Cloned Dog
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REPOSITORIES: ENA
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Project description:De novo copy number variations in cloned dogs from the same nuclear donor In this study, we aimed to identify de novo post-cloning CNV events and estimated the rate of CNV mosaicism in cloned dogs with the identical genetic background. We analyzed CNVs in seven cloned dogs using the nuclear donor genome as reference by array-CGH
2013-12-17 | E-GEOD-49092 | biostudies-arrayexpress
Project description:De novo copy number variations in cloned dogs from the same nuclear donor In this study, we aimed to identify de novo post-cloning CNV events and estimated the rate of CNV mosaicism in cloned dogs with the identical genetic background. We analyzed CNVs in seven cloned dogs using the nuclear donor genome as reference by array-CGH
2013-12-17 | E-GEOD-49123 | biostudies-arrayexpress
Project description:De novo copy number variations in cloned dogs from the same nuclear donor In this study, we aimed to identify de novo post-cloning CNV events and estimated the rate of CNV mosaicism in cloned dogs with the identical genetic background.
2013-12-17 | GSE49092 | GEO
Project description:De novo copy number variations in cloned dogs from the same nuclear donor In this study, we aimed to identify de novo post-cloning CNV events and estimated the rate of CNV mosaicism in cloned dogs with the identical genetic background.
2013-12-17 | GSE49123 | GEO
Project description:Studies on somatic mutations in cloned animals have revealed slight genetic variances between clones and their originals but have yet to identify the precise effects of these differences within the organism. Somatic mutations contribute to aging and are implicated in tumor development and other age-related diseases. To explore this, we compared whole genome sequencing data of an original dog with cloned dogs, identifying 8,155 candidate somatic mutations. By analyzing mutational signatures and rates within relevant genes, we identified potential associations with aging. Further analysis of 239 homozygous mutations within 189 genes revealed significant enrichment of traits related to chronotype, adult body size, height, spherical equivalent or myopia, and age at first sexual intercourse, suggesting these genes play roles in both growth and aging, as indicated by changes during adolescence.
2024-06-17 | E-MTAB-13924 | biostudies-arrayexpress
Project description:Free-breeding dogs have occupied the Galápagos islands at least since the 1830s, however, it was not until the 1900s that dog populations grew substantially, endangering wildlife and spreading disease. In 1981, authorities sanctioned the culling of free-roaming dogs. Yet there are currently large free-roaming dog populations of unknown ancestry on the islands of Isabela and Santa Cruz, whose ancestry has never been assessed on a genome-wide scale. Thus, we performed a complete genomic analysis of the current Galápagos dog population as well as historical Galápagos dogs sampled between 1969 and 2003, testing for population structure, admixture, and shared ancestry. Our dataset included samples from 187 modern and six historical Galápagos dogs, together with whole genome sequence from over 2,000 modern purebred and village dogs. Our results indicate that modern Galápagos dogs are recently admixed with purebred dogs but show no evidence of a population bottleneck related to the culling. Additionally, IBD analyses reveal evidence of shared shepherd-dog ancestry in the historical Galápagos dogs. Overall, our results demonstrate that the 1980s culling of dogs was ineffective in controlling population size and did little to reduce genetic diversity, instead producing a stable and expanding population with genomic signatures of historical dogs remaining today. The insights from this study can be used to improve population control strategies for the Galápagos Islands and other endangered endemic communities worldwide.
2024-10-01 | GSE276576 | GEO
Project description:Whereas cloning mammals by direct somatic cell nuclear transfer has been successful using a wide range of donor cell types, neurons from adult brain remain M-bM-^@M-^\unclonableM-bM-^@M-^] for unknown reasons. Here we examined whether neurons from adult mice could be cloned, using a combination of two epigenetic approaches. First, we used a specific antibody to discover cell types with reduced amounts of a repressive histone mark - dimethylated histone H3 lysine 9 (H3K9me2) - and identified CA1 pyramidal cells in the hippocampus and Purkinje cells in the cerebellum as candidates. Second, reconstructed embryos were treated with trichostatin A (TSA), a potent histone deacetylase inhibitor. Using CA1 cells, cloned offspring were obtained at high rates, reaching 10.2% and 4.6% (per embryos transferred) for male and female donors, respectively. Cerebellar Purkinje cell nuclei were too large to maintain their genetic integrity during nuclear transfer, leading to developmental arrest of embryos. However, gene expression analysis using cloned blastocysts corroborated a high rate of genomic reprogrammability of CA1 pyramidal and Purkinje cells. Neurons from the hippocampal dentate gyrus and cerebral cortex, which had higher amounts of H3K9me2, could also be used for producing cloned offspring, but the efficiencies were low. A more thorough analysis revealed that TSA treatment was essential for cloning adult neuronal cells. This study demonstrated for the first time that adult neurons could be cloned by nuclear transfer. Furthermore, our data imply that reduced amounts of H3K9me2 and increased histone acetylation appear to act synergistically to improve the development of cloned embryos. Comparative gene expression analyses using blastocysts of cloned embryos were performed by microarray. Cloned embryos were produced with three different types of donor cells (neonatal Sertoli cells, CA1 pyramidal cells and Purkinje cells) and all cloned embryos were treated with Trichostatin A (TSA). Each embryos were cultured for 96 h and blastocysts derived from each donor cell types were subjected to gene expression microarray. For comparison of gene expression, the data sets of control sex- and genotype-matched embryos produced by in vitro fertilization and SCNT-derived blastocysts from cumulus cells treated with TSA from our previous paper (Inoue K. et al. Science 2010) were also used.
2015-02-03 | E-GEOD-65497 | biostudies-arrayexpress
Project description:Somatic Mutation Patterns in Cloned Dogs: Implications for Aging
| PRJEB74060 | ENA
Project description:The inherent diversity of canines is closely intertwined with the unique color patterns of each dog population. These variations in color patterns are believed to have originated through mutations and selective breeding practices that occurred during and after the domestication of dogs from wolves. To address the significant gaps that persist in comprehending the evolutionary processes that underlie the development of these patterns, we generated and analyzed deep-sequenced genomes of 113 Korean indigenous Jindo dogs that represent five distinct color patterns to identify the associated mutations in CBD103, ASIP, and MC1R. The degree of linkage disequilibrium and estimated allelic ages consistently indicate that the black-and-tan dogs descend from the first major founding population on Jindo island, compatible with the documented literature. We additionally demonstrate that black-and-tan dogs, in contrast to other color variations within the breed, exhibit a closer genetic affinity to ancient wolves from western Eurasia than those from eastern Eurasia. Lastly, population-specific genetic variants with moderate effects were identified, particularly in loci associated with traits underlying body size and behavioral variations, potentially explaining the observed phenotypic diversity based on coat colors. Overall, comparisons of whole genome sequences of each coat color population diverged from the same breed provided an unprecedented glimpse into the properties of evolutionary processes maintaining variation in Korean Jindo dog populations that were previously inaccessible.
2024-04-05 | E-MTAB-13939 | biostudies-arrayexpress
Project description:To infer potential epigenetic variations during SCNT procedure that could occur and lead to abnormal sex-reversal phenotype, we performed whole genome bisulfite sequencing (WGBS) on DNAs extracted from primary fibroblast cells isolated from seven dog samples. These samples include two normal donors, two sex-reversed cloned dogs, one sex-reversed re-cloned dog as well as a pair of independent replicate samples taken as controls
2016-11-09 | GSE74225 | GEO