Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1189519 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Amblyraja radiata (thorny skate) genome, sAmbRad1, alternate haplotype
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Project description:The little skate, a cartilaginous fish evolutionarily distal from tetrapods, displays walking-like behavior and has conserved genetic programs and neuronal substrates for land-walking. Studies on little skate have been limited due to lack of high-quality genome assembly. Here, we generated an improved genome assembly of little skate reflecting precise gene annotation and structures and performed integrated analysis of gene expression and chromatin accessibility to investigate molecular mechanisms of fin motor neuron development. Through interspecies comparison of RNA expression, common and species-specific genes expressed in fin/limb/wing level motor neurons were identified. Moreover, by performing chromatin accessibility analysis with a pure fin motor neuron population the potential regulators controlling the gene expression in fin motor neurons were identified. Interspecies comparison of genomic data, gene expression, and chromatin accessibility assay suggest that the little skate has highly conserved gene regulatory mechanisms controlling tetrapod locomotion, which was not previously expected.
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Project description:Whole genome sequencing of CTVT, breed dogs, and wild canids reveals pathways that are important in cancer cell survival. Comparison of these mutations with breed dogs shows that the original tumor came from a dog very similar to one of the modern Arctic breeds.
2015-07-30 | GSE70454 | GEO
Project description:The little skate, a cartilaginous fish evolutionarily distal from tetrapods, displays walking-like behavior and has conserved genetic programs and neuronal substrates for land-walking. Studies on little skate have been limited due to lack of high-quality genome assembly. Here, we generated an improved genome assembly of little skate reflecting precise gene annotation and structures and performed integrated analysis of gene expression and chromatin accessibility to investigate molecular mechanisms of fin motor neuron development. Through interspecies comparison of RNA expression, common and species-specific genes expressed in fin/limb/wing level motor neurons were identified. Moreover, by performing chromatin accessibility analysis with a pure fin motor neuron population the potential regulators controlling the gene expression in fin motor neurons were identified. Interspecies comparison of genomic data, gene expression, and chromatin accessibility assay suggest that the little skate has highly conserved gene regulatory mechanisms controlling tetrapod locomotion, which was not previously expected.
2022-10-24 | GSE180336 | GEO
Project description:While retaining ancestral morphological and genomic traits, skates evolved a novel body plan with remarkably enlarged wing-like fins that allowed skates to thrive in benthic environments, but their molecular underpinnings remain elusive. Here we investigate the origin of this phenotypical innovation by assembling a high-quality chromosome-scale genome sequence for the little skate Leucoraja erinacea and by generating extensive regulatory profiling datasets in developing fins (gene expression, chromatin occupancy and conformation). We show that despite their derived morphology, the skate genome retains multiple features of the ancestral jawed vertebrate genome.
2023-01-12 | GSE188976 | GEO
Project description:While retaining ancestral morphological and genomic traits, skates evolved a novel body plan with remarkably enlarged wing-like fins that allowed skates to thrive in benthic environments, but their molecular underpinnings remain elusive. Here we investigate the origin of this phenotypical innovation by assembling a high-quality chromosome-scale genome sequence for the little skate Leucoraja erinacea and by generating extensive regulatory profiling datasets in developing fins (gene expression, chromatin occupancy and conformation). We show that despite their derived morphology, the skate genome retains multiple features of the ancestral jawed vertebrate genome.
2023-01-12 | GSE188972 | GEO