Dogs
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB16012 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:DNA structural variation (SV) comprises a major portion of genetic diversity, but its biological impact is unclear. We propose that the genetic history and extraordinary phenotypic variation of dogs make them an ideal mammal in which to study the effects of SV on biology and disease. The hundreds of existing dog breeds were created by selection of extreme morphological and behavioral traits. And along with those traits, each breed carries increased risk for different diseases. We used array CGH to create the first map of DNA copy number variation (CNV) or SV in dogs. The extent of this variation, and some of the gene classes affected, are similar to those of mice and humans. Most canine CNVs affect genes, including disease and candidate disease genes, and are thus likely to be functional. We identified many CNVs that may be breed or breed class specific. Cluster analysis of CNV regions showed that dog breeds tend to group according to breed classes. Our combined findings suggest many CNVs are (1) in linkage disequilibrium with flanking sequence, and (2) associated with breed specific traits. We discuss how a catalog of structural variation in dogs will accelerate the identification of the genetic basis of canine traits and diseases, beginning with the use of whole genome association and candidate CNV/gene approaches. Chen WK, Swartz JD, Rush LJ, Alvarez, CE. Mapping DNA structural variation in dogs. Genome Res. 2009. 19: 500 509 PMID: 19015322
2009-09-30 | GSE18317 | GEO
Project description:DNA structural variation (SV) comprises a major portion of genetic diversity, but its biological impact is unclear. We propose that the genetic history and extraordinary phenotypic variation of dogs make them an ideal mammal in which to study the effects of SV on biology and disease. The hundreds of existing dog breeds were created by selection of extreme morphological and behavioral traits. And along with those traits, each breed carries increased risk for different diseases. We used array CGH to create the first map of DNA copy number variation (CNV) or SV in dogs. The extent of this variation, and some of the gene classes affected, are similar to those of mice and humans. Most canine CNVs affect genes, including disease and candidate disease genes, and are thus likely to be functional. We identified many CNVs that may be breed or breed class specific. Cluster analysis of CNV regions showed that dog breeds tend to group according to breed classes. Our combined findings suggest many CNVs are (1) in linkage disequilibrium with flanking sequence, and (2) associated with breed specific traits. We discuss how a catalog of structural variation in dogs will accelerate the identification of the genetic basis of canine traits and diseases, beginning with the use of whole genome association and candidate CNV/gene approaches. Chen WK, Swartz JD, Rush LJ, Alvarez, CE. Mapping DNA structural variation in dogs. Genome Res. 2009. 19: 500 509 PMID: 19015322 Array comparitive genomic hybridization analysis of structural variation in 9 dogs, and 1 lymphoma cell line.
2010-05-22 | E-GEOD-18317 | biostudies-arrayexpress
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:Transcriptional profiling of dog muscle tissue comparing control dogs. tested, genomewide, for genes differentially expressed in muscle between the escapers and the affected dogs. Using Agilent mRNA SurePrint Canine arrays, we compared muscle gene expression of the two escapers, four affected, and four normal dogs at age 2 years.
2015-11-19 | GSE69040 | GEO
Project description:SNP genotyping was used to determine if the free living Highland Wild dogs of Papua, Indonesia are the ansestors of captive New Guinea Singing Dogs.
2020-03-31 | GSE143824 | GEO
Project description:Transcriptional profiling of dog muscle tissue comparing control dogs. tested, genomewide, for genes differentially expressed in muscle between the escapers and the affected dogs. Using Agilent mRNA SurePrint Canine arrays, we compared muscle gene expression of the two escapers, four affected, and four normal dogs at age 2 years. normal, affected DMD, and escapers
2015-11-19 | E-GEOD-69040 | biostudies-arrayexpress
Project description:Renal insufficiency is a risk factor for development of cardiovascular disease. In this study our aim was to investigate functional and structural changes in the heart of dogs with mild renal insufficiency induced by uninephrectomy (UNX). In addition to comprehensively assessing functional parameters 12 week after UNX or sham surgery, we harvested tissue for assessment of structural changes. Microarray analyses were performed on snap frosen tissue from the left atrium (LA) and left ventricle (LV) of UNX and sham operated animals. Gene expression in LA was compared between the groups, and gene expression in the LV was compared between the groups. We aimed to assess whether a potentially altered gene expression in the heart of the UNX group also included genes associated with cardiac remodeling. Six dogs were assigned to unineprectomy and 6 dogs were assigned to sham operation. Microarray analyses were performed on 5 samples from the left atrium of uninephrectomized animals and on 5 samples from the left atrium of sham operated animals. Further, microarray analyses were performed on 5 samples from the left ventricle of uninephcretomized animals and on 5 samples from the left ventricle of sham operated animals. No replicates were perfomed.
2013-06-13 | E-GEOD-47876 | 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-49092 | biostudies-arrayexpress