Automated DNA Library Construction using the NEBNext® Ultra II DNA Library Prep Kit for Illumina® on the Beckman Coulter Biomek FXP Automated Liquid Handler
The ability to construct DNA sequencing (DNASeq) libraries from a wide range of starting input masses is essential for many next generation sequencing (NGS) applications. The New England Biolabs NEBNext Ultra II DNA Library Preparation Kit for Illumina (Catalog Number E7645) provides users with the ability to construct high quality indexed DNASeq libraries from inputs ranging from 500 pg to 1 ug of starting DNA from sample inputs that include genomic DNA (gDNA), formalin fixed, paraffin embedded DNA (FFPE DNA) and chromatin immunoprecipitated DNA (ChIP DNA).
In this technical note, we describe the automation of the New England Biolabs NEBNext Ultra II DNA Library Preparation Kit for Illumina on the Beckman Coulter Biomek FXP Dual Arm Multi-channel 96 and Span-8 automated liquid handler (Biomek FXP) (Figure 1). The automation method utilizes an intuitive HTML-driven user interface (UI) which allows the user to specify the number of samples to be processed (1-96). The UI allows the user to select between seven size selection options and different indexing strategies including single and dual index systems. To increase the flexibility of the method, the user may enter a dilution factor for the NEBNext adaptor as appropriate for the input concentration of the user’s samples. In addition to these and other smaller features, the UI also allows the user to choose between off-deck incubations using an external thermocycler or to perform incubations on-deck with a Biometra TRobot thermocycler integrated to the Biomek FXP liquid handler for maximized walk-away time (Figure 2). The method also incorporates numerous stopping points through the workflow offering flexibility in the experimental planning (Figure 3). To help simplify and reduce errors during system setup, an HTML-driven reagent calculator is presented to the user with information on the required reagents, their respective volumes, and their location on the instrument deck based on the user’s input on number of samples and steps to be run. The automation method allows the user to prepare up to 96 individually indexed DNASeq libraries in approximately four hours (Figure 4).