Next Generation Sequencing of different ovine muscle's Transcriptomes
Ontology highlight
ABSTRACT:
ORGANISM(S): Ovis aries
PROVIDER: GSE43316 | GEO | 2013/12/01
SECONDARY ACCESSION(S): PRJNA185414
REPOSITORIES: GEO
Similar Datasets
Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of different ovine muscle's transcriptomes. 9.27 gigabases of sequence from two different breeds of sheep. Examination of 2 different muscle's transcriptomes in 2 breed types.
2013-12-01 | E-GEOD-43316 | biostudies-arrayexpress
Project description:Normal development in the brain requires temporal changes in gene expression. A better understanding of the genomics of the fetal brain during late gestation can help to improve our understanding of the molecular events that enable the newborn to survive extra-uterine life. The purpose of the present study is to model changes and coherence of gene expression in cerebral cortex, brainstem, hippocampus, and hypothalamus throughout the second half of gestation. We used the sheep as an animal model to identify co-expressed genes in different regions of the ovine fetal brain, from mid-gestation (80 days) to one day of postnatal life. In the ewe, gestation length varies from 142 to 152 days, with an average of 147 days. Using a newly-available ovine array and weighted gene co-expression network analysis (WGCNA), we tested the hypothesis that the resulting products of genes expressed in a similar pattern through the last stage of gestation in different brain regions are functionally related and could play an important role in the normal fetal development.
2014-06-30 | GSE50460 | GEO
Project description:In humans and other species, Longlong-term hypoxia (LTH) during pregnancy can lead to intrauterine growth restriction with reduced body/brain weight, dysregulation of cerebral blood flow (CBF), and other problems in humans and rodents. In contrast, sheep appear to undergo relatively successful acclimatization, not demonstrating any of the above-mentioned problems except at extremely high altitude. To identify the signal transduction genetic pathways and those critical molecules, which may be involved in acclimatization to high altitude LTH, we conducted microarray with advanced bioinformatic analysis on carotid arteries (CA) from the normoxic near-term ovine fetus at sea-level and those acclimatized to high altitude for 110+ days during gestation. In response to LTH acclimatization, in fetal CA we identified, mRNA from 38 genes upregulated (> 2 fFold; (P < 0.05) and 9 genes downregulated (> 2-f Fold; (P < 0.05). The major genes with upregulated mRNA were SLC1A3, Insulin-like growth factor (IGF) binding protein 3, IGF type 2 receptor, transforming growth factor (TGF) Beta-3, and genes involved in the AKT and BCL2 signal transduction networks. The majority of genes with upregulated mRNA have a common motif for Pbx/Knotted homeobox in the promoter region, and Sox family binding sites in the 3M-bM-^@M-^Y un -translated region (UTR). Genes with downregulated mRNA included those involved in the P53 pathway and 5-lipoxygenase activating proteins. The promoter region of all genes with downregulated mRNA, had a common 49 bp region, with a binding site for DOT6 and TOD6, components of the RPD3 histone deacetylase complex RPD3C(L). We also identified miRNA complementary to a number of the altered genes. Thus, the present study identified molecules in the ovine fetus, which may help it to play a role in the acclimatizatione successfully response to high-altitude associated LTH. In these series of experiments we examined changes in gene expression in sheep carotids. Pregnant sheep and non-pregnant adult sheep were exposed to 110 days of hypoxia at 3801 meters of altitude. Carotid arteries from fetuses from non-pregnant adult from sea-level controls and those from high-altitude were compared by Agilent ovine custom array
2013-08-15 | E-GEOD-49920 | biostudies-arrayexpress
Project description:Mannheimia haemolytica strain:ovine | isolate:ovine Genome sequencing and assembly
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Project description:Gastrointestinal nematode (GIN) infections are considered the most important disease of grazing sheep. Due to increasing anthelmintic resistance, chemical control alone is inadequate. Resistance to GIN infection is a heritable trait, and through natural selection many sheep breeds have higher resistance. Studying the transcriptome from GIN-exposed and GIN-unexposed sheep using RNA-Sequencing technology can provide measurements of transcript levels associated with the host response to GIN infection, and these transcripts may harbor genetic markers that can be used in selective breeding programs to enhance disease resistance. The objective of this study was to compare liver transcriptomes of sheep naturally exposed to GINs, with either high or low parasite burdens, to GIN-unexposed control sheep in order to identify key regulator genes and biological processes associated with GIN infection. Differential gene expression analysis revealed no significant differentially expressed genes (DEG) between sheep with a high or low parasite burden (P-value ≤ 0.01; False Discovery Rate (FDR) ≤ 0.05; and Fold-Change (FC) of > 2). However, when compared to the control group, low parasite burden sheep showed 159 DEG, and high parasite burden sheep showed 146 DEG (P-value ≤ 0.01; FDR ≤ 0.05; and FC of > 2). Among these two lists of significant DEG, 86 DEG were found in common between the two parasite burden groups compared to the control (GIN-unexposed sheep). Functional analysis of these significant 86 DEG found upregulated genes involved in immune response and downregulated genes involved in lipid metabolism. Results of this study offer insight into the liver transcriptome during natural GIN exposure that helps provide a better understanding of the key regulator genes involved in GIN infection in sheep.
2023-02-10 | GSE224936 | GEO
Project description:Normal development in the brain requires temporal changes in gene expression. A better understanding of the genomics of the fetal brain during late gestation can help to improve our understanding of the molecular events that enable the newborn to survive extra-uterine life. The purpose of the present study is to model changes and coherence of gene expression in cerebral cortex, brainstem, hippocampus, and hypothalamus throughout the second half of gestation. We used the sheep as an animal model to identify co-expressed genes in different regions of the ovine fetal brain, from mid-gestation (80 days) to one day of postnatal life. In the ewe, gestation length varies from 142 to 152 days, with an average of 147 days. Using a newly-available ovine array and weighted gene co-expression network analysis (WGCNA), we tested the hypothesis that the resulting products of genes expressed in a similar pattern through the last stage of gestation in different brain regions are functionally related and could play an important role in the normal fetal development. Tissues from cortex, brainstem, hippocampus and hypothalamus were collected from non treated fetuses at 80 (80d, n=4), 96M-bM-^@M-^S100 (100d, n=4), 120 (120d, n=4), 130 (130d, n=4), and 142M-bM-^@M-^S144 (145d, n=4) days of gestation and on the first (1d, n=4) day after delivery. Each group included one set of twin fetuses. None of the ewes showed any signs of impending labor.
2014-06-30 | E-GEOD-50460 | biostudies-arrayexpress
Project description:Mear prodution is the most important trait for sheep. In this study, we performed a Genome-wide association study (GWAS) by using Illumina Ovine SNP50 BeadChip in 329 purebred sheep phenotyped for 11 growth and meat production traits (birth weight, weaning weight, 6-month weight, eye muscle area, fat thickness, pre-weaning gain, post-weaning gain, daily weight gain, height at withers , chest girth and shin circumference). A total of 319 sheep and 48,198 SNPs were fitted using TASSEL 3.0 software as random effects in a mixed linear model. 36 chromosome-wise significant SNPs were identified for 7 traits and 10 of them reached genome-wide significance level consistently for post-weaning gain. Gene annotation was implemented based on the latest version3.1 ovine genome sequence (released October 2012), and meanwhile we referenced genomic information of human, bovine, mouse and rat. More than one-third SNPs (14 out of 36) were located within ovine genes , some other were located close to ovine genes (878bp-398165bp apart). 329 sheep DNA were scanned using OvineSNP50 Beadchip and the association is done between the SNP data and 11 different meat prodution traits
2015-05-01 | E-GEOD-46231 | biostudies-arrayexpress
Project description:The period of development from the last two weeks of gestation through the first two weeks of life spans a period of great functional and metabolic challenge to the fetal and neonatal lamb heart. Important changes in gene expression occur to meet these challenges. On this study, septa from sheep hearts at 130 days gestation (n=6), term (n=8, gestational lenght is around 145 days) and 14-days-old lambs (n=8) were used to model the changes in gene expression patterns during the perinatal period using Agilent 15k ovine microarrays. Weighted gene co-expression network analysis (WGCNA) determined five major patterns of co-expressed and functionally related genes during this critical period of cardiac transition.
2015-07-30 | GSE66725 | GEO
Project description:Ovine mastitis is defined as the inflammation of the sheep udder, most commonly caused in response to intramammary infections. Based on the occurrence of clinical signs, mastitis is characterized as either clinical or subclinical (SCM). The impact of ovine SCM on the overall sustainability of dairy sheep farms has been documented underpinning the significance of efficient diagnosis. Although SCM can be detected in cows, the performance and the validity of the methods used do not transfer in dairy sheep. This fact challenges the development of evidence-based ovine udder health management protocols and renders the detection and control of ovine mastitis rather problematic. Currently, cell culture-based models are being successfully used in biomedical studies and have also been effectively used in the case of bovine mastitis. The objective of the present study was to culture ovine primary mammary cells for the development of 2D and 3D cell culture-based models for the study of ovine SCM. Cells were infected by mastitis-inducing pathogens mimicking the pathogenesis of SCM as derived by natural intramammary infections. The secreted proteins were subjected to mass-spectrometry resulting in the identification of 79 distinct proteins. Among those, several had already been identified in healthy or mastitic milk, while others were detected for the first time in the ovine mammary secretome. The development of cell-based models for the early detection and the overall study of SCM has the potential to be applicable and beneficial for the udder health management in dairy sheep.
2022-11-03 | PXD036985 | Pride