Xenopus laevis
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ABSTRACT:
PROVIDER: PRJDB12234 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:RNA-seq of regenerating tails of il11ra.L knocked-down tadpoles
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Project description:Comparison of regenerating and non regenerating transgenic stage 52 Xenopus hind limbs
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Project description:Global analysis of gene expression in Xenopus hindlimbs during stage-dependent complete and incomplete regeneration
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Project description:Xenopus laevis tadpoles are capable of limb regeneration following amputation, in a process which initially involves the formation of a blastema. However, Xenopus has full regenerative capacity only through premetamorphic stages. We have used the Affymetrix Xenopus laevis Genome Genechip® microarray to perform a large-scale screen of gene expression in the regeneration-complete, stage 53 (st53), and regeneration-incomplete, stage 57 (st57), hindlimbs at 1 and 5 days post-amputation. Through an exhaustive reannotation of the Genechip® and a variety of comparative bioinformatic analyses, we have identified genes that are differentially expressed between the regeneration-complete and âincomplete stages, detected the transcriptional changes associated with the regenerating blastema, and compared these results with those of other regeneration researchers. We focus particular attention on striking transcriptional activity observed in genes associated with patterning, stress response, and inflammation. Overall, this work provides the most comprehensive views yet of a regenerating limb and different transcriptional compositions of regeneration-competent and deficient tissues. Experiment Overall Design: This experiment measures gene expression in regeneration competent stage 53 and regeneration non-competent stage 57 Xenopus laevis hindlimbs, at 1 and 5 days post-amputation. Four replicates for each condition were used. Hindlimbs at either st53 or st57 were amputated unilaterally or bilaterally at the mid-zeugopodia level. One (1dPA) and 5 days (5dPA) after amputation tissues were collected 1mm proximal to the original level of amputation. Total RNA was isolated using RNaqueous micro kit (Ambion, inc.). One microgram of total RNA was amplified with the the Affymetrix 2 cycle kit and assayed per Genechip using standard Affymetrix protocols.
2008-06-13 | E-GEOD-4738 | biostudies-arrayexpress
Project description:RNA-seq analysis after spinal cord injury in Xenopus laevis
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Project description:RNA-seq based identification of potential RARgamma target genes in Xenopus laevis
| PRJNA309946 | 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 | GSE245313 | 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 | GSE245312 | GEO
Project description: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. In the present study we investigated the transcriptome of regenerating half-embryos after sagittal and dorsal-ventral (D-V) bisections. Individual embryos were operated at midblastula with an eyelash hair and cultured until early gastrula (stage 10.5) or late gastrula (Stage 12) and analyzed the transcriptome of each half-embryo by RNAseq. Because many genes are activated by wound healing, stringent analyses were used to identify genes upregulated in identical twins but not in either dorsal or ventral fragments. At early gastrula cell division-related genes such as histones were identified, whereas at late gastrula pluripotency genes (such as sox2) and germ layer determining genes (such as eomesodermin, ripply2 and activing receptor ACVRI) and a number of secretory pathway components (serpinH1, fucoleptin and sialyl transferase). These findings are consistent with a model in which cell division is required to heal damage, while maintaining pluripotency to permit formation of the organizer with a displacement of 900 from its original site. In addition, the extensive transcriptomic data presented here (30 RNA-seq libraries of individual whole or regenerating half-embryos) provides a useful resource for data mining gene expression during early vertebrate development.
2019-02-01 | GSE124563 | GEO