College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
Nucleic Acids Res. 2018 Jan 4;46(D1):D1229-D1236. doi: 10.1093/nar/gkx725.
Real-time quantitative polymerase chain reaction (qPCR) is one of the most important methods for analyzing the expression patterns of target genes. However, successful qPCR experiments rely heavily on the use of high-quality primers. Various qPCR primer databases have been developed to address this issue, but these databases target only a few important organisms. Here, we developed the qPrimerDB database, founded on an automatic gene-specific qPCR primer design and thermodynamics-based validation workflow. The qPrimerDB database is the most comprehensive qPCR primer database available to date, with a web front-end providing gene-specific and pre-computed primer pairs across 147 important organisms, including human, mouse, zebrafish, yeast, thale cress, rice and maize. In this database, we provide 3331426 of the best primer pairs for each gene, based on primer pair coverage, as well as 47760359 alternative gene-specific primer pairs, which can be conveniently batch downloaded. The specificity and efficiency was validated for qPCR primer pairs for 66 randomly selected genes, in six different organisms, through qPCR assays and gel electrophoresis. The qPrimerDB database represents a valuable, timesaving resource for gene expression analysis. This resource, which will be routinely updated, is publically accessible at http://biodb.swu.edu.cn/qprimerdb.
实时定量聚合酶链反应（qPCR）是分析靶基因表达模式的最重要方法之一。然而，成功的 qPCR 实验在很大程度上依赖于高质量引物的使用。已经开发了各种 qPCR 引物数据库来解决这个问题，但这些数据库仅针对少数几个重要的生物体。在这里，我们开发了 qPrimerDB 数据库，该数据库基于自动基因特异性 qPCR 引物设计和基于热力学的验证工作流程。qPrimerDB 数据库是迄今为止最全面的 qPCR 引物数据库，具有一个网络前端，可提供 147 种重要生物体（包括人类、小鼠、斑马鱼、酵母、拟南芥、水稻和玉米）的基因特异性和预计算引物对。在这个数据库中，我们根据引物对覆盖率为每个基因提供了 3331426 对最佳引物对，以及 47760359 对可方便批量下载的替代基因特异性引物对。通过 qPCR 分析和凝胶电泳，对 66 个随机选择的基因在 6 个不同生物体中的 qPCR 引物对的特异性和效率进行了验证。qPrimerDB 数据库代表了一种有价值的、节省时间的基因表达分析资源。该资源将定期更新，并可在 http://biodb.swu.edu.cn/qprimerdb 上公开访问。
