PCRdrive: the largest qPCR assay archive to date and endless potential for lab workflow revitalization

• Published in: BMC bioinformatics 2018-11, Vol.19 (1), p.447-447, Article 447
• Main Authors: Burger, Florian, Angioni, Michele, Russo, Gianluca, Schad, Martina, Kallarackal, Jim
• Format: Article
• Language: English
• Subjects: Acids; Archives & records; Assay database; Assaying; Bioinformatics; Data integrity; Design; DNA Primers - genetics; Electronic lab notebook; Filtration; Gene expression; Genes; Genomes; Genomics; Internet; Online workspace; Optimization; Primers; Protein structure; Protocol (computers); Reagents; Real-Time Polymerase Chain Reaction - methods; Regeneration; Researchers; RT-qPCR assay; Secondary structure; Single-nucleotide polymorphism; SNP check; Software; Specificity check; Streamlining; Transcription; Workflow
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-018-2452-3

Primer design is a crucial step in establishing specific and sensitive qPCR assays. Even though numerous tools for primer design exist, the majority of resulting assays still requires extensive testing and optimisation or does not allow for high quality target amplification. We developed a workflow for designing qPCR assays. Unlike other tools, we compute a PCR assay including primer design, concentrations and the optimal PCR program. Gene expression assays were already generated in a total of 283,226 genes from three species and are continued for all genes of the major model species. The results are available online at https://pcrdrive.com/lab#/assay-database . The workflow involves filtering Primer3-generated primers by considering diverse parameters including specificity, single-nucleotide polymorphisms (SNPs), secondary structure as well as compatibility with standard qPCR assay conditions. The resulting assays consist of transcript-specific primer sequences, a reagents protocol as well as instrument settings which are provided in a web-based tool called PCRdrive. PCRdrive was designed to support PCR users in their PCR-related tasks and is equipped with handy functions, components of an electronic lab notebook (ELN) as well as teamworking opportunities. High quality ready to use qPCR assays for gene expression analysis are provided within the online platform PCRdrive. A built-in primer designer enables easy generation of assays which is not supported by any other tool. The wet lab optimisation of new assays can be transparently documented and shared within the team. PCRdrive also contains an archive of public PCRs which is updated regularly. Users may use the archive to publish their PCR to the community which makes it easy for other researchers worldwide to reproduce and validate the PCR. PCRdrive is a growing network of PCR users, simplifying and streamlining research through its useful existing features and continuous developments from the active development team.