Project description:Expression of known and predicted genes in tissues of Xenopus tropicalis (frog) pooled from multiple healthy individuals. Two-colour experiments with two different tissues hybridized to each array. Each tissue is arrayed in replicate with dye swaps. Tissues: Brain, Cartilage, Esophagus, Eye, Fat body, Femur, Gallbladder, Heart, Kidney, Large intestine, Liver, Lung, Muscle, Ovary, Oviduct, Skin, Small intestine, Spleen, Stomach, Testis
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.
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.
Project description:DNA methylation clocks have been widely used for accurate age prediction, but most studies have been carried out on mammals. Here we present an epigenetic clock for the aquatic frog Xenopus tropicalis, a widely used model organism in developmental biology and genomics. To construct the clock, we collected DNA methylation data from 192 frogs using targeted bisulfite sequencing at genomic regions containing CpG sites previously shown to have age-associated methylation in Xenopus. We found highly positively and negatively age-correlated CpGs are enriched in heterochromatic regions marked with H4K20me3 and H3K9me3. Positively age-correlated CpGs are enriched in bivalent chromatin and gene bodies with H3K36me3, and tend to be proximal to lowly expressed genes. These epigenetic features of aging are similar to those found in mammals, suggesting evolutionary conservation of epigenetic aging mechanisms. Our clock enables future aging biology experiments that leverage the unique properties of amphibians.
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.
