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RNA-seq of a time course of spinal cord regeneration following tail amputation in Xenopus tropicalis tadpoles at stage 50

ABSTRACT: RNA-seq of a time course of spinal cord regeneration following tail amputation in Xenopus tropicalis tadpoles at stage 50

PROVIDER: PRJEB36722 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3895411.fastq.gz	Fastqsanger.gz
	ERR3895412.fastq.gz	Fastqsanger.gz
	ERR3895413.fastq.gz	Fastqsanger.gz
	ERR3895414.fastq.gz	Fastqsanger.gz
	ERR3895415.fastq.gz	Fastqsanger.gz

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single cell RNAseq on isolated spinal cord cells before and 3 day post tail amputation in Xenopus tropicalis tadpoles at stage NF50

Project description:The tails of stage NF50 Xenopus tropicalis tadpoles were amputated and samples were collected at 0 and 3 days post amputation. 10 spinal cords were isolated for each time point. After cell dissociation, single cell RNAseq was performed using 10X Genomics platform

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RNA-seq of a time course of spinal cord regeneration following tail amputation in Xenopus tropicalis tadpoles at stage 50

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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.

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single cell RNAseq on isolated spinal cord cells before and 3 day post tail amputation in Xenopus tropicalis tadpoles at stage NF50

Project description:single cell RNAseq on isolated spinal cord cells before and 3 day post tail amputation in Xenopus tropicalis tadpoles at stage NF50

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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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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.

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Project description:Tadpoles of the anuran species Rana pirica can undergo predator-specific morphological responses. Exposure to a predation threat by larvae of the salamander Hynobius retardatus results in formation of a bulgy body (bulgy morph) with a higher tail. Whereas, dragon fly also induced higher tail tadpole. The tadpoles revert to a normal phenotype upon removal of the larval salamander or dragon fly threat. The objective of the present study was to use Affymetrix Xenopus Genechip to profile gene expression in the tail tissue by different predation threat. Tadpoles of Rana pirica treated with larvae salamander for 8days (S1, S2, S3) or dragon fly for 8days (Y1,Y2, Y3) were analyzed with triplicate. Removal experiments were also treated with predators for 4days and then removed predators from tadpoles (-S1,-S2, -S3) or (-Y1,-Y2,-Y3). Controls were cultured for 8days without predators (C2, C3). Tails from tadpoles after 8days of each treatment were dissected for RNA extraction and gene expression analysis using Affymetrix Xenopus Genechip arrays.

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Gene expression in the tail tissue of tadpoles [Rana pirica] by larvae salamander or dragon fly

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Project description:RNA-seq of a time course of spinal cord regeneration following tail amputation in Xenopus tropicalis tadpoles at stage 50

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