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PROVIDER: PRJNA820034 | ENA |
REPOSITORIES: ENA
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Project description:The purpose of this study was the identification of RNAs contained in the urinary exosome (UExo) from dogs and cats. The quality of total RNA in isolated urinary exosome (UExo)-derived total RNAs obtained from the column-based method (urine 1 mL) was checked by using a Bioanalyzer, and samples from normal renal function (NR) group and kidney disease (KD) group were pooled as one sample for each group. We collected NR dogs (n = 37), KD dogs (n = 47), NR cats (n=43), and KD cats (n = 45). For the next generation sequencing, libraries were prepared according to the manufacturer’s protocols and sequenced using 50-base reads acquired by using a HiSeq 2000 platform. The December 2011 (GRCm38/mm10) mouse (Mus musculus) genome data were used as reference. As a result, we could identify the miRNA from these samples.
2018-12-10 | GSE121156 | GEO
Project description:Staphylococcus haemolyticus from Dogs and Cats WGS
| PRJNA821205 | ENA
Project description:WGS of dogs and cats with suspected heritable conditions
| PRJEB52248 | ENA
Project description:Canine gastric dilatation-volvulus (GDV) is a common life-threatening condition occurring primarily in large and giant breeds with a 3.9% to 36.7% lifetime risk. GDV is a complex disease with risk factors including age, diet, behavior, family history, and genetics. The genetic correlates of GDV have not previously been systematically explored. We undertook multiplatform genome-wide association analysis (GWAS) of 253 dogs including 106 healthy dogs and 147 dogs with at least one GDV episode. The study included ten dog breeds enriched for Borzoi, German Shepherd (GSD), Great Dane, and Standard Poodle. SNP array genotyping was performed on constitutional DNA from all 241 samples to identify GDV-associated SNPs and CNVs. To increase the coverage of our study we performed imputation analysis of the SNP data as well as additional whole genome sequencing (WGS) on a subset of 33 dogs (15 healthy dogs and 18 GDV patients from the three most represented breeds). Twenty-one patients were genotyped by both SNP and WGS platforms. The GWAS was conducted across breeds as well as on specific breeds using a mixed linear model adjusting for relatedness, population structure and sex. After genome-wide Bonferroni correction, we identified a significant protective GDV-associated SNP, rs851737064, occurring in an intergenic region, across all breeds. The signal was most significant in Collies, German Shorthaired Pointers, and Great Danes. Subsequent focused analysis across these three breeds identified 12 additional independent, protective and deleterious SNPs with significant GDV association. Additional GWAS conducted on Borzoi, GSD and Great Dane yielded significant genome-wide GDV associations in 11 independent SNPs, while that in Borzoi alone identified 2 independent GDV-associated SNPs. We then used WGS data to validate the imputation analysis. Notable significant SNPs included genes involved in gastric tone and motility including VHL, NALCN, and PRKCZ. From the WGS data we also detected two independent GDV-associated SNPs in Borzoi, GSD and Great Dane breeds on an intergenic region on chromosome 7 not covered by previous analyses. These data provide important new information regarding canine GDV risk factors and facilitate generation of hypotheses regarding the genetic and molecular underpinnings this syndrome.
2020-12-01 | GSE141128 | GEO
Project description:BACKGROUND: Meticillin-resistant Staphylococcus aureus (MRSA) infections remain important medical and veterinary challenges. The MRSA isolated from dogs and cats typically belong to dominant hospital-associated clones, in the UK mostly EMRSA-15 (CC22 SCCmecIV), suggesting original human-to-animal transmission. Nevertheless, little is known about host-specific genetic variation within the same S. aureus lineage. HYPOTHESIS/OBJECTIVES: To identify host-specific variation amongst MRSA CC22 SCCmecIV by comparing isolates from pets with those from in-contact humans using whole-genome microarray. METHODS: Six pairs of MRSA CC22 SCCmecIV from human carriers (owners and veterinary staff) and their respective infected in-contact pets were compared using a 62-strain whole-genome S. aureus microarray (SAM-62). The presence of putative host-specific genes was subsequently determined in a larger number of human (n = 47) and pet isolates (n = 93) by PCR screening. RESULTS: Variation in mobile genetic elements (MGEs) occurred frequently and appeared largE: The variation found amongst MGEs highlights that genetic adaptation in MRSA continues. However, host-specific MGEs were not detected, which supports the hypothesis that pets may not be natural hosts of MRSA CC22 and emphasizes that rigorous hygiene measures are critical to prevent contamination and infection of dogs and cats. The host specificity of individual heavy-metal resistance genes warrants further investigation into different selection pressures in humans and animals.
2013-11-02 | E-BUGS-138 | biostudies-arrayexpress
Project description:Background: Ultra-Conserved-Non-coding Elements (UCNEs) are genomic sequences that exhibit >95% sequence identity between human, mammals, birds, reptiles and fishes. Recent findings reported their functional role in cancer. Aim of this study was to evaluate their DNA methylation modifications in squamous cell carcinoma (SCC) from different mammal species Methods: Fifty SCC from 26 humans, 17 cats, 3 dogs, 1 horse, 1 bovine, 1 badger and 1 porcupine were investigated. Fourteen feline stomatitis and normal samples from 36 healthy human donors, 7 cats, 5 dogs, 5 horses, 2 bovines and 1 badger were collected as normal controls. Bisulfite Next Generation Sequencing evaluated the DNA methylation level from seven UCNEs (uc.160, uc.283, uc.416, uc.339, uc.270, uc.299, uc.328). Results: 57/59 CpGs were significantly different according to the Kruskal-Wallis test (P<0.05) comparing normal vs SCC. A common DNA hypermethylation pattern was observed in SCC from all the species evaluated in this study, with an increasing trend of hypermethylation starting from normal mucosa, through stomatitis to SCC. Conclusions: Our findings indicate that UCNEs are hypermethylated in human SCC, and this behavior is also conserved among different species of mammals.
2020-09-04 | GSE157436 | GEO