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The effect of upper-respiratory infection on transcriptomic changes in the CNS

ABSTRACT: Purpose: The goal of this study was to determine the effect of an upper-respiratory infection on changes in RNA transcription occuring in the cerebellum and spinal cord. post infection. Methods: Gender matched eight week old C57BL/6 mice were inoculated saline or with Influenza A (Puerto Rico/8/34; PR8, 1.0 HAU) by intranasal route and transcriptomic changes in the cerebellum and spinal cord tissues were evaluated by RNA-seq (100bp paired end reads) at days 0 (non-infected), 4 and 8 Results: After trimming and excluding multi-mappeing reads an average of 92.07% (cerebellum) and 91.71% (spinal cord) of genes were uniquely mapped to a gene. The average number of single end reads per sample was 36.42 and 37 million for the spinal cord and cerebellum respectively. Infection caused significant changes to the transcriptome of each tissue, which was most prominent at day 8 post infection. Conclusion: This study represents the first to use RNA-seq tecnology to evaluate the effect of peripheral influenza a infection on changes in gene expression of the cerebellum and spinal cord.

ORGANISM(S): Mus musculus

PROVIDER: GSE96870 | GEO | 2017/06/14

SECONDARY ACCESSION(S): PRJNA379959

REPOSITORIES: GEO

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Project description:We have investigated the process of disease-induced functional perturbation and the related transcriptional changes occurring in thoraco-lumbar spinal cord extracted from Sprague-Dawley rats heterozygous for the G93A SOD1 gene mutation (Emerging Model 2148 Het Male, Taconic USA; Wyeth and Amyotrophic Lateral Sclerosis Association 2002) using spinal cord from wild type females littermates as reference tissues. Rats were obtained from a breeding project at Taconic Breeding Services (USA). We have applied large-scale gene expression analysis to define the pattern or transcriptional changes occurring in spinal cord from the G93A SOD1 rat model from a pre-symptomatic stage, at disease onset and at end-stage disease, using Bead Array analysis (Illumina, San Diego, USA). We have pooled spinal cord from N:5 transgenic rats for each of the time points considered, using the same pools of spinal cord from sex and age-matched WT rats as reference. In this specific project, the aim was to obtain a gene ontology (GO) pathway analysis of the transcriptional changes induced by the G93A SOD1 mutation in rat spinal cord. Hence, we have opted for a sample pooling strategy, well aware that in so doing, we would not obtaineed information about individuals genes variation across the samples in study but an overall view of the activation of multi-genes molecular signals. Total RNA was isolated from the spinal cords of mutant (G93A SOD1 gene mutation) female rats sacrificed at a pre-symptomatic stage (10-week old), at disease onset and at end stage disease and from age and sex-matched wild type (WT) littermates. RNA samples obtained from spinal cord extracted from rats of the same genetic types and sacrificed at the same time points (e.g. 5 RNA samples from mutant spinal cord from end-stage rats; 5 RNA samples from mutant spinal cord from rats at disease onset; 5 RNA samples from mutant pre-symptomatic rats and 5 RNA samples from spinal cord obtained from age-matched WT rats sacrificed at each of the 3 time points) were pooled and used for gene expression analysis and Ontology analysis of the expression profiles.

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The effect of upper-respiratory infection on transcriptomic changes in the CNS

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