Use of the Affymetrix Human GeneChip array and genomic DNA hybridisation probe selection to study ovine transcriptomes
Use of the Affymetrix Human GeneChip array and genomic DNA hybridisation probe selection to study ovine transcriptomes
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DOI：
10.1017/s1751731110002533
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发表时间：
2011-06-01
期刊：
影响因子：
3.6
通讯作者：
Parr, T.
中科院分区：
文献类型：
--
作者：
Graham, N. S.;May, S. T.;Parr, T.
基因芯片微阵列是研究全球基因表达谱的有力工具，已被用于许多物种。然而，目前没有羊特异性的Affyssin基因芯片，牛阵列的覆盖范围和注释相当有限。以前，开发了一种基于基因组DNA（gDNA）杂交的探针选择方法，这使得基因芯片能够用于它们未被设计的物种。这种方法可以大大增加潜在的注释基因的数量，这些基因可以在目前可用的基因之外进行研究，特别是对于没有全面表征基因组的物种。在这项研究中，我们证明了基于gDNA的探针选择的Affyellow人类U133+2基因芯片阵列可用于研究绵羊组织中的基因表达谱。在绵羊骨骼肌和肝脏样品中检测到超过20 000个转录物，这比使用市售的绵羊特异性微阵列可能的要多。已知每个组织的前15个差异表达基因中的大多数以组织特异性方式表达或与该组织的特定功能相关。差异表达基因的基因本体分析揭示了两种组织之间基因表达谱的预期差异。除了证明探针选择方法可用于研究绵羊转录组之外，这种方法的好处是，它可以大大增加注释和新基因的数量，这些基因可以使用绵羊或牛特异性微阵列进行研究。同样的方法也有可能允许研究其他物种，其中物种特异性微阵列不可用或其基因组尚未得到全面表征。
Affymetrix GeneChip microarrays are a powerful tool to study global gene expression profiles and have been used on many species. However, no sheep-specific Affymetrix GeneChip is currently available and the bovine array is fairly limited in its coverage and annotation. Previously, a probe-selection method based on hybridisation of genomic DNA (gDNA) was developed, which enables GeneChips to be used for species that they were not designed for. This approach can greatly increase the number of potential annotated genes that can be studied beyond that which is currently available, particularly for species that do not have comprehensively characterised genomes. In this study, we demonstrate that gDNA-based probe selection on the Affymetrix Human U133+2 GeneChip array can be used to study gene expression profiles in sheep tissues. More than 20 000 transcripts were detected in triplicate ovine skeletal muscle and liver samples, which is more than would be possible using the commercially available sheep-specific microarray. The majority of the top 15 differentially expressed genes for each tissue were known to either be expressed in a tissue-specific manner or relate to specific functions of that tissue. Gene ontology analysis of the differentially expressed genes revealed the expected differences in gene expression profiles between the two tissues. Besides demonstrating that the probe selection method can be used to study the ovine transcriptome, the benefits of this approach are that it can greatly increase the number of annotated and novel genes that can be studied beyond those currently possible using ovine-or bovine-specific microarrays. This same method also has the potential to allow the study of other species where species-specific microarrays are not available or whose genomes have not been comprehensively characterised.