Spotted long oligonucleotide arrays for human gene expression analysis
Spotted long oligonucleotide arrays for human gene expression analysis
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DOI：
10.1101/gr.1048803
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发表时间：
2003-07-01
期刊：
影响因子：
7
通讯作者：
Erle, DJ
中科院分区：
文献类型：
--
作者：
Barczak, A;Rodriguez, MW;Erle, DJ
通过沉积（或“点样”）每个基因的单个长寡核苷酸探针产生的 DNA 微阵列可能是其他类型阵列的有吸引力的替代品。我们使用两个类似 70 聚体探针的大集合生产了点状寡核苷酸阵列，并使用这些阵列来分析两个不同的人类 RNA 样本中的基因表达。还使用通过原位合成每个基因的多组短（25 聚体）寡核苷酸组产生的阵列（Affymetrix GeneChips）对这些样品进行了分析。我们比较了长寡核苷酸探针集合和原位合成的 25 聚体阵列中代表的 7344 个基因的表达测量结果。我们发现用点状长寡核苷酸探针和原位合成的 25 聚体探针组进行的相对基因表达测量之间存在很强的相关性 (r = 0.8-0.9)。点状长寡核苷酸阵列适用于未扩增的 cDNA 和扩增的 RNA 靶标，并且是许多功能基因组学应用的经济高效的替代方案。大多数先前报道的微阵列技术评估都集中在对相对较少数量的基因进行的表达测量。这里描述的方法涉及更多的基因表达测量，并为比较基因组规模表达分析的现有和新兴技术提供了一种有用的方法。
DNA microarrays produced by deposition (or 'spotting') of a single long oligonucleotide probe for each gene may be an attractive alternative to other types of arrays. We produced spotted oligonucleotide arrays using two large collections of similar to70-mer probes, and used these arrays to analyze gene expression in two dissimilar human RNA samples. These samples were also analyzed using arrays produced by in situ synthesis of sets of multiple short (25-mer) oligonucleotides for each gene (Affymetrix GeneChips). We compared expression measurements for 7344 genes that were represented in both long oligonucleotide probe collections and the in situ-synthesized 25-mer arrays. We found strong correlations (r = 0.8-0.9) between relative gene expression measurements made with spotted long oligonucleotide probes and in situ-synthesized 25-mer probe sets. Spotted long oligonucleotide arrays were suitable for use with both unamplified cDNA and amplified RNA targets, and are a cost-effective alternative for many functional genomics applications. Most previously reported evaluations of microarray technologies have focused on expression measurements made on a relatively small number of genes. The approach described here involves far more gene expression measurements and provides a useful method for comparing existing and emerging techniques for genome-scale expression analysis.