Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Temporal and Spatial Transcriptomic Dynamics across Brain Development in Xenopus laevis tadpoles

ABSTRACT: Temporal and Spatial Transcriptomic Dynamics across Brain Development in Xenopus laevis tadpoles

PROVIDER: PRJNA759592 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR15687739_1.fastq.gz	Fastqsanger.gz
	SRR15687739_2.fastq.gz	Fastqsanger.gz
	SRR15687740_1.fastq.gz	Fastqsanger.gz
	SRR15687740_2.fastq.gz	Fastqsanger.gz
	SRR15687741_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 60

Similar Datasets

Transcription profiling of brains, hindlimbs and tails of Xenopus laevis tadpoles after treatment with thyroid hormone

Project description:Premetamorphic Xenopus laevis tadpole tail respond to thyroid hormone by resorption. The goal of this experiment is to identify the genes involved in the TH-induced resorption tadpole tail and compare it to TH-induced proliferation and differentiation program in tadpole limb and brain. Xenopus tadpoles (NF54) were treated with 100 nM T3(triioodthyronine) in 0.1 x MMR for another 24h and 48h or without T3 for 48h (control group). NF 61 tadpoles were in 0.1 X MMR till they reached NF stage 62. The tails were dissected after the experiment.

2006-11-08 | E-MNIA-94 | biostudies-arrayexpress

Single cell RNA-seq of tail tissue from regeneration-competent and -incompetent Xenopus laevis tadpoles

Project description:Xenopus laevis tadpoles differ in their regenerative potential according to their developmental stage. Here, we focus on tail regeneration following amputation. By comparing the regenerative response during the naturally occurring regeneration-competent and -incompetent stages, scRNAseq can reveal cell type changes that are required for successful regeneration.

2019-04-23 | E-MTAB-7716 | biostudies-arrayexpress

Single cell RNA-seq of limb tissue from regeneration-competent, -restricted and -incompetent Xenopus laevis tadpoles

Project description:Xenopus laevis tadpoles display a decreasing capacity to regenerate their limbs following injury according to developmental stage. By comparing the regenerative response during the naturally occurring regeneration-competent, -restricted and -incompetent stages, scRNAseq can reveal cell type changes that are required for successful regeneration.

2021-05-17 | E-MTAB-9104 | biostudies-arrayexpress

RNA-seq Analysis of intestinal tubes from the Unfed and Fed Xenopus laevis tadpoles

Project description:In this study, we assessed nutrient-dependent organ morphogenesis in Xenopus laevis. We performed the RNA-seq analysis of the gastrointestinal (GI) tract for both fed and unfed tadpoles to identify feeding-dependent inter-organ transmitters secreted from GI tract post-prandially during development. We found that one of the GI hormones, glucose-dependent insulinotropic polypeptide (GIP), is required for thyroid morphogenesis.

2022-01-24 | GSE194146 | GEO

Comparison of RNA localization during oogenesis within Acipenser ruthenus and Xenopus laevis [Xenopus laevis]

Project description:In this study we analyzed the spatial and temporal localization of maternal transcripts during oogenesis in Xenopus laevis. The occurrence of transcript asymmetry in X. laevis has been described at a global level only in matured eggs, while the establishment of the asymmetry during oogenesis has been described only for a few transcripts. In this model it was discerned that there exist three pathways (early, intermediate, late) for the establishment of the vegetal gradient, while for the animal gradient not much is known for its production. In this study we assessed the temporal establishment of the transcript localization at a global level for Xenopus laevis. We were able to determine that there are many transcripts that show temporal variability in the establishment of their localization. We observed the previously described early, intermediate (predefined) and also late pathways but found more member transcripts within these groups. We also described, perhaps for the first time, an early, intermediate (predefined) and late pathway for the animal genes as well. Additionally, we showed that some maternal transcripts are dynamic during oogenesis with degradation and de novo production being observed. Our study showed that in additional to spatial orientation to the transcripts, there is a strong temporal factor. The discovery of these new temporal profiles should help to better understand the driving forces during embryogenesis.

2022-08-23 | GSE211415 | GEO

Thyroid hormone induced resorption of tail in Xenopus laevis tadpole

Project description:Premetamorphic Xenopus laevis tadpole tail respond to thyroid hormone by resorption. The goal of this experiment is to identify the genes involved in the TH-induced resorption tadpole tail and compare it to TH-induced proliferation and differentiation program in tadpole limb and brain. Xenopus tadpoles (NF54) were treated with 100 nM T3 in 0.1 x MMR for another 24h and 48h or without T3 for 48h (control group). NF 61 tadpoles were in 0.1 X MMR till they reached NF stage 62. The tails were dissected after the experiment. Keywords: development or differentiation design,organism part comparison design,reference design,replicate design,time series design

2005-10-04 | GSE3405 | GEO

Thyroid hormone induced changes in Xenopus laevis tadpole brain

Project description:Premetamorphic Xenopus laevis tadpoles brain ventricle cells respond to thyroid hormone by proliferation and subsequent differentiation. The goal of this experiment is to identify the genes involved in the TH-induced proliferation pathway in tadpole brain and compare it to TH-induced proliferation and differentiation program in tadpole limb. Xenopus tadpoles (NF54) were treated with 1 mM methimazole in 0.1 X MMR solution for 1 week to block the endogenous TH production and reduce the TH present in the system of the tadpole. They were then treated with 100 nM T3 in 1 mM methimazole and 0.1 x MMR for another 24h and 48h or without T3 for 48h (control group). Brains from the tadpoles were dissected at the end of the experiment. Keywords: development or differentiation design,organism part comparison design,reference design,replicate design,time series design

2005-10-04 | GSE3402 | GEO

Xenopus laevis

Project description:Xenopus laevis

| PRJNA269132 | ENA

Temporal and Spatial Transcriptomic Dynamics across Brain Development in Xenopus laevis tadpoles

Project description: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. We also found that at the start of metamorphosis, neural progenitor populations appeared to be similar across the fore-, mid-, and hindbrain regions. Genes pertaining to negative regulation of differentiation were upregulated in the spinal cord compared to the rest of the brain. Finally, we found that regulation of biological processes like cell fate commitment and synaptic signaling follow similar trajectories in the brain across early tadpole metamorphosis and mid- to late-embryonic mouse development.

2022-02-22 | GSE183193 | GEO

Identification of genes associated with lens regeneration from the cornea in Xenopus laevis tadpoles

Project description:Surgical removal of the lens from larval Xenopus laevis results in a rapid transdifferention of central corneal cells to form a new lens. The trigger for this process is understood to be an induction event arising from the unprecedented contact between the cornea and the vitreous humour that occurs following lens removal. The identity of this trigger is unknown. Here, we have used a functional transgenic approach to show that BMP signalling is required for lens regeneration and a microarray approach to identify genes that are upregulated specifically during this process. Analysis of the array data strongly implicates Wnt signalling and Pitx transcription factors in this process. Pluripotency genes, in contrast, are not upregulated, supporting the idea that corneal cells transdifferentiate without returning to a stem cell state. Furthermore, several genes from the array were expressed in the forming lens during embryogenesis. One of these, nipsnap1, is a known direct target of BMP signalling. We suggest that, as with tail regeneration, activation of multiple developmental signalling pathways could drive lens regeneration from the cornea. Three biological replicates of each of three sample types were analysed. For each replicate, lens tissue (L) was derived from 5 lenses dissected from stage 50 tadpoles. Similarly, 7-8 corneas dissected from stage 50 tadpoles from which the lens had been removed 3 days previously were pooled for each biologocal replicate (R). These samples should contain tissue that is changing from cornea to lens, to regenerate the missing lens. Finally, 7-8 corneas from eyes of tadpoles at the same stage that had the cornea lifetd but the lens left in place 3 days earlier were pooled for each biological replicate (sham operated corneas, designated S).

2011-09-13 | E-GEOD-28014 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data