Benchmarking the CATMA microarray. A novel tool for Arabidopsis transcriptome analysis
Benchmarking the CATMA microarray. A novel tool for Arabidopsis transcriptome analysis
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DOI：
10.1104/pp.104.051300
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发表时间：
2005-02-01
期刊：
影响因子：
7.4
通讯作者：
Kuiper, MTR
中科院分区：
文献类型：
--
作者：
Allemeersch, J;Durinck, S;Kuiper, MTR
转录谱分析对于研究生物系统至关重要，并且已经实施了各种平台来在基因组尺度上调查mrna。我们评估了为拟南芥转录组分析设计的CATMA微阵列的性能，并将其与Agilent和Affymetrix商业平台进行了比较。CATMA阵列由150 ~ 500 bp的基因特异性序列标签、60mer寡核苷酸的Agilent（拟南芥2）阵列和25mer寡核苷酸的Affymetrix基因芯片（ATH1）组成。我们将每个探针库与拟南芥基因组注释（the Institute for Genomic Research release 5.0）进行匹配，并确定它们之间的对应关系。通过与来自8个RNA样品的标记靶标杂交，分析了阵列的性能，这些样品由芽总RNA和校准的14个对照转录本组成。CATMA阵列显示最大的动态范围可以延伸到3到4个测井段。Agilent和Affymetrix阵列显示的范围较窄，可能是因为转录本浓度超过每个细胞1,000拷贝时发生信号饱和。三种平台的灵敏度相当。对于Affymetrix GeneChip数据，RMA软件包在所有调查标准上都优于Microarray Suite 5.0，证实了错配寡核苷酸提供的信息没有附加价值。此外，利用我们数据集中的重复，我们对平台产生假阳性和假阴性差异表达基因的倾向进行了稳健的统计分析，并给出了令人满意的结果。结果表明，CATMA阵列是Affymetrix和Agilent平台的成熟替代品。
Transcript profiling is crucial to study biological systems, and various platforms have been implemented to survey mRNAs at the genome scale. We have assessed the performance of the CATMA microarray designed for Arabidopsis (Arabidopsis thaliana) transcriptome analysis and compared it with the Agilent and Affymetrix commercial platforms. The CATMA array consists of gene-specific sequence tags of 150 to 500 bp, the Agilent (Arabidopsis 2) array of 60mer oligonucleotides, and the Affymetrix gene chip (ATH1) of 25mer oligonucleotide sets. We have matched each probe repertoire with the Arabidopsis genome annotation (The Institute for Genomic Research release 5.0) and determined the correspondence between them. Array performance was analyzed by hybridization with labeled targets derived from eight RNA samples made of shoot total RNA spiked with a calibrated series of 14 control transcripts. CATMA arrays showed the largest dynamic range extending over three to four logs. Agilent and Affymetrix arrays displayed a narrower range, presumably because signal saturation occurred for transcripts at concentrations beyond 1,000 copies per cell. Sensitivity was comparable for all three platforms. For Affymetrix GeneChip data, the RMA software package outperformed Microarray Suite 5.0 for all investigated criteria, confirming that the information provided by the mismatch oligonucleotides has no added value. In addition, taking advantage of replicates in our dataset, we conducted a robust statistical analysis of the platform propensity to yield false positive and false negative differentially expressed genes, and all gave satisfactory results. The results establish the CATMA array as a mature alternative to the Affymetrix and Agilent platforms.