Felis catus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA311549 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3160242.fastq.gz | Fastqsanger.gz | |||
| SRR3160243.fastq.gz | Fastqsanger.gz | |||
| SRR3160244.fastq.gz | Fastqsanger.gz |
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Project description:Various breeds of domestic cat (Felis catus) whole genome sequence
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Project description:De novo mutations in domestic cat - A whole genome sequencing study
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Project description:TWIST1 is thought to be a novel oncogene. Understanding the molecular mechanisms regulating the TWIST1 gene expression profiles in tumor cells may give new insights regarding prognostic factors and novel therapeutic targets in veterinary oncology. In the present study we partially isolated the TWIST1 gene in Felis catus and performed comparative studies. Several primer combinations were used based on the alignments of homologous DNA sequences. After PCR amplification, three bands were obtained, purified and sequenced. Several bioinformatic tools were utilized to carry out the comparative studies. Higher similarity was found between the isolated TWIST1 gene in Felis catus and Homo sapiens (86%) than between Homo sapiens and Rattus norvegicus or Mus musculus (75%). Partial amino acid sequence showed no change in the four species analyzed. This confirmed that coding sequences presented high similarity (~96%) between man and cat. These results give the first insights regarding the TWIST1 gene in cat but further studies are required in order to establish, or not, its role in tumor formation and progression in veterinary oncology.
| S-EPMC2878985 | biostudies-literature
Project description:BackgroundDomestic cats enjoy an extensive veterinary medical surveillance which has described nearly 250 genetic diseases analogous to human disorders. Feline infectious agents offer powerful natural models of deadly human diseases, which include feline immunodeficiency virus, feline sarcoma virus and feline leukemia virus. A rich veterinary literature of feline disease pathogenesis and the demonstration of a highly conserved ancestral mammal genome organization make the cat genome annotation a highly informative resource that facilitates multifaceted research endeavors.FindingsHere we report a preliminary annotation of the whole genome sequence of Cinnamon, a domestic cat living in Columbia (MO, USA), bisulfite sequencing of Boris, a male cat from St. Petersburg (Russia), and light 30× sequencing of Sylvester, a European wildcat progenitor of cat domestication. The annotation includes 21,865 protein-coding genes identified by a comparative approach, 217 loci of endogenous retrovirus-like elements, repetitive elements which comprise about 55.7% of the whole genome, 99,494 new SNVs, 8,355 new indels, 743,326 evolutionary constrained elements, and 3,182 microRNA homologues. The methylation sites study shows that 10.5% of cat genome cytosines are methylated. An assisted assembly of a European wildcat, Felis silvestris silvestris, was performed; variants between F. silvestris and F. catus genomes were derived and compared to F. catus.ConclusionsThe presented genome annotation extends beyond earlier ones by closing gaps of sequence that were unavoidable with previous low-coverage shotgun genome sequencing. The assembly and its annotation offer an important resource for connecting the rich veterinary and natural history of cats to genome discovery.
| S-EPMC4138527 | biostudies-literature
Project description:The association of host histones with parvoviral DNA is poorly understood. We analyzed the chromatinization and histone acetylation of canine parvovirus DNA during infection by confocal imaging and in situ proximity ligation assay combined with chromatin immunoprecipitation and high-throughput sequencing. We found that at late infection parvovirus replication bodies were rich in histones bearing modifications characteristic of transcriptionally active chromatin, i.e. histone H3 lysine acetylation (H3K27ac). The H3K27ac, in particular, was located in close proximity to the viral DNA-binding protein NS1. Importantly, our results show for the first time that in the chromatinized parvoviral genome, particularly the two viral promoters were rich in H3K27ac. Histone acetyltransferase (HAT) inhibitorefficiently interfered with expression of viral proteins and infection progress. Altogether, our data suggest that acetylation of histones on parvoviral DNA is essential for viral gene expression and completion of viral life cycle. Examination of H3K27 acetylation in CPV infected and non-infected NLFK (Norden laboratory feline kidney) cells. Please note that the result in this study, considering the sequencing, is the fact that the viral genome is chromatinized. Processed data in this case would be the aligned read percentages in control cells (of which 0% aligns to parvoviral genome) and infected cells (of which ~9% only aligns to parvoviral genome and not to the cat genome), which is basically the output of the read aligner software without further processing steps (no peaks or regions were identified for the associated publication). Therefore no processed data was provided, and an exception to GEO processed data requirement was made.
2016-02-11 | E-GEOD-77785 | biostudies-arrayexpress