A Methodical Microarray Design Enables Surveying of Expression of a Broader Range of Genes in Ciona intestinalis
A Methodical Microarray Design Enables Surveying of Expression of a Broader Range of Genes in Ciona intestinalis
复制标题
有条不紊的微阵列设计能够调查玻璃海鞘更广泛的基因表达
作者：
Matsumae H;et al.
我们基于NimbleGen 12-plex× 135 k格式，提供了一种新的玻璃海鞘寡核苷酸芯片。该阵列代表106，285个探针，这是目前可用的44 k微阵列的探针数量的两倍多。这些探针覆盖了2008年发表的KyotoHoya（KH）模型中99.2%的转录本，并且它们包含了UniGene数据库中不包括在KH模型中的条目的81.1%。在本文中，我们表明，这种新的135 K微阵列测量的基因表达水平是高度相关的，与现有的44 K微阵列获得的基因共同的两个阵列。我们还研究了基因表达的样本，从卵巢和神经复合体的成年C。结果表明，组织特异性基因的表达与以前的报道一致。在135 k微阵列中鉴定的高表达基因中，约有一半未包括在先前的微阵列中。这种微阵列对基因模型的高覆盖率使得识别给定转录本的剪接变体成为可能。135 k微阵列在研究尚未很好表征的基因功能方面很有用。关于这个135 k微阵列的详细信息可以从补充材料，NCBI基因表达综合（GEO）和http://marinegenomics.oist.jp免费获得。
We provide a new oligo-microarray for Ciona intestinalis, based on the NimbleGen 12-plex×135k format. The array represents 106,285 probes, which is more than double the probe number of the currently available 44k microarray. These probes cover 99.2% of the transcripts in the KyotoHoya (KH) models, published in 2008, and they contain 81.1% of the entries in the UniGene database that are not included in the KH models. In this paper, we show that gene expression levels measured by this new 135k microarray are highly correlated with those obtained by the existing 44k microarray for genes common to both arrays. We also investigated gene expression using samples obtained from the ovary and the neural complex of adult C. intestinalis, showing that the expression of tissue-specific genes is consistent with previous reports. Approximately half of the highly expressed genes identified in the 135k microarray are not included in the previous microarray. The high coverage of gene models by this microarray made it possible to identify splicing variants for a given transcript. The 135k microarray is useful in investigating the functions of genes that are not yet well characterized. Detailed information about this 135k microarray is accessible at no charge from supplemental materials, NCBI Gene Expression Omnibus (GEO), and http://marinegenomics.oist.jp.