GEO DataSets

(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) 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

(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

(Submitter supplied) We conducted differential gene expression analyses of the developing X. laevis tadpole midbrain between stages 44 and 61, and across brain regions at stage 46. We found that genes pertaining to positive regulation of neural progenitor cell proliferation as well as known progenitor cell markers were upregulated in the midbrain prior to metamorphic climax; concurrently, expression of cell cycle timing regulators decreased across this period. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

30 Samples

Download data: TXT

(Submitter supplied) Xenopus laevis are able to regenerate the spinal cord during larvae stages through the activation of neural stem progenitor cells (NSPC). Here, we use high-resolution expression profiling to characterize the early transcriptome changes induced after spinal cord injury, and identify the signals that trigger NSPC proliferation. The analysis delineates a pathway that starts with a rapid and transitory activation of immediate early genes, followed by migration processes and immune response genes, the pervasive increase of NSPC specific ribosome biogenesis factors, and genes involved in stem cell proliferation. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22393 GPL17682

111 Samples

Download data: TXT

(Submitter supplied) Xenopus embryonic ectodermal cells are responsive to various inducing factors. Mesoderm is specified and patterned by extracellular factors including FGF, Nodal, BMP and Wnt families. Pinhead is another secreted protein implicated in mesoderm formation. We found that Pinhead physically interacts with and antagonizes ADMP (anti-dorsalizing morphogenetic protein) that acts as BMP-like protein to promote ventral mesoderm formation. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

8 Samples

Download data: XLSX

(Submitter supplied) Among the three embryonic germ layers, mesoderm plays a central role in the establishment of the vertebrate body plan. Mesoderm is specified by secreted signaling proteins from the FGF, Nodal, BMP and Wnt families. No new classes of extracellular mesoderm-inducing factors have been identified in more than two decades. Here we show that the Xenopus pinhead (pnhd) gene encodes a novel secreted protein that activates specific mesodermal markers in presumptive ectoderm. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

8 Samples

Download data: XLSX

(Submitter supplied) Changes in gene expression are required to orchestrate changes in cell state during development. Most cells change patterns of gene expression through transcriptional regulation. In contrast, oocytes are transcriptionally silent and use changes in mRNA poly-A tail length to control protein production. Recent technical advances have enabled genome-wide measurement of poly-A tail length. Poly-A tail lengthening is correlated with translational activation and poly-A tail shortening is correlated with translational repression at a global level during early development. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL18936 GPL17682

32 Samples

Download data: TXT

(Submitter supplied) Over the past few years, interest in the field of neuroimmunology has expanded dramatically. While recent data and hypotheses suggest immunity as the ‘seventh sense’ to inform brain about microorganisms, the role of the brain to protect against infection is unknown. We demonstrate here that the brain signaling is an essential part of the innate immunity. In absence of a brain, survival rates of embryos injected with pathogenic E.coli decreased significantly. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

8 Samples

Download data: XLSX

(Submitter supplied) It has become clear that DNA repair factors function not only in the maintenance of genomic integrity but also in active DNA demethylation and epigenetic gene regulation. This dual role raises the question if phenotypic abnormalities resulting from deficiency of DNA repair factors are due to DNA damage or impaired DNA demethylation. Here we investigate the bifunctional DNA glycosylases/lyases NEIL1 and NEIL2, which act in repair of oxidative lesions and in epigenetic demethylation.

Organism:

Xenopus laevis; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17682 GPL13112

45 Samples

Download data: TSV

(Submitter supplied) It was shown that neil2 is required for neural crest development in Xenopus (Schomacher et al. 2016; doi:10.1038/nsmb.3151). To gain further insights into the underlying molecular mechanism leading to neural crest defects and microcephaly in neil2 Morpholino injected Xenopus embryos, we performed RNA-seq transcriptome analysis of neil2 Morpholino versus control Morpholino injected embryos.

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

6 Samples

Download data: TSV

(Submitter supplied) Animal embryos have the remarkable property of self-organization. Over 125 years ago Hans Driesch separated the two blastomeres of sea urchin embryos and obtained twins, in what was the foundational experiment of experimental embryology. Since then, embryonic twinning has been obtained experimentally in many animals by diverse methods. In a recent study, we developed bisection methods that generate identical twins reliably from Xenopus blastula embryos. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

30 Samples

Download data: XLSX

(Submitter supplied) The induction of limb repair depends on signals that initiate regeneration and the successful transmission of those signals in vivo. Here, we characterize the effects of an integrated device-based in vivo delivery of drug compounds in adult Xenopus laevis, which normally regenerate only a cartilaginous spike after limb amputation. A wearable bioreactor containing a silk protein-based hydrogel containing progesterone that was applied to the wound site immediately after hind-limb amputation for 24 hours induced regeneration of flattened paddle-like structures in adult frogs. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

27 Samples

Download data: XLSX

(Submitter supplied) Determining how size is controlled is a fundamental question in biology that is poorly understood at the organismal, cellular and subcellular levels. The Xenopus species, X. laevis and X. tropicalis differ in size at all three of these levels. Despite these differences, fertilization of X. laevis eggs with X. tropicalis sperm gives rise to viable hybrid animals that are intermediate in size. Hybrid and X. more...

Organism:

Xenopus tropicalis x Xenopus laevis; Xenopus laevis; Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17682 GPL22797 GPL21874

8 Samples

Download data: FA, TXT

(Submitter supplied) We combined cryosectining of oocytes along the animal-vegetal axis (first developmental axis) and RNA-Seq to determine localization profiles of coding and noncoding RNAs. It provides complete view on RNA localization. We found that nearly all RNAs are localized, but only small percentage is actively transported during oogenesis.

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

15 Samples

Download data: TXT

(Submitter supplied) Retinoic acid (RA) is required for pancreas specification in Xenopus and other vertebrates. However, the gene network that is directly induced by RA-signalling in this context remains to be defined. We identified the transcription factor Hnf1β and the Wnt-receptor Fzd4/Fzd4s as direct RA-target genes through RNA-sequencing of in vitro generated pancreatic explants. Functional analyses of Hnf1β and Fzd4/Fzd4s in programmed pancreatic explants and whole embryos revealed their requirement for pancreatic progenitor formation and differentiation. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

8 Samples

Download data: TXT

(Submitter supplied) The Xenopus laevis embryo has been subjected to almost saturating screens for molecules specifically expressed in dorsal Spemann organizer tissue. In this study, we performed high-throughput RNA sequencing of ectodermal explants, called animal caps, which normally give rise to epidermis. We analyzed dissociated animal cap cells that, through sustained activation of MAPK, differentiate into neural tissue. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

16 Samples

Download data: XLSX

(Submitter supplied) During vertebrate neurulation, the embryonic ectoderm is patterned into lineage progenitors for neural plate, neural crest, placodes and epidermis. Here, we use Xenopus laevis embryos to analyze the spatial and temporal transcriptome of distinct ectodermal domains in the course of neurulation, during the establishment of cell lineages. In order to define the transcriptome of small groups of cells from a single germ layer, and to retain spatial information, dorsal and ventral ectoderm was subdivided along the anterior-posterior and medial-lateral axes by microdissections. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

79 Samples

Download data: TXT

(Submitter supplied) Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates.The most recent vertebrate genome duplication is that in Xenopus laevis, which resulted from the hybridization of two closely related species about 17 million years ago. Here we generated epigenetic profiles and determined gene expression in X.laevis embryos to study the consequences of this duplication at the level of the genome, the epigenome and gene expression.

Organism:

Xenopus laevis; Xenopus tropicalis x Xenopus laevis; Xenopus tropicalis

Type:

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

Platforms:

GPL21874 GPL22797 GPL17682

22 Samples

Download data: BED, TXT

(Submitter supplied) RNA-seq reveals the downstream gene regulatory network of wild-type Ptf1a, Neurog2 and Ptf1aW224A/W242A

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

16 Samples

Download data: GFF3, TXT