Gene expression profiles of various tissues under different physiological conditions

Rice is one of important crop and, the genome has been already completely sequenced. Moreover we collected more than 30K rice FL-cDNA clones as transcriptome resources. However, the cDNA collection did not reveal the transcription activity and specificity of expression. So, we designed 60-mer oligo array based on the array system of Agilent Technologies (GPL477) as custom array. For validation of the array, we tested the reproducibility of labeling and hybridization. After this validation, 22K rice oligo array was supplied from Agilent Technologies (GPL892). 1: reproducibility of labeling: mRNA of shoot sample was amplified and labeled more than 10 times with Cy3 and Cy5, and both Cy3- and Cy5-labeled cRNA was hybridized on a slide (self-hybridization), and validate the reproducibility of labeling. In addition, we also amplified and labeled mRNA of other samples with Cy3 and Cy5, and made a self-hybridization. The intensity data of these array was also indicated transcription activity of genes in these samples. Keywords: variety among tissues organisms: Oryza sativa ssp. japonica (Nipponbare) tissue: shoot, root, germinated seed, panicle, callus derived from more than 100 plants treatement1: cold stress (10 degreeC) time course1: 24, 48, 72 hours tissue1: shoot treatment2: drought stress (25% polyethylene glycol 6000) time course2: 1, 9, 24 hours tissue: shoot treatment3: flood and lay-down stress time course3: 1, 6, 24, 48 hours tissue3: shoot treatment4: flood stress time course4: 1, 24, 48, 72 hours tissue4: shoot treatment5: osmotic stress (260mM mannitol) for 24 hours tissue5: shoot treatment6: 150mM NaCl for 24 hours tissue6: shoot hybridization : two dye method hybridization: self-hybridization replication: Hybridization of shoot replicated 11 times, and germinated seed was twice. Other samples did not replicated. array: 1 array per 1 experiment (total 39 arrays)

水稻是重要粮食作物之一，其基因组已完成全序列测定。此外，我们收集了超过3万个水稻全长互补DNA（full-length cDNA, FL-cDNA）克隆作为转录组研究资源。但现有cDNA文库无法揭示基因的转录活性与表达特异性。为此，我们基于安捷伦科技（Agilent Technologies）的GPL477芯片平台定制了60聚体寡核苷酸芯片（60-mer oligo array）。为验证该芯片的可靠性，我们对荧光标记与杂交流程的重复性开展了测试。完成验证流程后，安捷伦科技推出了编号为GPL892的22K水稻寡核苷酸芯片。
1. 标记重复性验证实验：以地上组织样本的mRNA为材料，分别使用Cy3和Cy5荧光染料进行10次以上的扩增与标记，将两种荧光标记的cRNA进行玻片自身杂交（self-hybridization），以此验证标记流程的重复性。此外，我们还对其余样本的mRNA进行Cy3、Cy5双标记并开展自身杂交实验。上述芯片的荧光强度数据可反映对应样本中基因的转录活性水平。
关键词：组织间表达差异；实验生物：粳稻（Oryza sativa ssp. japonica）日本晴（Nipponbare）
样本组织：地上组织、根系、萌发种子、穗部以及100株以上材料诱导的愈伤组织
处理1：低温胁迫（10℃），时间梯度：24、48、72小时，样本组织：地上组织
处理2：干旱胁迫（25%聚乙二醇6000），时间梯度：1、9、24小时，样本组织：地上组织
处理3：淹水+倒伏胁迫，时间梯度：1、6、24、48小时，样本组织：地上组织
处理4：淹水胁迫，时间梯度：1、24、48、72小时，样本组织：地上组织
处理5：渗透胁迫（260mM甘露醇），处理时长24小时，样本组织：地上组织
处理6：150mM氯化钠胁迫，处理时长24小时，样本组织：地上组织
杂交方式：双荧光标记法，杂交类型：自身杂交
生物学重复：地上组织样本杂交重复11次，萌发种子样本杂交重复2次，其余样本无生物学重复
芯片使用规则：每个实验对应1张芯片，本数据集共包含39张芯片的杂交数据