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Nucleic Acids Res. 2018 Jan 4;46(D1):D1229-D1236. doi: 10.1093/nar/gkx725.

qPrimerDB: a thermodynamics-based gene-specific qPCR primer database for 147 organisms.

Lu K1,2, Li T3, He J4,5, Chang W1,4, Zhang R1, Liu M1, Yu M1, Fan Y1, Ma J1,4, Sun W1, Qu C1,2, Liu L1,2, Li N2,5, Liang Y1,2, Wang R1,2, Qian W1, Tang Z1, Xu X1,2, Lei B6,7, Zhang K1, Li J1,2.

Author information

1
College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
2
Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
3
State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China.
4
Shennong Class, Southwest University, Beibei, Chongqing 400715, China.
5
College of Resources and Environment, Southwest University, Chongqing 400715, China.
6
Key Laboratory of Molecular Genetics, China National Tobacco Corporation, Guizhou Academy of Tobacco Science, Guiyang 550081, China.
7
Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China.

Abstract

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.

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