Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays
Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays
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DOI：
10.1093/toxsci/69.2.383
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发表时间：
2002-10-01
影响因子：
3.8
通讯作者：
Johnson, JA
中科院分区：
文献类型：
--
作者：
Li, J;Pankratz, M;Johnson, JA
DNA微阵列可以根据阵列探针分为寡核苷酸（Affytek）或长cDNA（IncyteGenomics）。不幸的是，缺乏这两种流行的全球筛查阵列系统的比较数据。本研究旨在评估两个平台从相同样本生成的数据集的可靠性。我们已经建立了一个模型，通过用叔丁基对苯二酚（tBHQ）处理8和24小时，在人神经母细胞瘤细胞系中上调一组抗氧化反应元件（ARE）驱动的基因。选择HuGene FL（Affytectin）、U95 Av 2（Affytectin）和UniGem V 2.0（IncyteGenomics）对8-和24-h样品进行比较研究。从U95 Av 2芯片产生的Affyphin数据表明，在tBHQ处理8小时后，218个（占总克隆的2.3%）基因的mRNA增加。这份清单包含了大多数已知的ARE驱动基因，其中9个基因与RT-PCR结果显示出高度一致性。IncyteGenomics称有四个基因增加，没有基因减少。同样的四个基因也被Affyandroid微阵列调用。当比较两个平台时，所选基因的灵敏度（荧光强度）和特异性（倍数）非常不同。交叉杂交被证明部分导致了两个平台生成的数据的差异。根据我们的研究结果，从寡核苷酸微阵列产生的数据是更可靠的询问基因表达的变化比长cDNA微阵列的数据。
DNA microarrays can be classified into oligonucleotides (Affymetrix) or long cDNAs (IncyteGenomics) based on the arrayed probes. Unfortunately, data are lacking on the comparison of these two popular global screening array systems. The present study was designed to assess the reliability of datasets generated by the two platforms from the same samples. We have already established a model for upregulation of a cluster of antioxidant responsive element (ARE)-driven genes in a human neuroblastoma cell line by treatment with tert-butylhydroquinone (tBHQ) for 8 and 24 h. HuGene FL (Affymetrix), U95 Av2 (Affymetrix), and UniGem V 2.0 (IncyteGenomics) were chosen to do the comparative study on 8- and 24-h samples. The Affymetrix data generated from U95Av2 chips demonstrated that the mRNA of 218 (2.3% of total clones) genes was increased after 8 h of tBHQ treatment. This list included most of the known ARE-driven genes, and nine selected genes showed a high consistency with RT-PCR results. IncyteGenomics called four genes increased and no genes were decreased. These same four genes were also called by the Affymetrix microarray. The sensitivity (fluorescence intensity) and specificity (fold) were very different for selected genes when comparing the two platforms. Cross-hybridization was shown to partially contribute to the discrepancies of the data generated by the two platforms. According to our results, the data generated from oligonucleotide microarrays is more reliable for interrogating changes in gene expression than data from long cDNA microarrays.