Ontology highlight
ABSTRACT:
PROVIDER: PRJNA661439 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12588506_1.fastq.gz | Fastqsanger.gz | |||
| SRR12588506_2.fastq.gz | Fastqsanger.gz | |||
| SRR12588507_1.fastq.gz | Fastqsanger.gz | |||
| SRR12588507_2.fastq.gz | Fastqsanger.gz | |||
| SRR12588508_1.fastq.gz | Fastqsanger.gz |
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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 .
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Project description:Investigation of whole genome gene expression level changes in porcine alveolar macrophage response to co-infection of PRRSV and M. hyopneumoniae The results in this study will be further described in Bin li et al., 2013. BMC genomics. A 24 chip study using total RNA recovered from four separate group include control, PRRSV, M. hyopneumoniae and PRRSV+M. hyopneumoniae.
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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:Pan-viral DNA array (PVDA) and high-throughput sequencing (HTS) are useful tools to identify novel virus of emerging diseases. However, both techniques have difficulties to identify viruses in clinical samples because of host genomic DNA (hgDNA) contamination. Both propidium monoazide (PMA) and ethidium bromide monoazide (EMA) have the capacity to bind free DNA but are cell membrane-impermeable and thus are unable to bind protected DNA and RNA such as viral genomic material. DNA modified by EMA or PMA is not amplifiable by polymerase. In order to assess the capacity of EMA or PMA to lower hgDNA, serum or lung tissue homogenates were spiked with porcine reproductive and respiratory virus (PRRSV) and were processed with different combination of treatment: with or without ultracentrifugation and incubation with or without different concentration of EMA or PMA. PVDA and HTS were used to evaluate the capacity of both techniques to detect the presence of PRRSV from each sample. Negative results were obtained by PVDA and low amount of PRRSV specific reads were obtained by HTS with untreated samples or samples treated only by ultracentrifugation. An increase capacity of PRRSV detection was observable by PVDA in EMA and PMA treated samples but PVDA best results were obtained following PMA treatment, with or without ultracentrifugation. HTS sensitivity was also improved by a treatment with EMA or PMA, but the number of reads was significantly higher in PMA treated samples. These results support the use of PMA as a treatment to increase sensitivity of PVDA and HTS. A non specific DNA probe is used as a negative hybridization control. Also, specifics probes targeting pUC19 plasmid DNA is used as a DNA array positive control as well as a localization control. Finally, there are 34 probes of 70 nucleotides spotted in duplicate were selected to target PRRSV conserved regions. A total of 80 different tests were done by DNA array in order to evaluate different treatments conditions with EMA or PMA, with or without ultracentrifugation. A total of 58 samples were tested on specific lung tissue homogenates spiked with different concentration of PRRSV and 12 samples were serum samples spiked with one concentration of PRRSV. Finally. A total of six samples
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Project description:Investigation of whole genome gene expression level changes in porcine alveolar macrophage response to co-infection of PRRSV and M. hyopneumoniae The results in this study will be further described in Bin li et al., 2013. BMC genomics.
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