Expression data from subcutaneous adipose tissue of barrows and boars
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ABSTRACT:
ORGANISM(S): Sus scrofa
PROVIDER: GSE45710 | GEO | 2013/04/08
SECONDARY ACCESSION(S): PRJNA195911
REPOSITORIES: GEO
Similar Datasets
Project description:The male hypogonadism is closely associated with adipose tissue metabolism. Domestic pig has been a widely used experimental animal in biomedical research because of their similarity to humans in body size and other physiological/anatomical features. However, the transcriptional responses of pigs to male hypogonadism in subcutaneous adipose tissue remain unclear so far. We used microarrays to detail the transcriptional profiles of barrows and boars, and determined the gene networks regulated by castration-induced sex hormone deficiency. This study will help to provide a significant addition to knowledge about fat accumulation and lipid metabolism in hypogonadal man. The subcutaneous adipose tissue of barrows and boars were acquired at 175 d of age for RNA extraction and hybridization on Affymetrix microarrays. All the fifteen pairs of full sibs were divided into six subgroups. An equal amount of total RNA from 5 boars was pooled in a subgroup, and RNA from 5 barrows in each pair of full sibs was pooled in another subgroup. Each pooled RNA sample was hybridized to a separate array. A total of 6 gene chips were used in this study, resulting in three biological duplicates.
2013-04-08 | E-GEOD-45710 | biostudies-arrayexpress
Project description:Skatole is one of the compounds causing boar taint in meat of uncastrated male pigs. This study focuses on differences in gene expression of 50 Danish Landrace boars with high and low skatole levels. The animals were divided into 2 groups based on the skatole measurements, with animals having a skatole concentration of less than 0.01 ppm in one group, and above 0.275 ppm in the other group. Gene expression was assessed using porcine oligonucleotide microarrays. We report differential expression of CYP2E1, CYP2A13 and suggests involvement of FMO1, HSD17B13, CBR4 and several transcription factors. Gene expression study of liver, comparison of 25 boars with high and 25 boars with low skatole levels, using in-house printed porcine two-colour oligonucleotide microarrays.
2015-06-15 | E-GEOD-29974 | biostudies-arrayexpress
Project description:Domestication of pig results in modifications of many traits, including fatness traits, which are important in pig production since they have effect on meat quality, fattening efficiency, reproduction and immunity.In this study, we investigate 3D genome organization and transcriptomic characterization of adipose tissues (ATs) between wild boars and Bama pig, a typical indigenous domestic pig in China, to uncover molecular mechanisms of fatness-phenotypic shifts.
2022-01-14 | GSE183447 | GEO
Project description:Skatole is one of the compounds causing boar taint in meat of uncastrated male pigs. This study focuses on differences in gene expression of 50 Danish Landrace boars with high and low skatole levels. The animals were divided into 2 groups based on the skatole measurements, with animals having a skatole concentration of less than 0.01 ppm in one group, and above 0.275 ppm in the other group. Gene expression was assessed using porcine oligonucleotide microarrays. We report differential expression of CYP2E1, CYP2A13 and suggests involvement of FMO1, HSD17B13, CBR4 and several transcription factors.
2015-06-15 | GSE29974 | GEO
Project description:Salmonella in Swedish wild boars
| PRJEB52521 | ENA
Project description:We investigated the nutritional effects on gene expression in sperm cells of F0 boars from a three generation Large White pig feeding experiment. A group of experimental (E) F0 boars were fed a standard diet supplemented with high amounts of methylating micronutrients whereas a control (C) group of F0 boars received a standard diet. These differentially fed F0 boars sired F1 boars which then sired 60 F2 pigs which were investigated in a previous study. The aim of this study was to investigate if the nutrition affects gene expression in sperm cells of differentially fed boars and thus carry information in the form of RNA molecules to the next generation. Four RNA samples from sperm cells of these differentially fed boars were analyzed by RNA-Seq methodology. We found no differential RNA expression in sperm cells of the two groups based on the adjusted P-value > 0.05. Nevertheless, we performed a pathway analysis with 105 genes that differed in gene expression on the level of nominal P-value < 0.05 between the two diet groups. We found a significant number of these differentially expressed genes were enriched for the pathway maps of bacterial infections in cystic fibrosis (CF) airways, glycolysis and gluconeogenesis p.3 and cell cycle_Initiation of mitosis. The GO processes including a significant portion of differentially expressed genes were viral transcription and viral genome expression, viral infectious cycle, cellular protein localization, cellular macromolecule localization, nuclear-transcribed mRNA catabolic process and nonsense-mediated decay. In summary, the results of the pathway analysis are also inconclusive and it is concluded that RNA expression in sperm cells is not significantly affected by extensive supplementation of methylating micronutrients. Consequently, RNA molecules could not be established as epigenetic marks in this feeding experiment.
2013-09-16 | GSE48777 | GEO
Project description:We investigated the nutritional effects on gene expression in testes of F0 boars from a three generation Large White pig feeding experiment. A group of experimental (E) F0 boars were fed a standard diet supplemented with high amounts of methylating micronutrients whereas a control (C) group of F0 boars received a standard diet. These differentially fed F0 boars sired F1 boars which then sired 60 F2 pigs which were investigated in a previous study. The aim of this project was to investigate if the nutrition affects gene expression in testis of differentially fed boars and thus impact on spermatogenesis. We found a small number of 70 genes that were differentially expressed (fc ≥ 1) on the P<0.01 significance level. The false discovery rate (FDR) was 0.82 indicating that only a small portion of these genes are real positives. Nevertheless, we performed a pathway analysis and found this moderate differential expression associated with pathways maps of development_A2B receptor: action via G-protein alpha s, cell adhesion_Tight junctions and cell adhesion_Endothelial cell contacts by junctional mechanisms. The gene ontology (GO) processes that matched the gene expression data in boars’ testes were positive regulation of nucleobase-containing compound metabolic process, cellular response to hormone stimulus and cellular process. The pathway maps and GO processes associated with gene expression differences do not indicate a simple relationship between nutritional influences and gene expression in testes. Nevertheless the Adenosine A2B receptor influences cell differentiation and proliferation and has thus far reaching consequences. Similar applies to those GO processes positive regulation of nucleobase-containing compound metabolic process, cellular response to hormone stimulus and cellular process that were associated with differentially expressed genes between the testes samples. The expression result is thus not conclusive of whether the diet affects processes related to transmittable epigenetic marks. The results, however, indicate that the extreme supplementation of methylating micronutrients from month one to month ten of age has a very moderate (if any) effect on gene expression in boar testes as measured by microarray analysis.
2013-09-16 | GSE48597 | GEO
Project description:We investigated the nutritional effects on gene expression in testes of F0 boars from a three generation Large White pig feeding experiment. A group of experimental (E) F0 boars were fed a standard diet supplemented with high amounts of methylating micronutrients whereas a control (C) group of F0 boars received a standard diet. These differentially fed F0 boars sired F1 boars which then sired 60 F2 pigs which were investigated in a previous study. The aim of this project was to investigate if the nutrition affects gene expression in testis of differentially fed boars and thus impact on spermatogenesis. We found a small number of 70 genes that were differentially expressed (fc ≥ 1) on the P<0.01 significance level. The false discovery rate (FDR) was 0.82 indicating that only a small portion of these genes are real positives. Nevertheless, we performed a pathway analysis and found this moderate differential expression associated with pathways maps of development_A2B receptor: action via G-protein alpha s, cell adhesion_Tight junctions and cell adhesion_Endothelial cell contacts by junctional mechanisms. The gene ontology (GO) processes that matched the gene expression data in boars’ testes were positive regulation of nucleobase-containing compound metabolic process, cellular response to hormone stimulus and cellular process. The pathway maps and GO processes associated with gene expression differences do not indicate a simple relationship between nutritional influences and gene expression in testes. Nevertheless the Adenosine A2B receptor influences cell differentiation and proliferation and has thus far reaching consequences. Similar applies to those GO processes positive regulation of nucleobase-containing compound metabolic process, cellular response to hormone stimulus and cellular process that were associated with differentially expressed genes between the testes samples. The expression result is thus not conclusive of whether the diet affects processes related to transmittable epigenetic marks. The results, however, indicate that the extreme supplementation of methylating micronutrients from month one to month ten of age has a very moderate (if any) effect on gene expression in boar testes as measured by microarray analysis. Gene expression in testes from differentially fed F0 boars was measured. F0 boars received either a standard diet or a standard diet supplemented with methylating micronutrients. These boars were used to study transgenerational epigenetic inheritance in a three generation pig pedigree. Therefore it was of interest if the diet affects gene expression in testes and so could impact spermatogenesis.
2013-09-16 | E-GEOD-48597 | biostudies-arrayexpress
Project description:We investigated the nutritional effects on gene expression in sperm cells of F0 boars from a three generation Large White pig feeding experiment. A group of experimental (E) F0 boars were fed a standard diet supplemented with high amounts of methylating micronutrients whereas a control (C) group of F0 boars received a standard diet. These differentially fed F0 boars sired F1 boars which then sired 60 F2 pigs which were investigated in a previous study. The aim of this study was to investigate if the nutrition affects gene expression in sperm cells of differentially fed boars and thus carry information in the form of RNA molecules to the next generation. Four RNA samples from sperm cells of these differentially fed boars were analyzed by RNA-Seq methodology. We found no differential RNA expression in sperm cells of the two groups based on the adjusted P-value > 0.05. Nevertheless, we performed a pathway analysis with 105 genes that differed in gene expression on the level of nominal P-value < 0.05 between the two diet groups. We found a significant number of these differentially expressed genes were enriched for the pathway maps of bacterial infections in cystic fibrosis (CF) airways, glycolysis and gluconeogenesis p.3 and cell cycle_Initiation of mitosis. The GO processes including a significant portion of differentially expressed genes were viral transcription and viral genome expression, viral infectious cycle, cellular protein localization, cellular macromolecule localization, nuclear-transcribed mRNA catabolic process and nonsense-mediated decay. In summary, the results of the pathway analysis are also inconclusive and it is concluded that RNA expression in sperm cells is not significantly affected by extensive supplementation of methylating micronutrients. Consequently, RNA molecules could not be established as epigenetic marks in this feeding experiment. Gene expression in sperm cells from differentially fed F0 boars was measured. F0 boars received either a standard diet or a standard diet supplemented with methylating micronutrients. These boars were used to study transgenerational epigenetic inheritance in a three generation pig pedigree. Therefore it was of interest if the diet affects gene expression in sperm cells which could then be transmitted to next generations.
2013-09-16 | E-GEOD-48777 | biostudies-arrayexpress
Project description:Purpose: The goal of this study was to perform a transcriptome-wide analysis of variation in brain gene expression between domesticated pig and wild boars using illumina sequencing strategy. Methods: Brain mRNA profiles of wild boars and Rongchang pigs were generated by deep sequencing, in triplicate, using Illumina Hiseq2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: We identified 808 widely-expressed conserved and 697 species-specific novel miRNAs in two species. In addition, although two organs showed similar high expression miRNAs, larger differentiation was present in lung than heart between two species. In addition, miRNAs with significantly differentiated patterns of expression in two organs exhibited obvious co-operation effect in high altitude adaptation in form of miRNA family and cluster. Functional analysis revealed that a large amount of differentially expressed miRNAs were enriched in hypoxia-related pathways, such as VEGF signaling pathway, HIF-1α signaling pathway, insulin signaling pathway, DNA damage response, apoptosis, fatty acid metabolism and glucose metabolism. These results suggested the diverse degrees of epigenetic variation in different tissues between yak and cattle, and revealed extensive roles of miRNAs in high altitude adaptation. Conclusions: First, we totally identified 20,805 genes in two groups, of which 18,904 in wild boar and 17,980 in Rongchang pigs, respectively. Second, we detected substantial variation in expression profiles between wild boar and Rongchang pig, including substantial wild boar/Rongchang specifically expressed genes and differentially expressed genes. The functional enrichment analysis revealed immune response was enriched for genes upregulated in wild boars. Finally, we compared our results against previous study and identified seven genes that were associated with domestication.The work performed here will provide a typical demonstration for future deciphering the mechanism of pig domestication.
2018-04-05 | GSE98108 | GEO