<strong>Dataset of DNA microarray probe for every gene in the genome of </strong><em><strong>Escherichia coli</strong></em><strong> K-12</strong>
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Prior to the maturation of RNA-seq technology, DNA microarray is the go-to tool for understanding the genome-level gene expression pattern of particular organism. However, the probes used to fish out the mRNA are often designed by commercial companies, which although useful, could not tailor to the specific research needs of individual researchers in different fields. This work presents a dataset of DNA microarray probe for every gene in the genome of <em>Escherichia coli</em> K-12 designed by an in-house MATLAB software through automated algorithm. Each probe targets the front part of every gene, and the specificity check (TRUE / FALSE) reveals that not every probe is specific for each gene. This means that the probe could also fish out mRNA from other genes in the same genome. A count is provided for the number of genes that could be targeted for a given probe. Naturally, a higher count meant that the probe could target more genes, and is thus, not specific. Overall, this work represents an initial attempt to design a software for automatic design of probes for each gene in the genome of <em>E. coli</em> K-12. The result is a satisfactory list of probes useful for the tasks, but there are a number of genes that requires more refined strategies for developing more specific probes.
在RNA测序（RNA-seq）技术成熟之前，DNA微阵列（DNA microarray）是探究特定生物体全基因组水平基因表达模式的主流工具。然而，用于捕获信使RNA（mRNA）的探针通常由商业公司开发，尽管此类探针具备一定实用性，但难以适配不同领域研究者的个性化研究需求。本研究构建了一套针对大肠杆菌（Escherichia coli）K-12全基因组每个基因的DNA微阵列探针数据集，该数据集由自研MATLAB软件通过自动化算法设计生成。每条探针靶向对应基因的前端序列，特异性验证结果（TRUE/FALSE）显示，并非所有探针都能仅特异性结合目标基因——这意味着此类探针同时也可能捕获同一基因组中其他基因的信使RNA（mRNA）。数据集同时提供了单条探针的可靶向基因数统计：可靶向基因数目越多，说明该探针的特异性越差。整体而言，本研究首次尝试开发一款自动化探针设计软件，用于大肠杆菌K-12全基因组每个基因的探针设计。最终得到的探针列表可满足多数研究需求，但仍有部分基因需要采用更精细的设计策略，以获得特异性更强的探针。
