback signalling that in turn regulates gene expression in the chordamesoderm and neuroectoderm is unclear. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21046

6 Samples

Download data: XLSX

(Submitter supplied) To identify regulators of activity-dependent neural progenitor cell fate, we used RNA-Seq to profile the transcriptomes of proliferating neural progenitor cells and newly-differentiated immature neurons. We identified six DE transcription factors which are predicted to regulate the majority of the other DE transcripts. We investigated the effect of BRCA1 and ELK-1 on activity-regulated neurogenesis in the tadpole visual system and found that knockdown of either BRCA1 or ELK-1 altered the fates of neural progenitor cells, and furthermore that the effects of visual experience on neurogenesis depend on BRCA1 expression, while the effects of visual experience on neuronal differentiation depend on ELK-1 expression. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

6 Samples

Download data: FA, GFF3, XLSX

(Submitter supplied) As part of the EcoToxChip project, 49 distinct exposure studies were conducted on three lab model species (Japanese quail, fathead minnow, African clawed frog) and three ecologically relevant species (double crested cormorant, rainbow trout, northern leopard frog), at multiple life stages (embryo, adult), exposed to eight chemicals of environmental concern (ethinyl estradiol-EE2, hexabromocyclododecane-HBCD, lead-Pb, selenomethionine-SeMe, 17β trenbolone-TB, chlorpyrifos-CPF, fluoxetine-FLX, and benzo [a] pyrene-BaP. more...

Organism:

Lithobates pipiens; Phalacrocorax auritus; Pimephales promelas; Oncorhynchus mykiss; Xenopus laevis; Coturnix japonica

Type:

Expression profiling by high throughput sequencing

9 related Platforms

724 Samples

Download data: TXT

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

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18936

24 Samples

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(Submitter supplied) We investigated whether normal embryonic developmental cues are only at the level of cells within the embryo or whether they exist in interactions between embryos. To explore this, we subjected groups of embryos with disruptors of normal development while varying group size. RNA-seq analysis revealed a small set of transcripts specific for teratogen response in large groups but not small ones.

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18936

12 Samples

Download data: CSV, TSV

(Submitter supplied) We investigated whether normal embryonic developmental cues are only at the level of cells within the embryo or whether they exist in interactions between embryos. To explore this, we subjected groups of embryos with disruptors of normal development while varying group size. RNA-seq analysis revealed a small set of transcripts specific for teratogen response in large groups but not small ones.

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18936

12 Samples

Download data: TSV, XLSX

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

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL21248 GPL28901

63 Samples

Download data: CSV, JPG, JSON, MTX, PNG, TSV, XLSX

(Submitter supplied) In this experiment, we revealed the critical steps for regeneration initiation. We discovered Regeneration Initiating Cells (RICs) using single cell and spatial transcriptomics of the regenerating Xenopus laevis tail. RICs are formed transiently from the basal epidermal cells and are critical for the modification of the surrounding extracellular matrix to allow for migration of other cell types that promote regeneration. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21248

32 Samples

Download data: XLSX

(Submitter supplied) In this experiment, we revealed the critical steps for regeneration initiation. We discovered Regeneration Initiating Cells (RICs) using single cell and spatial transcriptomics of the regenerating Xenopus laevis tail. RICs are formed transiently from the basal epidermal cells and are critical for the modification of the surrounding extracellular matrix to allow for migration of other cell types that promote regeneration. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21248

27 Samples

Download data: XLSX

(Submitter supplied) In this experiment, we revealed the critical steps for regeneration initiation. We discovered Regeneration Initiating Cells (RICs) using single cell and spatial transcriptomics of the regenerating Xenopus laevis tail. RICs are formed transiently from the basal epidermal cells and are critical for the modification of the surrounding extracellular matrix to allow for migration of other cell types that promote regeneration. more...

Organism:

Xenopus laevis

Type:

Other

Platform:

GPL28901

3 Samples

Download data: CSV, JPG, JSON, MTX, PNG, TSV, XLSX

(Submitter supplied) In this experiment, we revealed the critical steps for regeneration initiation. We discovered Regeneration Initiating Cells (RICs) using single cell and spatial transcriptomics of the regenerating Xenopus laevis tail. RICs are formed transiently from the basal epidermal cells and are critical for the modification of the surrounding extracellular matrix to allow for migration of other cell types that promote regeneration. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28901

1 Sample

Download data: MTX, TSV, XLSX

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

Organism:

Homo sapiens; Xenopus laevis

Type:

Expression profiling by array

Platforms:

GPL16686 GPL10756

22 Samples

Download data: CEL

(Submitter supplied) In early embryonic development, the organiser functions in multiple developmental processes, including neural induction, dorsoventral patterning of the mesoderm, and formation of the axial mesoderm. Chordin is a central molecule for the activity of the Spemann’s organiser and abundantly secreted from the Spemann’s organiser in Xenopus laevis. However, so far, a whole picture of the gene expression profile regulated by Chordin has not been examined. more...

Organism:

Xenopus laevis

Type:

Expression profiling by array

Platform:

GPL10756

12 Samples

Download data: CEL