期刊
FRONTIERS IN IMMUNOLOGY
卷 5, 期 -, 页码 1-12出版社
FRONTIERS MEDIA SA
DOI: 10.3389/fimmu.2014.00396
关键词
Mycobacterium bovis; tuberculosis; RNA-seq; biomarker; cattle; microarray; peripheral blood
类别
资金
- Science Foundation Ireland [SFI/01/F.1/B028, SFI/08/IN.1/B2038]
- Department of Agriculture, Food and the Marine [RSF 06 405]
- European Union [KBBE-211602-MACROSYS]
- UCD Wellcome Trust Computational Infection Biology Ph.D. Programme [097429/Z/11/Z]
- Wellcome Trust [097429/Z/11/Z] Funding Source: Wellcome Trust
Bovine tuberculosis, caused by infection with Mycobacterium bovis, is a major endemic disease affecting cattle populations worldwide, despite the implementation of stringent surveillance and control programs in many countries. The development of high-throughput functional genomics technologies, including gene expression microarrays and RNA-sequencing (RNA-seq), has enabled detailed analysis of the host transcriptome to M. bovis infection, particularly at the macrophage and peripheral blood level. In the present study, we have analyzed the peripheral blood leukocyte (PBL) transcriptome of eight natural M. bovis-infected and eight age- and sex-matched non-infected control Holstein-Friesian animals using RNA-seq. In addition, we compared gene expression profiles generated using RNA-seq with those previously generated using the high-density Affymetrix (R) GeneChip (R) Bovine Genome Array platform from the same PBC-extracted RNA. A total of 3,250 differentially expressed (DE) annotated genes were detected in the M. bovis-infected samples relative to the controls (adjusted P-value <= 0.05), with the number of genes displaying decreased relative expression (1,671) exceeding those with increased relative expression (1,579). Ingenuity Systems Pathway Analysis (IPA) of all DE genes revealed enrichment for genes with immune function. Notably, transcriptional suppression was observed among several of the top-ranking canonical pathways including Leukocyte Extravasation Signaling. Comparative platform analysis demonstrated that RNA-seq detected a larger number of annotated DE genes (3,250) relative to the microarray (1,398), of which 917 genes were common to both technologies and displayed the same direction of expression. Finally, we show that RNA-seq had an increased dynamic range compared to the microarray for estimating differential gene expression.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据