Evaluation of Affymetrix Gene Chip sensitivity in rat hippocampal tissue using SAGE analysis
Evaluation of Affymetrix Gene Chip sensitivity in rat hippocampal tissue using SAGE analysis
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DOI：
10.1046/j.1460-9568.2002.02097.x
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发表时间：
2002-08-01
影响因子：
3.4
通讯作者：
Akil, H
中科院分区：
文献类型：
--
作者：
Evans, SJ;Datson, NA;Akil, H
DNA微阵列是同时监测数千个转录水平的有力工具。然而，使用DNA微阵列研究中枢神经系统面临着一些挑战。这些包括检测高度复杂组织中的低丰度转录本，以及估计响应实验操作的转录本水平的相对低幅度的变化。许多对脑功能很重要的转录物的表达水平很低，或者在相对较少的细胞中表达，这使得它们难以在复杂的脑组织背景中检测到。本研究的目的是评估基因芯片检测转录本的敏感性，通过使用基因表达系列分析（SAGE）研究的结果。比较结果表明，Affymetrix基因芯片（如SAGE）只能可靠地检测中高丰度转录本，而低丰度转录本的检测则不一致，其中许多转录本与大脑生物功能有很大相关性。具体来说，我们估计，基因芯片可靠地检测不超过30%的海马转录组时，使用总海马解剖作为源组织。这份报告提供了第一个广泛的评估Affyssin基因芯片的敏感性相关的研究大脑。
DNA microarrays are a powerful tool for monitoring thousands of transcript levels simultaneously. However, the use of DNA microarrays in studying the central nervous system faces several challenges. These include the detection of low-abundance transcripts in highly complex tissue as well as estimating relatively low-magnitude changes in transcript levels in response to experimental manipulation. Many transcripts important to brain function have low expression levels or are expressed in relatively few cells, making them difficult to detect in the complex background of brain tissue. The aim of the present study is to evaluate the sensitivity of Gene Chip detection of transcripts in brain by using results from serial analysis of gene expression (SAGE) studies. The results of this comparison indicate that Affymetrix Gene Chips, like SAGE, only reliably detect medium- to high-abundance transcripts and that detection of low-abundance transcripts, many of which have great relevance to biological function in brain, is inconsistent. Specifically, we estimate that Gene Chips reliably detect no more than 30% of the hippocampal transcriptome when using a gross hippocampal dissection as the source tissue. This report provides the first broad evaluation of Affymetrix Gene Chip sensitivity relevant to studying the brain.