RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis.
RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis.
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来自牛肉菌感染的牛的外周血白细胞的RNA-seq转录分析。
DOI：
10.3389/fimmu.2014.00396
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发表时间：
2014
影响因子：
7.3
通讯作者：
MacHugh DE
中科院分区：
文献类型：
--
作者：
McLoughlin KE;Nalpas NC;Rue-Albrecht K;Browne JA;Magee DA;Killick KE;Park SD;Hokamp K;Meade KG;O'Farrelly C;Gormley E;Gordon SV;MacHugh DE
牛结核病是由牛分枝杆菌感染引起的，是一种影响全球牛种群的主要地方性疾病，尽管许多国家实施了严格的监测和控制计划。高通量功能基因组学技术的发展，包括基因表达微阵列和RNA测序(RNA-seq)，使详细分析宿主转录组对牛分枝杆菌感染的影响成为可能，特别是在巨噬细胞和外周血水平。在本研究中，我们用RNA-seq技术分析了8只自然感染的牛分枝杆菌和8只年龄和性别匹配的非感染对照荷斯坦-弗里斯动物的外周血白细胞(PBL)转录组。此外，我们比较了使用RNA-seq生成的基因表达谱与之前使用高密度Affymetrix®GeneChip®牛基因组阵列平台从相同的PBL提取的RNA生成的基因表达谱。在感染牛分枝杆菌的样本中，与对照组相比，总共检测到3,250个差异表达(DE)注释基因(调整后的P值≤为0.05)，其中相对表达降低的基因(1,671个)超过相对表达增加的基因(1,579个)。所有DE基因的Invenity®系统路径分析(IPA)显示具有免疫功能的基因丰富。值得注意的是，在包括白细胞外渗信号在内的几个顶级典型通路中观察到转录抑制。比较平台分析表明，相对于微阵列(1,398)，RNA-SEQ检测到更多的注释DE基因(3,250)，其中917个基因是两种技术共同的，并且显示出相同的表达方向。最后，我们表明，与微阵列相比，RNA-SEQ在估计差异基因表达方面具有更大的动态范围。
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® GeneChip® Bovine Genome Array platform from the same PBL-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.
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影响因子：
64.8
作者：
通讯作者：
--
影响因子：
5.4
作者：
Frick, C;Odermatt, A;Parkos, CA
通讯作者：
Parkos, CA
影响因子：
14.9
作者：
Barrett T;Troup DB;Wilhite SE;Ledoux P;Evangelista C;Kim IF;Tomashevsky M;Marshall KA;Phillippy KH;Sherman PM;Muertter RN;Holko M;Ayanbule O;Yefanov A;Soboleva A
通讯作者：
Soboleva A
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
3.3
作者：
Gormley, E;Doyle, MB;Collins, JD
通讯作者：
Collins, JD