Oas1b-dependent Immune Transcriptional Profiles of West Nile Virus Infection in the Collaborative Cross
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE91003 | GEO | 2017/01/03
SECONDARY ACCESSION(S): PRJNA356625
REPOSITORIES: GEO
Similar Datasets
Project description:To accurately identify the unique transcriptional signatures in collaborative cross mice after exposure to West Nile Virus (or mock/no virus) , RNA isolated from spleen tissue and was analyzed using the nanostring immunology panel.
2016-09-01 | GSE86000 | GEO
Project description:Here, we characterize the RIX line CC(032x013)F1, which serves as a mouse model of chronic WNV infection. While studies using C57BL/6 mice have shown that WNV RNA can persist in the CNS up to 3 months post infection in a limited fraction of mice (Appler et al., 2010), to date there is a lack of a robust mouse model of chronic West Nile virus infection that can be used to elucidate the immune responses associated with this viral persistence and chronicity of symptoms described in human patients. Here, we characterize this line in comparison with lines showing either no disease symptoms or significant disease, and suggest a mechanism by which WNV infection can become chronic through alterations in immune responses.
2016-06-01 | GSE82046 | GEO
Project description:The Collaborative Cross (CC) recombinant inbred panel was conceived as an ideal resource for mammalian system genetics. The pre-CC is a proof-of-concept experiment involving CC lines that have undergone at least five generations of inbreeding. Siblings from these lines were each involved in one of four distinct phenotyping arms, then genotyped on a high-density Affymetrix platform. The genetic profile of these emerging lines reveals high diversity, balanced allele frequencies, and well-distributed recombination – all ideal qualities for a mapping panel. We have mapped white spot, a discrete trait; body weight, a highly polygenic complex trait; and more than 11,000 liver gene expression traits. These analyses provide a glimpse of the potential mapping power and resolution of the CC. The goal of this project was to identify eQTLs for genome-wide gene expression from liver tissue in pre-CC mice.
2010-12-01 | GSE22297 | GEO
Project description:The Collaborative Cross (CC) recombinant inbred panel was conceived as an ideal resource for mammalian system genetics. The pre-CC is a proof-of-concept experiment involving CC lines that have undergone at least five generations of inbreeding. Siblings from these lines were each involved in one of four distinct phenotyping arms, then genotyped on a high-density Affymetrix platform. The genetic profile of these emerging lines reveals high diversity, balanced allele frequencies, and well-distributed recombination – all ideal qualities for a mapping panel. We have mapped white spot, a discrete trait; body weight, a highly polygenic complex trait; and more than 11,000 liver gene expression traits. These analyses provide a glimpse of the potential mapping power and resolution of the CC. The goal of this project was to identify eQTLs for genome-wide gene expression from liver tissue in pre-CC mice. Gene expression profiling from liver tissue from pre-CC males. Pre-Collaborative Cross (CC) mice are partially inbred strains created by intercrossing eight founder (parental) strains: 129S1/SvImJ, (129S1), A/J (AJ), C57BL/6J (B6), CAST/Ei (CAST), NOD/LtJ (NOD), NZO/H1LtJ (NZO), PWK/Ph (PWK), and WSB/Ei (WSB). Sister-brother mating in 220 families was done for 4-11 generations. One animal was sampled from 157 pre-CC strain. Hybridizations were performed at the Gene Expression Core Facility at The Jackson Laboratory. Samples were divided in six batches of about 11 to 24 samples. Two batches were performed per day. Probe-level data was summarized by a custom CDF file based on Ensembl genes (NCBI 37, Ensembl 49; htttp://brainarray.mbni.med.umich.edu). The parental strains are not part of this submission.
2010-12-01 | E-GEOD-22297 | biostudies-arrayexpress
Project description:Here, we characterize the RIX line CC(032x013)F1, which serves as a mouse model of chronic WNV infection. While studies using C57BL/6 mice have shown that WNV RNA can persist in the CNS up to 3 months post infection in a limited fraction of mice (Appler et al., 2010), to date there is a lack of a robust mouse model of chronic West Nile virus infection that can be used to elucidate the immune responses associated with this viral persistence and chronicity of symptoms described in human patients. Here, we characterize this line in comparison with lines showing either no disease symptoms or significant disease, and suggest a mechanism by which WNV infection can become chronic through alterations in immune responses. Microarrays were performed on spleen samples from mice collected at days 7,12,21,28 post-infection with west nile virus or from time-matched mock-infected animals.
2016-06-01 | E-GEOD-82046 | biostudies-arrayexpress
Project description:The Collaborative Cross (CC) recombinant inbred panel was conceived as an ideal resource for mammalian system genetics. The pre-CC is a proof-of-concept experiment involving CC lines that have undergone at least five generations of inbreeding. Siblings from these lines were each involved in one of four distinct phenotyping arms, then genotyped on a high-density Affymetrix platform. These mice were initially described in the following reference. Genome Research 2011 Aug;21(8):1213-22 (PMID: 21406540). The goal of this specific project was to identify gene expression QTL using lung tissue from pre-CC mice that were sensitized and challenged with house dust mite allergen (namely, Der p 1).
2013-11-15 | GSE51768 | GEO
Project description:West Nile virus (WNV) is a mosquito-borne RNA flavivirus and the cause of more than 31,000 cases in the USA from 1999-2011 including 1, 262 fatalities. WNV infections are typically asymptomatic, but some patients, especially the elderly and immunocompromised, may experience severe neurological disease and even death. Control of WNV infection by the immune system is multifactorial. We profiled antibody, cytokine responses and gene expression from a stratified cohort of WNV subjects to define immune responses that contribute to disease severity and outcome. Differential gene expression by human PBMCs from asymptomatic and severe patients with WNV infection were generated by microarray.
2012-12-29 | E-GEOD-43190 | biostudies-arrayexpress
Project description:The Collaborative Cross (CC) recombinant inbred panel was conceived as an ideal resource for mammalian system genetics. The pre-CC is a proof-of-concept experiment involving CC lines that have undergone at least five generations of inbreeding. Siblings from these lines were each involved in one of four distinct phenotyping arms, then genotyped on a high-density Affymetrix platform. These mice were initially described in the following reference. Genome Research 2011 Aug;21(8):1213-22 (PMID: 21406540). The goal of this specific project was to identify gene expression QTL using lung tissue from pre-CC mice that were sensitized and challenged with house dust mite allergen (namely, Der p 1). We analyzed whole lung RNAs from 138 pre-Collaborative Cross mice using Illumina WG6v2 arrays. Pre-Collaborative Cross (CC) mice are partially inbred strains created by intercrossing eight founder (parental) strains: 129S1/SvImJ, (129S1), A/J (AJ), C57BL/6J (B6), CAST/Ei (CAST), NOD/LtJ (NOD), NZO/H1LtJ (NZO), PWK/Ph (PWK), and WSB/Ei (WSB). Sister-brother mating in 220 families was done for 5-12 generations. One animal was sampled from 138 unique pre-CC strains, each designated by the prefix OR which denotes Oak Ridge National Laboratory as the original source of these mice. The parental strains are not part of this submission. Hybridizations were performed at the National Human Genome Research InstituteM-bM-^@M-^Ys Gene Expression Core Facility.The resulting data were initially processed using Illumina Genome Studio software and then imported into R (v2.9.2) for post-processing. Normalization was conducted using RMA with quantile normalization and log2 transformation.
2013-11-15 | E-GEOD-51768 | biostudies-arrayexpress
Project description:The flavivirus genus has conserved NS4B residues at P54, L56, and W103. We sought to determine both in vitro and in vivo which mutations displayed attenuated characteristics for use as potential vaccine candidates.
2023-10-06 | E-MTAB-9408 | biostudies-arrayexpress
Project description:The oligoadenylate-synthetase (Oas) gene locus provides innate immune resistance to virus infection. In mouse models, variation in the Oas1b gene influences host susceptibility to flavivirus infection. However, the impact of Oas variation on overall innate immune programming and global gene expression among tissues and in different genetic backgrounds has not been defined. We examined how Oas1b acts in spleen and brain tissue to limit West Nile virus (WNV) susceptibility and disease across a range of genetic backgrounds. The laboratory founder strains of the mouse Collaborative Cross (CC) (A/J, C57BL/6J, 129S1/SvImJ, NOD/ShiLtJ, and NZO/HlLtJ) all encode a truncated, defective Oas1b, whereas the three wild-derived inbred founder strains (CAST/EiJ, PWK/PhJ, and WSB/EiJ) encode a full-length OAS1B protein. We assessed disease profiles and transcriptional signatures of F1 hybrids derived from these founder strains. F1 hybrids included wild-type Oas1b (F/F), homozygous null Oas1b (N/N), and heterozygous offspring of both parental combinations (F/N and N/F). These mice were challenged with WNV, and brain and spleen samples were harvested for global gene expression analysis. We found that the Oas1b haplotype played a role in WNV susceptibility and disease metrics, but the presence of a functional Oas1b allele in heterozygous offspring did not absolutely predict protection against disease. Our results indicate that Oas1b status as wild-type or truncated, and overall Oas1b gene dosage, link with novel innate immune gene signatures that impact specific biological pathways for the control of flavivirus infection and immunity through both Oas1b-dependent and independent processes.
| S-EPMC5473748 | biostudies-literature