RNA-seq of early responses to ASFV
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Sus scrofa
SUBMITTER: Geert van Geest
PROVIDER: E-MTAB-11634 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Brain gene expression in pigs housed in a pen during a tail biting outbreak compared with pigs housed in control pens.
2012-09-30 | E-MEXP-3643 | biostudies-arrayexpress
Project description:Gene expression in the hypothalamus and pre frontal cortex in pigs performing and receiving tail biting behaviour was compared with expression in pigs not performing or receiving tail biting
2013-11-12 | E-MEXP-3630 | biostudies-arrayexpress
Project description:The objective of this experiment was to use transcriptional profiling of skeletal muscle and adipose tissue to develop a better understanding of the metabolic basis for poor weaned-pig transition. A total of 1,054 pigs were reared in commercial conditions and weighed at birth, weaning, and 3 weeks post- weaning. Transition average daily gain (tADG) was calculated as the average daily gain for the 3-week period post-weaning. Nine pigs from each of the lowest 10th percentile (low tADG) and the 60th-70th percentile (high tADG) were harvested at 3 weeks post-weaning. Differential expression analysis was conduced in both tissues using RNA-Seq methodology mRNA profiling in two different tissues (skeletal muscle and adipose tissue) harvested at 3 weeks post-weaning
2015-02-25 | E-GEOD-65983 | biostudies-arrayexpress
Project description:In this study, we used Two-dimensional gel electrophoresis (2-DE)-based Western blotting coupled with MALDI-TOF / TOF-MS / MS to separate and identify the T. pseudospiralis adult worms (Ad) ES products immunoreaction-positive proteins. In total, 400 protein spots were separated by 2-DE. 28 protein spots were successfully identified using the sera from infected pigs and were characterized to correlate with twelve different proteins of T. pseudospiralis.
2018-11-22 | PXD007783 | Pride
Project description:To understand the host transcriptional response to S. enterica serovar Choleraesuis (S. Choleraesuis), the first generation Affymetrix porcine GeneChip® was used to identify differentially expressed genes in the mesenteric lymph nodes responding to infection at acute (8 hours (h), 24h, 48h post-inoculation (pi)) and chronic stages (21 days (d) pi); The objectives of this study were to identify and examine the stereotypical gene expression response within the host mesenteric lymph nodes to S. Choleraesuis infection, and to characterize the global host responses by revealing the specific features of the hostâs innate immunity. Experiment Overall Design: Fifteen piglets from Salmonella spp.-free sows were weaned at 10 days (d) of age, shipped to the National Animal Disease Center, Ames, IA and raised in isolation facilities. To confirm that all piglets were free of Salmonella spp. prior to challenge, bacteriological cultures were performed on rectal swabs twice. Seven week old pigs were randomly divided into 2 groups, 3 non-infected pigs and 12 infected pigs. Three non-infected control pigs were necropsied 3 days prior to experimental infection. On day 0, pigs in the infected groups were intranasally challenged with 1 billion CFU of Salmonella enterica serotype Choleraesuis x3246. Three infected pigs were necropsied at 8 hours post-inoculation (hpi), 24 hpi, 48 hpi and 21 day post-inoculation (dpi). Tissue samples from the mesenteric lymph nodes (MLN) were collected and immediately frozen in liquid nitrogen for RNA isolation.
2008-06-15 | E-GEOD-7314 | biostudies-arrayexpress
Project description:Analysis of gene expression in the lungs of pigs from high and low litter birth weight groups (HBW and LBW) inoculated with swine influenza virus. The aim of the experiment is to determine whether litter birth weight has an effect on the innate immune response to infection in pigs, and whether differences in gene expression can be linked to epigenetic differences between the two birth weight groups. A two condition experiment: lung tissue RNA from HBW and LBW SIV-infected pigs. 16 biological replicates for each condition, each hybridized with a reference to separate arrays. 32 arrays in total.
2015-10-27 | E-GEOD-62765 | biostudies-arrayexpress
Project description:The aim of this experiment was to identify changes in gene expression in muscle and liver between pigs that were divergent in feed efficiency. The animals were selected from two different farms of origin. 48 animals were utilized in this study. Following slaughter RNA Total RNA was extracted from liver and muscle ((25 mg) tissue using Trizol Reagent (Sigma-Aldrich, Arklow, Ireland) according to the manufacturer’s instructions, the crude RNA extract was further purified using the GenElute Mammalian Total RNA Miniprep Kit (RTN70, Sigma-Aldrich). Library construction and sequencing was performed by the next generation sequencing facility at the Institute of Molecular Medicine, University of Leeds, United Kingdom. The RNA-seq libraries were constructed using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA) per the manufacturer’s instructions. One hundred base paired-end sequencing was run on an Illumina HiSeq2000 platform with each pool ran on two lanes on a flow cell.
2019-04-24 | E-MTAB-7435 | biostudies-arrayexpress
Project description:The presence of variability in the response of pigs to Porcine Reproductive and Respiratory Syndrome virus (PRRSv) infection, and recent demonstration of significant genetic control of such responses, leads us to believe that selection towards more disease resistant pigs could be a valid strategy to reduce its economic impact on the swine industry. To find underlying molecular differences in PRRS susceptible versus more resistant pigs, 100 animals with extremely different growth rates and viremia levels after PRRSv infection were selected from a total of 600 infected pigs. A microarray experiment was conducted on whole blood RNA samples taken at 0, 4 and 7 days post infection (dpi) from these pigs. From these data, we examined associations of gene expression with weight gain and viral load phenotypes. The single nucleotide polymorphism (SNP) marker WUR10000125 (WUR) on the porcine 60K SNP chip was shown to be associated with viral load and weight gain after PRRSv infection, and so, additionally, the effect of the WUR10000125 (WUR) genotype was examined. Limited information was obtained through linear modeling of blood gene differential expression (DE) that contrasted pigs with extreme phenotypes, for growth or viral load or between animals with different WUR genotype. However, using network-based approaches, molecular pathway differences between extreme phenotypic classes could be identified. Several gene clusters of interest were found when Weighted Gene Co-expression Network Analysis (WGCNA) was applied to 4dpi contrasted with 0dpi data. The expression pattern of one such cluster of genes correlated with weight gain and WUR genotype, contained numerous immune response genes such as cytokines, chemokines, interferon type I stimulated genes, apoptotic genes and genes regulating complement activation. In addition, Partial Correlation and Information Theory (PCIT) identified differentially hubbed (DH) genes between the phenotypically divergent groups. GO enrichment revealed that the target genes of these DH genes are enriched in adaptive immune pathways. There are molecular differences in blood RNA patterns between pigs with extreme phenotypes or with a different WUR genotype in early responses to PRRSv infection, though they can be quite subtle and more difficult to discover with conventional DE expression analyses. Co-expression analyses such as WGCNA and PCIT can be used to reveal network differences between such extreme response groups. three timepoints from 100 animals are hibridized following a blocked reference design; Blood gene expression of pigs 4 days post infection
2015-06-04 | E-GEOD-69513 | biostudies-arrayexpress
Project description:The presence of variability in the response of pigs to Porcine Reproductive and Respiratory Syndrome virus (PRRSv) infection, and recent demonstration of significant genetic control of such responses, leads us to believe that selection towards more disease resistant pigs could be a valid strategy to reduce its economic impact on the swine industry. To find underlying molecular differences in PRRS susceptible versus more resistant pigs, 100 animals with extremely different growth rates and viremia levels after PRRSv infection were selected from a total of 600 infected pigs. A microarray experiment was conducted on whole blood RNA samples taken at 0, 4 and 7 days post infection (dpi) from these pigs. From these data, we examined associations of gene expression with weight gain and viral load phenotypes. The single nucleotide polymorphism (SNP) marker WUR10000125 (WUR) on the porcine 60K SNP chip was shown to be associated with viral load and weight gain after PRRSv infection, and so, additionally, the effect of the WUR10000125 (WUR) genotype was examined. Limited information was obtained through linear modeling of blood gene differential expression (DE) that contrasted pigs with extreme phenotypes, for growth or viral load or between animals with different WUR genotype. However, using network-based approaches, molecular pathway differences between extreme phenotypic classes could be identified. Several gene clusters of interest were found when Weighted Gene Co-expression Network Analysis (WGCNA) was applied to 4dpi contrasted with 0dpi data. The expression pattern of one such cluster of genes correlated with weight gain and WUR genotype, contained numerous immune response genes such as cytokines, chemokines, interferon type I stimulated genes, apoptotic genes and genes regulating complement activation. In addition, Partial Correlation and Information Theory (PCIT) identified differentially hubbed (DH) genes between the phenotypically divergent groups. GO enrichment revealed that the target genes of these DH genes are enriched in adaptive immune pathways. There are molecular differences in blood RNA patterns between pigs with extreme phenotypes or with a different WUR genotype in early responses to PRRSv infection, though they can be quite subtle and more difficult to discover with conventional DE expression analyses. Co-expression analyses such as WGCNA and PCIT can be used to reveal network differences between such extreme response groups. three timepoints from 100 animals are hibridized following a blocked reference design; Blood gene expression of pigs 7 days post infection
2015-06-04 | E-GEOD-69514 | biostudies-arrayexpress
Project description:To gain insight into the role of testosterone in modulating hepatic fat accumulation, we collected liver tissues from high fat diet-fed intact male pigs, castrated male pigs, and castrated male pigs with testosterone replacement. RNA-Seq was employed to profile hepatic gene expression in pigs with different testosterone levels. Liver mRNA profiles of intact male pigs fed a HFC diet, castrated male pigs fed a HFC diet, and castrated male pigs treated with testosterone fed a HFC diet were generated by deep sequencing, using Illumina HiSeq 2000.
2015-01-08 | E-GEOD-62696 | biostudies-arrayexpress