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GSE52626
Sus scrofa
101 Downloadable Samples
Affymetrix Porcine Genome Array (porcine)
Description
The integration of the results of QTL fine-mapping with microarray expression data offers a promising tool for understanding the genetic mechanisms influencing complex traits as fatty acid composition in pigs. The expression level of each probe may be treated as a quantitative trait and the marker genotypes used to map loci with regulatory effect on the gene expression level (eQTL)
Publication Title
Genome-wide analysis of porcine backfat and intramuscular fat fatty acid composition using high-density genotyping and expression data.
Sample Metadata Fields
Sex, Age
View Samples- Sus scrofa
- 26 Downloadable Samples
- Affymetrix Porcine Genome Array (porcine)
Description
We studied the influence of genetic type (pure Iberian pigs vs crossbred with Duroc) on l.dorsi transcriptome
Publication Title
Longissimus dorsi transcriptome analysis of purebred and crossbred Iberian pigs differing in muscle characteristics.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Bos taurus
- 18 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Sexual dimorphism in mammals is mostly attributable to sex-related hormonal differences in fetal and adult tissues; however, this may not be the sole determinant. Though genetically-identical for autosomal chromosomes, male and female preimplantation embryos could display sex-specific transcriptional regulation which can only be attributted to the differences in sexual chromosome dosage.
Publication Title
Sex determines the expression level of one third of the actively expressed genes in bovine blastocysts.
Sample Metadata Fields
Sex, Specimen part
View Samples- Sus scrofa
- 16 Downloadable Samples
- Affymetrix Porcine Genome Array (porcine)
Description
Breed, gender and diet are factors affecting porcine metabolism. The aim of this study has been to investigate the gene expression patterns of the major sites for lipid metabolism, liver and fat, conditional on gender and on a moderate feeding restriction in Iberian pigs, as a model of obese porcine breed. Our results show that tissue effect account for more differentially expressed genes than gender or feeding restriction. The results obtained from the comparison between tissues support the studies showing adipose tissue is not only a fat-storage depot, we report a high number of upregulated genes in adipose tissue which represent relevant biological functions such as carbohydrate and energy metabolisms and endocrine function. Besides, key genes implicated in lipid metabolism are specifically overrepresented in liver or fat, particularly the differentially expressed genes related to fatty acid synthesis support previous studies showing that in pig, as in cattle or sheep, this process largely occurs in fat. We identified metabolic differences between genders such as oxidation capacity or response to toxins, reflected at gene expression level in liver but no in adipose tissue, contrarily to previous studies. Finally, our results seem to indicate that a moderate feeding restriction does not have large effects on liver or fat gene expression of obese pigs. Although the list of differentially expressed genes due to the effect of feeding restriction is limited, we could identify expression differences in genes related to antiageing mechanisms associated with feeding restriction as enhancement of immune response and anticoagulation and the balance between prosurvival and cell-death.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part
View Samples- Sus scrofa
- 16 Downloadable Samples
- Affymetrix Porcine Genome Array (porcine)
Description
The aim of this study was to identify genes, gene clusters and networks involved in sexual dimorphism and in the response to nutritional restriction in porcine skeletal muscles, through the analysis of gene expression differences. Full sib Iberian piglets from three litters composed of two males and two females per family were randomly assigned to two dietary treatments which differed in the feeding level during 15 wk. At the end of the trial, 27 wk of age, significant phenotypic differences were detected between genders and between feeding levels for growth, fatness, fatty acid composition and primary cuts weights. RNA samples from two skeletal muscles, diaphragm and Psoas major, were hybridized with Affymetrix microarrays and the expression data were analyzed using a mixed model and a FDR<0.01. The successfully performed validations by qRT-PCR of six selected genes supported the reliability of our microarray results. Ina a first step, the main gene expression differences between both muscles were established, identifying 181 differentially expressed genes, which represented almost exclusively anatomical structural differences. The analysis between genders reported expression differences of 59 unique genes, mainly implicated in muscle growth and stress response, including well known genes, such as IGF1, apart from others potentially associated to meat quality such as ANKRD1. The analysis of the feeding level effect restriction reported up-regulation of 76 genes and down-regulation of other 60 genes. Functional annotation showed that the moderated nutritional restriction applied led to a reduced growth through down-regulation of key genes implicated in enhancing growth and up-regulation of genes implicated in inhibiting growth. Besides, the restriction led to an increase of muscular aminoacid metabolism and decrease of lipid metabolism as adaptive response. Changes in expression patterns of genes determining meat characteristics, such as PDK4 implicated in water holding, CTSD associated to muscle transformation during meat processing and SCD involved in the determination of fatty acids profiles, were also reported. Finally, we identify relevant expression differences in ADAM12, CA2, UCHL1 and ESRRG genes, which are involved in human obesity and have not been previously studied in pig.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Sus scrofa
- 15 Downloadable Samples
- Affymetrix Porcine Genome Array (porcine)
Description
We studied the influence of the oleic acid content of the diet on adipose tissue transcriptome.
Publication Title
Dietary energy source largely affects tissue fatty acid composition but has minor influence on gene transcription in Iberian pigs.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Sus scrofa
- 12 Downloadable Samples
- Affymetrix Porcine Genome Array (porcine)
Description
Previous results from a genome scan in a F2 Iberian by Meishan intercross showed several chromosome regions associated with litter size traits. In order to identify candidate genes underlying these QTL we have performed an ovary gene expression analysis during pregnancy. F2 sows were ranked by their estimated breeding values for prolificacy, the six sows with higher EBV (HIGH prolificacy) and the six with lower EBV (LOW prolificacy) were selected. Samples were hybridized to Affymetrix porcine expression microarrays. The statistical analysis with a mixed-model approach identified 221 differentially expressed probes, representing 189 genes. These genes were functionally annotated in order to identify the genetic pathways overrepresented. Among the most represented functional groups the first one was immune system response activation against external stimulus. The second group was made up of genes which regulate the maternal homeostasis by complement and coagulation cascades. The last group was involved on lipid and fatty acid enzymes of metabolic processes, which participate in steroidogenesis pathway. In order to identify powerful candidate genes for prolificacy, the second approach of this study was merging microarray data with position information of QTL affecting litter size, previously detected in the same experimental cross. According to this, we have identified 27 differentially expressed genes co-localized with QTL for litter size traits, which fulfill the biological, positional and functional criteria.
Publication Title
Differential gene expression in ovaries of pregnant pigs with high and low prolificacy levels and identification of candidate genes for litter size.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 9 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
We performed a tranascriptomic analysis of Ler, ebs and shl-2 plants in order to reveal targets whose transcription is regulated by EBS and SHL.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Sus scrofa
- 8 Downloadable Samples
- Affymetrix Porcine Genome Array (porcine)
Description
Liver plays major roles in vital functions including responses to energy deprivation. It is known that body composition and fuel metabolism differs between genders. However there are many unclear aspects related to metabolic pathways affected by feeding level and gender, which could be addressed by transcriptome analyses. To date, no published study in porcine liver has investigated the effects of both gender and feeding level on global gene expression level.We performed a gene expression analysis, using microarrays, in hepatic samples of pigs of the obese Iberian breed to analyze feeding level and gender effects. Results showed that feeding level leads to small expression differences, while gender leads to larger ones. Biological interpretation of the differentially expressed genes conditional on feeding level showed an overrepresentation of genes implicated in general metabolic processes, responses to stimulus and stress, oxidoreductase activity, calcium ion binding and lipid, organic acid and carbohydrate metabolisms. We validated the expression difference of PHYHD1 by qRT-PCR; however we could not validate the expression differences of other relevant genes. Curiously, validation of PGK1, considered reference gene, confirmed expression differences conditional on feeding level and gender. The annotation of the differentially expressed probes for gender effect allowed to observe sex-chromosome enrichment and dosage compensation phenomena in liver. Biological interpretation showed overrepresentation of genes related with oxidoreductase and transferase activities, lipid, organic acid, carbohydrate and steroid metabolisms and genes related with metabolites generation and energy and electron transport. Aside from 13 consistently across tissue differentially expressed genes between gender, gender hepatic expression dimorphism of key genes involved in lipid, carbohydrate and protein metabolisms and antioxidant capacity were also detected. A deeper qRT-PCR analysis showed a downregulation in entire males of all major genes implicated in hepatic degradation processes of androstenone and skatole. We have identified changes in hepatic gene expression conditional on feeding and gender. Reduction of around 25% in feeding level do not lead to great differences but gender effect leads not only to a larger number of differentially expressed probes, but much larger expression differences. Validation of microarray results is needed mainly for small expression differences.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part
View Samples- Arabidopsis thaliana
- 30 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Comparative transcriptomic analysis of Arabidopsis thaliana yda11 plants (in Col-0 background), and wild-type plants (Col-0) non-infected or infected with the necrotrophic fungal pathogen Plectosphaerella cucumerina BMM (PcBMM)
Publication Title
YODA MAP3K kinase regulates plant immune responses conferring broad-spectrum disease resistance.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples