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.
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.
Project description:We used Drop-seq and next generation sequencing to determine gene expression differences in dogs with atopic dermatitis and healthy dogs in peripheral blood mononuclear cells in an unbiased way. Using Seurat, we find 13 discrete immune cells clusters, including a cluster enriched for Gata3 expressing T cells with 95 differentially expressed genes between healthy and allergic dogs.
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
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
Project description:The import of nuclear transcribed RNAs into mitochondria is an emerging area that presents tremendous opportunity to develop human metabolic therapeutics. However, our knowledge base is quite limited. Much remains to be discovered regarding specific RNA localization and mechanisms of import. In order to identify novel RNAs imported into mitochondria, all RNAs within the mitochondria were characterized using next generation sequencing technology. Several nuclear transcribed RNAs were found within mitochondrial RNA samples, including nuclear ribosomal RNAs, gamma satellite RNA and VL30 retroelement RNA. The presence of these RNAs within mitochondria coupled with RNA sequencing data (RNAseq) from other laboratories investigating mitochondrial RNA processing, lead us to hypothesize that nuclease treatment of mitoplasts is insufficient for removing contaminating cytoplasmic RNAs. In contrast to traditional methodology, mitochondrial import was evaluated by qRT-PCR after stepwise removal of the outer mitochondrial membrane and subsequent lysis of mitochondria. This allowed identification of RNAs lost from the mitochondria with the same kinetics as mtDNA-transcribed RNAs. This approach provided an improved evaluation of nuclear RNA enrichment within mitochondrial membranes in order to characterize nuclease protection and mitochondrial import and identify false-positive detection errors. qRT-PCR results confirmed the presence of VL30 retroelement RNA within mitochondria and question the hypothesis that the RNA component of RNase P is imported. These results illustrate a reliable approach for evaluating the presence of RNAs within mitochondria and open new avenues of investigation relating to mitochondrial RNA biology and in targeting mitochondrial based therapeutics.
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.
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.