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Xenopus tropicalis

ABSTRACT: RNA-Seq of Xenopus tail regeneration

PROVIDER: PRJNA349464 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4435590.fastq.gz	Fastqsanger.gz
	SRR4435591.fastq.gz	Fastqsanger.gz
	SRR4435592.fastq.gz	Fastqsanger.gz
	SRR4435593_1.fastq.gz	Fastqsanger.gz
	SRR4435593_2.fastq.gz	Fastqsanger.gz

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Transcription profiling of Xenopus tropicalis tadpole tail tissue regeneration following removal

Project description:In this experiment, we show transcription profiling of the Xenopus tropicalis tadpole tail tissue regeneration following removal. The tail tissues include its spinal cord, notochord, muscle, and dorsal aorta. We characterized the early, intermediate, and late stages of Xenopus tropicalis tail regeneration using the Xenopus tropicalis Affymetrix genome array in biological replicate.

2010-10-01 | E-MEXP-2420 | biostudies-arrayexpress

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ATAC-Seq of Xenopus tail regeneration

Project description:Mammals possess limited regeneration capabilities, where the few examples of scarless healing tend to be restricted to early development. In light of this, it is of great interest to study animals that can faithfully regrow complete appendages, and uncover the biological properties that facilitate this process. Xenopus tropicalis tadpoles are excellent vertebrate models of regeneration, as they rapidly recover lost tails within just one week post amputation. Though we have some understanding of what pathways are required for tail regeneration, we have yet to systematically chronicle the regulatory events that coordinate this specialized response to injury. Here, we highlight a striking phenomenon in Xenopus regeneration, whereby nuclei within the fin epithelium of an amputated tail change shape in a dramatic and stereotyped manner during regeneration. We assess chromatin accessibility dynamics through ATAC-Seq of nine time points of regeneration, and find that large scale changes in chromatin state are highly correlated to changes in nuclear shape. To identify critical regulators of these chromatin dynamics, we describe and apply a machine learning method, PFBoost, which integrates information from motifs underlying dynamically accessible ATAC-Seq peaks and differentially expressed transcription factors from time-matched RNA-Seq data to predict chromatin state. To functionally evaluate PFBoost-predicted regeneration regulators, we developed an inducible CRISPRi system utilizing the FKBP derived destabilizing domain, and knockdown expression of these regulators during the early hours of regeneration. With this methodology, we identified and describe two novel regulators of regeneration, spib and chd8. We provide not only an abundant resource for chromatin dynamics in tail regeneration, but also chronicle an intriguing mechanism of regeneration regulation in the form of nuclear shape change and coordinate changes in chromatin state.

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Next generation sequencing identifies differentially localized transcripts in Xenopus laevis and Xenopus tropicalis oocytes

Project description:RNA-seq technology was used to identify differentially localized transcripts from Xenopus laevis and Xenopus tropicalis stage VI oocytes. Besides the discovery of a group of novel animally enriched RNAs, this study revealed a surprisingly low conservation of vegetal RNA localization between the two frog species. mRNA profiles of Xenopus laevis and Xenopus tropicalis animal and vegetal oocyte halves were generated by RNA-seq technology. For Xenopus laevis, animal and vegetal oocyte RNA preparations from two different females were generated in duplicates. For Xenopus tropicalis, animal and vegetal oocyte RNA preparations from two different females were analyzed.

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MicroRNA editing in Xenopus tropicalis

Project description:We collected small RNA sequencing data from brain and heart of an adult Xenopus tropicalis individual to investigate the conservation of site-specific miRNA editing events identified in mammals.

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RNA-Seq of Xenopus tail regeneration

Project description:In contrast to humans, many amphibians are able to rapidly and completely regenerate complex tissues, including complete appendages. Following tail amputation, Xenopus tropicalis tadpoles quickly regenerate muscle, spinal cord, cartilage, vasculature and skin, all properly patterned in three dimensions. To better understand the molecular basis of this regenerative competence, we performed a transcriptional analysis of regeneration using RNA-Seq. We profiled the transcriptome at 6 timepoints during tail regeneration, and used clustering analysis to identify biological processes that are prioritized during different transitions in the regeneration process. Our work expands significantly on previous expression analyses of tail regeneration. We are able to refine the windows during which many key biological signaling processes act, including embryonic patterning signals, immune responses, bioelectrical signaling and apoptosis. By including multiple timepoints within the first 24 hours post-amputation, we have also identified new processes that are highly prioritized early in regeneration, including axonogenesis, chemotaxis, and RNA metabolism. Our work provides a deep database for researchers interested in appendage regeneration, and highlights new avenues for further study.

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