期刊
JOURNAL OF DAIRY SCIENCE
卷 102, 期 2, 页码 1761-1767出版社
ELSEVIER SCIENCE INC
DOI: 10.3168/jds.2018-15516
关键词
baySeq; crossbred dairy cow; Cuffdiff 2; edgeR
资金
- Coordination for the Improvement of Higher Education Personnel (Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior, CAPES, Brazil)/Embrapa scholarship
- Foundation for Research Support of the State of Minas Gerais (Fundacao de Amparo a Pesquisa do Estado de Minas Gerais FAPEMIG, Minas Gerais, Brazil) [APQ-00095-15]
- National Council for Scientific and Technological Development (Conselho Nacional de Desenvolvimento Cientifico e Tecnologico, CNPq, Brazil) [473414/2011-2]
- Sao Paulo Research Foundation (Fundacao de Amparo a Pesquisa do Estado de Sao Paulo-FAPESP, Sao Paulo, Brazil) [2016/22940-3, 2015/25096-6]
The aim of this study was to elucidate the differential gene expression in the RNA sequencing transcriptome of isolated perfused udders collected from 4 slaughtered Holstein x Zebu crossbred dairy cows experimentally inoculated with Streptococcus agalactiae. We studied 3 different statistical tools (edgeR, baySeq, and Cuffdiff 2). In summary, 2 quarters of each udder were experimentally inoculated with Strep. agalactiae and the other 2 were used as a control. Mammary tissue biopsies were collected at times 0 and 3 h after infection. The total RNA was extracted and sequenced on an Illumina HiSeq 2000 (Illumiria Inc., San Diego, CA). Transcripts were assembled from the reads aligned to the bovine UMD 3.1 reference genome, and the statistical analyses were performed using the previously mentioned tools (edgeR, baySeq, and Cuffdiff 2). Finally, the identified genes were submitted to pathway enrichment analysis. A total of 1,756, 1,161, and 3,389 genes with differential gene expression were identified when using edgeR, baySeq, and Cuffdiff 2, respectively. A total of 122 genes were identified by the overlapping of the 3 methods; however, only the platelet activation presented a significantly enriched pathway. From the results, we suggest the FCER1G, GNAI2, ORAI1, and VASP genes shared among the 3 methods in this pathway for posterior biological validation.
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