Pippin Prep DNA Size Selection System

This application note demonstrates an optimized Pippin Prep protocol for use with the NEBNext Small RNA library kits. The Pippin Prep protocol provides all of the sequence quality benefits of the standard manual gel protocol, but with greatly enhanced ease-of-use and reproducibility.

Automated size selection is a superior alternative to manual gel extraction, allowing scientists to save time and money, improve the efficiency of sequencing runs and analysis, and perform new applications with next-gen sequencers. This white paper describes the use of the Pippin Prep and Blue Pippin size selection platforms for automated DNA size selection.

This case study demonstrates how scientists in the prominent core facility at the Dana-Farber Cancer Institute, have paired Pippin Prep size selection with Illumina’s Nextera to build better, more reproducible libraries that yield improved genome assemblies.

This case study demonstrates how a new, massively parallel genotyping technique from a research team at Harvard relies on automated size selection and next-generation sequencing to boost accuracy and lower costs.

For low-input DNA studies such as viral metagenomics, there is no room for error in library protocols. This application note describes a case study in which scientists at the University of Arizona have optimized methods for sequencing sample prep. This study emphasizes the need for efficient and precise size selection.

ChIP-Seq analysis is valuable for identifying genomic DNA sequences that are associated with immunoprecipitable proteins, such as modified histones or transcription factors, in vivo. One of the technically challenging and labor-intensive steps in ChIP-Seq is the size selection of DNA fragments during the NGS library construction and is a source of sample loss and sample cross contamination. This application note compares two methods for the size-selection step.

Gel purification of cDNA and RNA-Seq libraries is the gold standard for purification options but these methods are time consuming and so most protocols have standardized on bead or column purification methods. This scientific poster compares two systems for library purification steps in NGS. The Pippin Prep, a preparative gel electrophoresis system, is shown to offer several advantages over other protocols for this application including efficient removal of low molecular weight library contaminants (primer/adapter artifacts) and accurate size-selection of the library.

This poster outlines the expanded NGS Applications for the Pippin Prep DNA Size Selection System, initially showcased at a meeting during 2011.

Watch this informative video to learn more about the use of the Sage Science Pippin Prep, designed for Illumina library construction. Through a series of slides, we see that the Pippin Prep is a fast and easy method for selecting any DNA fragment size determined by the user.

This video highlights the use of the various tests preformed to ensure that the Pippin Prep machine is fully operational and fully optimized. TF ChIP-Seq and Histone Mark ChIP seq libraries utilize the Pippin Prep. The Pippin Prep automates preparative gel electrophoresis for the construction of next gen sequencing libraries. By setting a new standard for sample quality of size-selected DNA, effort is reduced, bioinformatics are improved, and costly sequencing runs are more fully utilized.

This presentation highlights the benefits of using an automated preparative gel electrophoresis system for the construction of next gen sequencing libraries. The Pippin Prep is designed to improve library quality whilst reducing the amount of DNA needed. Results of the use of the Pippin Prep have shown to result in consistent increased yields, more diverse and unique libraries.

Watch this interview with Sage Science to learn about the Pippin Prep, a new gel electrophoresis platform designed to automate size selection of DNA for next-generation sequencing applications. The instrument features a computer-controlled power supply and an integrated optical system, which enables user-defined size fractions to be collected automatically, avoiding time intensive manual gel pouring and gel cutting processes. Gel cassettes use an external DNA size standard run in a dedicated sample lane to determine the timing of size-selected collections. SelectScience.tv interview at AACR 2011.

Watch this video to see the quick and easy set-up process of the Pippin Prep, a new electrophoresis platform for the preparation of size-fractionated DNA samples. The step-by-step guide takes you through from out of the box to sample ready. The kit includes an LCD computer monitor, documentation and a rinse cassette.

This video clearly demonstrates all the steps for automated DNA size selection and collection using the Pippin Prep. The video covers how to test the system, set up a protocol for different cut sizes and load the gels. This system is a new electrophoresis platform using pre-cast agarose gel cassettes.

This video demonstrates how the Pippin Prep selects and collects 100bp, 200bp, 300bp and 400bp DNA fragments over 80 minutes. Gel Cassettes use an external DNA size standard run in a dedicated sample lane to determine the timing of size-selected collections. Four lanes are used for samples, and one extraction can be collected per lane according to user input size ranges. Sample lanes are physically separate and tapered to shorten run times and improve resolution.