Transcription analysis of the porcine alveolar macrophage M-oM-
Ontology highlight
ABSTRACT:
ORGANISM(S): Sus scrofa
SUBMITTER: li bin
PROVIDER: E-GEOD-49882 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The goal of this study was to produce a deep, global analysis of gene expression changes that occured following infection of normal porcine alveolar macrophages (PAMs) with PRRSV. The goal was to examine the gene expression changes to help determine the mechanisms that result in reduced function and immunosuppression observed in PRRSV-infected pigs. Keywords: time course of infection The PAMs were infected in culture at an MOI of 10 with PRRSV strains VR-2332 and incubated at 37C until 6, 12, 16 or 24 hours post infection. Total cellular RNA was collected from each at the appropriate time. SAGE libraries were prepared from each infected time point as well as from noninfected PAMs. The SAGE libraries were sequenced to at least 95,000 tags each.
2008-09-01 | E-GEOD-10346 | biostudies-arrayexpress
Project description:Porcine reproductive and respiratory disease (PRRS) is the most important disease in swine industry worldwide. However, strategies such as vaccination and good biosecurity are not consistently successful to eliminate PRRSV. Although some gene expression pathways have been explored recently, host molecular pathways blocked by PRRSV and the protective immune response expressed in pigs resistant to PRRSV are largely unknown. In order to answer these questions, we herein characterize changes in blood gene expression in pigs responding differentially to infection with a well characterized type 2 (North American) PRRSV isolate. Samples are those collected through the PRRS Host Genetics Consortium (PHGC). Samples were those from Tempus tube collected blood of PHGC pigs selected from four response groups according to their serum viral load (0-21 days post infection) and weight gain (0-42 dpi) and characterized as low vs. high viral load and low vs high weight gain . block reference design was used to accommodate samples from 4 treatment groups.
2012-09-26 | E-GEOD-41144 | biostudies-arrayexpress
Project description:Porcine reproductive and respiratory syndrome (PRRS), which caused by the porcine reproductive and respiratory syndrome virus (PRRSV), is a serious viral disease affecting global swine industry. At present, PRRSV vaccines fail to prevent this disease. Consequently, new antiviral strategies to compensate for the inefficacy of available vaccines are urgently required. Lysine acetylation is an important post-translational modification (PTM) regulating an array of pathological and physiological conditions. In this study, we profiled the global acetylome using acetylation specific antibody based enrichment and Tandem mass tag (TMT) label LC-MS in PRRSV-infected pulmonary alveolar macrophages (PAMs). As a result, 3731 lysine acetylation sites on 1421 cellular proteins were identified and quantified 6 hours post infection (hpi). Bioinformatics analysis of the differentially acetylated proteins revealed their involvement in various biological processes, including the host immune response and energy metabolism.
2020-12-11 | PXD016927 | Pride
Project description:We investigated for the first time the in vitro response of PRRSV-infected porcine DCs and monocytes to S. suis. We first assessed the effect of PRRSV infection on the phagocytosis and intracellular survival of S. suis by these two cell populations. We then used a genomic approach to compare the gene expression profiles of both type of cells infected with S. suis, with or without a previous infection with PRRSV. Total RNA obtained from porcine monocytes and dendritic cells infected with S. suis, PRRSV, or S. suis & PRRSV. Four replicates in all groups.
2016-06-01 | E-GEOD-75687 | 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:By analyzing the changes of miRNAs of piglet PAMs 6h after PRRSV infection,we can find porcine miRNAs associated with viral infection and possible target sites in both PRRSV and pig genome and their roles in protection against viral infections. Then these targets will screened by bioinformatics methods to find the susceptibility genes, resistance genes and immune related genes, and formed molecular biology network of miRNAs at gene and protein level . PAM cells were isolated from 60d old healthy piglets and inoculated with HuN4,a strain of highly pathogenic porcine reproductive and respitory syndrome virus (HP-PRRSV) and were collected at 6h post-inoculation (pi). The uninfected cells served as mock-infected cells.The miRNA chip was according to the porcine miRNA sequences in Sanger miRBase Release 17.0 (http://www.sanger.ac.uk/Software/Rfam/mirna/)added with some miRNAs we found in reference. Microarray hybridization and data analysis helps to find the susceptibility genes, resistance genes and immune related genes, and formed molecular biology network of miRNAs at gene and protein level .
2013-11-01 | E-GEOD-52014 | biostudies-arrayexpress
Project description:Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most relevant por-cine pathogens worldwide. Active control of the disease relies on modified live virus vaccines (MLVs), as most inactivated vaccines provide very limited protection. Neutralizing antibodies occur late in infection, therefore CD8+ T cells are considered important correlates of protection and are a frequent focus of investigation. Our aim was to identify viral peptides naturally bound by the class I major histocompatibility complex (MHC-I), and to confirm their ability to stimu-late CD8+ T cells. For this purpose, we immunoprecipitated MHC-I/peptide complexes of PRRSV (strain AUT15-33) -infected cells (SLA-I Lr-Hp 35.0/24mod) to isolate the viral epitopes and ana-lyzed them with liquid chromatography coupled to mass spectrometry (LC-MS). Furthermore, we employed these identified peptides to stimulate peripheral blood mononuclear cells (PBMCs) of previously PRRSV infected pigs and measured the PRRSV-specific CD8+ T cell re-sponse with an intracellular cytokine staining (ICS). Our data reveals that PRRSV non-structural proteins (NSPs) encoded in open reading frame 1a and 1b (ORF1) present the major source of MHC-I presented peptides. Additionally, we show that our identified epitopes are able to trig-ger IFNγ responses in vitro. These findings are a basis for understanding the proteasomal degra-dation of PRRSV proteins, the cellular ability to display them via MHC-I, and their potential to restimulate CD8+ T cells.
2022-10-14 | PXD035499 | Pride
Project description:Cell lines derived from Chlorocebus sabaeus kidney were infected with an isolate of PRRSV-1 or PRRSV-2 and ribosome profiling was performed (this entry) in parallel with RNASeq (see related accession number). These datasets were used to analyse the viral and host translatome, frameshifting on the viral genome, and putative frameshift-related ribosome pausing events. For the PRRSV-1 experiments, MA-104 cells were infected with an isolate based on the Porcilis vaccine strain (KJ127878.1 but with several accumulated mutations, see associated publication) and harvested at 8 hpi after pre-treatment with cycloheximide (CHX). For the PRRSV-2 experiments, MARC-145 cells were infected with SD95-21 PRRSV (KC469618.1), and a mutant thereof (KO2). One group of samples was harvested at 9 hpi after pre-treatment with CHX, and another group of samples was harvested at 3, 6, 9 and 12 hpi by flash-freezing without CHX pre-treatment. For all samples, RNase I treatment was carried out, following which ribosomes and enclosed RNA were isolated by centrifugation through a sucrose cushion. RNA was extracted, ribosomal RNA was removed using Illumina's RiboZero kit, and remaining RNA was gel purified to select fragments 25-34 nt (PRRSV-1-infected samples, CHX-pre-treated PRRSV-2- or mock-infected samples, and non-CHX-pre-treated PRRSV-2- or mock-infected 9 hpi replicate one samples) or 19-34 nt long (all other samples). Fragments were cloned into adapters based on the TruSeq small RNA adapters. For all PRRSV-2-infected (or mock-infected) libraries, adapters with an additional seven random nucleotides at the 5′-end of the 3′-adapter and the 3′-end of the 5′-adapter were used. For PRRSV-1 replicate one, no random nucleotides were present on the adapters, and for PRRSV-1 replicate two, 14 random nucleotides were present at the 5′-end of the 3′-adapter. Libraries were sequenced on the Illumina NextSeq 500 platform as a single-end run. Non-CHX-pre-treated PRRSV-2-infected 9 hpi replicate two libraries were uploaded under a separate accession number due to differences in the size selection and sequencing protocol - see associated paired-end entry. Note that sample nomeclature (including replicate numbers) is consistent between this and the two related accessions, and RiboSeq libraries are matched with RNASeq libraries, which were prepared from the same lysate. The noCHX_Ribo_9hpi_mock_3 library is deliberately absent as this was a poor quality library.
2022-03-09 | E-MTAB-10621 | biostudies-arrayexpress
Project description:Cell lines derived from Chlorocebus sabaeus kidney were infected with an isolate of PRRSV-1 or PRRSV-2 and RNASeq was performed (this entry) in parallel with ribosome profiling (see related accession numbers). These RNASeq datasets provide information on the transcriptome of PRRSV-infected cells and were used to detect novel viral transcripts and perform differential gene expression analysis on host transcripts. For the PRRSV-1 experiments, MA-104 cells were infected with an isolate based on the Porcilis vaccine strain (KJ127878.1 but with several accumulated mutations, see associated publication) and harvested at 8 hpi after pre-treatment with cycloheximide (CHX). For the PRRSV-2 experiments, MARC-145 cells were infected with SD95-21 PRRSV (KC469618.1), and a mutant thereof (KO2). One group of samples was harvested at 9 hpi after pre-treatment with CHX, and another group of samples was harvested at 3, 6, 9 and 12 hpi by flash-freezing without CHX pre-treatment. For all samples, RNA was extracted, ribosomal RNA was removed using Illumina's RiboZero kit, and remaining RNA was gel purified to select fragments 25-34 nt (PRRSV-1-infected samples, CHX-pre-treated PRRSV-2- or mock-infected samples, and non-CHX-pre-treated PRRSV-2- or mock-infected 9 hpi replicate one samples) or ~50 nt long (all other samples). Fragments were cloned into adapters based on the TruSeq small RNA adapters. For all PRRSV-2-infected (or mock-infected) libraries, adapters with an additional seven random nucleotides at the 5′-end of the 3′-adapter and the 3′-end of the 5′-adapter were used. For PRRSV-1 replicate one, no random nucleotides were present on the adapters, and for PRRSV-1 replicate two, 14 random nucleotides were present at the 5′-end of the 3′-adapter. Libraries were sequenced on the Illumina NextSeq 500 platform as a single-end run. For one NextSeq run, some potyvirus amplicons, indexed using TruSeq small RNA indices 1-48, was spiked in to the pool directly before sequencing, therefore some libraries (noCHX_RNA_9hpi_KO2_1, noCHX_RNA_9hpi_KO2_2, noCHX_RNA_9hpi_mock_1, noCHX_RNA_9hpi_mock_2, noCHX_RNA_9hpi_WT_1, noCHX_RNA_9hpi_WT_2) have a small proportion of potyvirus reads, but this does not represent co-infection in the biological sample and does not affect the conclusions of the study. Note that sample nomeclature (including replicate numbers) is consistent between this and the two related accessions, and RiboSeq libraries are matched with RNASeq libraries, which were prepared from the same lysate.
2022-03-09 | E-MTAB-10623 | biostudies-arrayexpress