ATAC-Seq of Xenopus tail regeneration
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA575367 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10215912_1.fastq.gz | Fastqsanger.gz | |||
| SRR10215912_2.fastq.gz | Fastqsanger.gz | |||
| SRR10215913_1.fastq.gz | Fastqsanger.gz | |||
| SRR10215913_2.fastq.gz | Fastqsanger.gz | |||
| SRR10215914_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 36 |
Similar Datasets
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.
2020-01-31 | GSE138303 | GEO
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
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.
2017-01-30 | GSE88975 | GEO
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
Project description: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. Absence or deregulation of RICs leads to excessive extracellular matrix deposition and regeneration defects.
2023-11-30 | GSE245312 | GEO
Project description:Characterization of regeneration initiating cells during Xenopus laevis tail regeneration [scRNA-Seq]
| PRJNA1027818 | ENA
Project description: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. Absence or deregulation of RICs leads to excessive extracellular matrix deposition and regeneration defects.
2023-11-30 | GSE245318 | GEO
Project description: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. Absence or deregulation of RICs leads to excessive extracellular matrix deposition and regeneration defects.
2023-11-30 | GSE245317 | GEO
Project description: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. Absence or deregulation of RICs leads to excessive extracellular matrix deposition and regeneration defects.
2023-11-30 | GSE245313 | GEO
Project description:Amphibians such as the salamanders and the African clawed frog Xenopus are great models for regeneration studies because they can fully regenerate their lost organs. While axolotl can regenerate damaged organs throughout its lifetime, Xenopus has a limited regeneration capacity after metamorphosis. The ecotropic viral integrative factor 5 (Evi5), a cell-cycle-regulated protein that prevents cells from entering mitosis prematurely, is of great interest for it is highly upregulated in the limb blastema of axolotls, but its expression level remains unchanged in the fibroblastema of postmetamorphic frogs. Yet, its role in regeneration competent context in Xenopus has not been fully analyzed. Here we show that Evi5 is also upregulated in Xenopus tadpoles after limb and tail amputation, as it is in axolotls. Down-regulation of Evi5 with morpholino antisense oligos (Mo) impairs wound healing and blastema formation in limbs and tails in both axolotls and Xenopus tadpoles, suggesting a conserved function for Evi5 in regeneration. Using skin punch as a healing model we show that Evi5 is also involved in cell migration during wound healing. RNA-sequencing analysis shows that in addition to reduced signaling of Lepr, Pdgfa, Gdf5, evi5 Mo also downregulate lysine demethylases kdm6b and kdm7a, which are also required for limb regeneration. Thus, our results demonstrate that Evi5 plays a critical role in the regeneration of multiple systems in amphibians.
2022-11-24 | GSE218034 | GEO