Canis lupus familiaris
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA130301 | ENA |
REPOSITORIES: ENA
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Project description:Effects of ad libitum feeding on canine skeletal muscle gene expression
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Project description:Adipose, once considered an inert storage depot, is now known to be an active endocrine tissue involved in total body homeostasis and metabolism, which exerts effects on multiple systems including food intake, immune function, and blood glucose regulation. During the development of obesity, adipose undergoes major expansion and remodeling, but the biological processes involved in this transition are not well understood. Thus, we used canine microarrays to analyze gene expression profiles of subcutaneous adipose tissue during the transition from a lean to obese phenotype. Subcutaneous adipose tissue samples were collected from 9 intact female beagles (4 yr-old; 4 control; 5 ad libitum) at baseline, 4, 8, 12 and 24 wk after beginning ad libitum feeding.
2010-09-14 | E-GEOD-24099 | biostudies-arrayexpress
Project description:Subcutaneous and gonadal adipose tissue transcriptome differences in lean and obese female dogs
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Project description:Adipose, once considered an inert storage depot, is now known to be an active endocrine tissue involved in total body homeostasis and metabolism, which exerts effects on multiple systems including food intake, immune function, and blood glucose regulation. Adipose tissue depots are known to have unique metabolic and gene expression profiles in vivo and when cultured in vitro. Differences in adipose tissue depot function could be important in determining chronic disease risk. Few comparisons of depot gene expression have been performed in the dog. Utilizing microarray technology, our objective was to identify differentially expressed genes and enriched functional pathways between subcutaneous and gonadal adipose of lean and obese dogs. Subcutaneous and gonadal adipose tissue samples were collected from 9 intact female beagles (4 yr-old; 4 lean controls; 5 obese ad libitum-fed) after 24 wk of ad libitum feeding.
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Project description:Comparative oncology is a developing research discipline that is being used to assist our understanding of human neoplastic diseases. Companion canines are a preferred animal oncology model due to spontaneous tumor development and similarity to human disease at the pathophysiological level. We use a paired RNA sequencing (RNA-Seq)/microarray analysis of a set of four normal canine lymph nodes and ten canine lymphoma fine needle aspirates to identify technical biases and variation between the technologies and convergence on biological disease pathways. Surrogate Variable Analysis (SVA) provides a formal multivariate analysis of the combined RNA-Seq/microarray data set. Applying SVA to the data allows us to decompose variation into contributions associated with transcript abundance, differences between the technology, and latent variation within each technology. A substantial and highly statistically significant component of the variation reflects transcript abundance, and RNA-Seq proved more sensitive for detection of transcripts expressed at low levels. Latent random variation among RNA-Seq samples is also distinct in character from that impacting microarray samples. In particular, we observed variation between RNA-Seq samples that reflects transcript GC content. Platform-independent variable decomposition without a priori knowledge of the sources of variation using SVA represents a generalizable method for accomplishing cross-platform data analysis. We identified genes differentially expressed between normal lymph nodes of disease free dogs and a subset of the diseased dogs diagnosed with B-cell lymphoma using each technology. There is statistically significant overlap between the RNA-Seq and microarray sets of differentially expressed genes. Analysis of overlapping genes in the context of biological systems suggests elevated expression and activity of PI3K signaling in B-cell lymphoma biopsies compared with normal biopsies, consistent with literature describing successful use of drugs targeting this pathway in lymphomas.
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Project description:Skeletal muscle, as a large and insulin sensitive tissue, is an important contributor to metabolic homeostasis and energy expenditure. Obese dogs exhibit skeletal muscle insulin resistance, but the causes of these changes are unclear. Thus, we used canine microarrays to analyze gene expression profiles of skeletal muscle tissue collected from obese dogs, after 24 wk of ad libitum feeding. Skeletal muscle tissue samples were collected from 9 intact female beagles (4 yr-old; 4 control; 5 ad libitum) after 24 wk of ad libitum feeding.
2012-01-15 | E-GEOD-29279 | biostudies-arrayexpress
Project description:Comparative oncology is a developing research discipline that is being used to assist our understanding of human neoplastic diseases. Companion canines are a preferred animal oncology model due to spontaneous tumor development and similarity to human disease at the pathophysiological level. We use a paired RNA sequencing (RNA-Seq)/microarray analysis of a set of four normal canine lymph nodes and ten canine lymphoma fine needle aspirates to identify technical biases and variation between the technologies and convergence on biological disease pathways. Surrogate Variable Analysis (SVA) provides a formal multivariate analysis of the combined RNA-Seq/microarray data set. Applying SVA to the data allows us to decompose variation into contributions associated with transcript abundance, differences between the technology, and latent variation within each technology. A substantial and highly statistically significant component of the variation reflects transcript abundance, and RNA-Seq proved more sensitive for detection of transcripts expressed at low levels. Latent random variation among RNA-Seq samples is also distinct in character from that impacting microarray samples. In particular, we observed variation between RNA-Seq samples that reflects transcript GC content. Platform-independent variable decomposition without a priori knowledge of the sources of variation using SVA represents a generalizable method for accomplishing cross-platform data analysis. We identified genes differentially expressed between normal lymph nodes of disease free dogs and a subset of the diseased dogs diagnosed with B-cell lymphoma using each technology. There is statistically significant overlap between the RNA-Seq and microarray sets of differentially expressed genes. Analysis of overlapping genes in the context of biological systems suggests elevated expression and activity of PI3K signaling in B-cell lymphoma biopsies compared with normal biopsies, consistent with literature describing successful use of drugs targeting this pathway in lymphomas. RNA was extracted from 10 lymphoma fine needle aspirates attained from companion canines. 4 normal lymph node samples were obtained from a Beagle breeding colony at Pfizer, including two samples that were taken from the same dog but different lymph nodes. This Series represents the Affymetrix gene expression only, not RNA-Seq referenced above. RNA-Seq data have been submitted to SRA as SRA059558.
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