Genomics & Bioinformatics Core Facility

BluePippin Size Selection

The BluePippin instrumentation, Sage Science’s automated DNA size selection system, is new addition to the Next-Generation Sequencing workflow. In an effort to reduce hands on time, Sage Sciences has developed a convenient streamline system for size selecting DNA that is much faster and easier than traditional gel cutting methods. The system produces consistent and reproducible results.

How Does the BluePippin Work?

Pulsed-field electrophoresis separates and extracts DNA fragments. Using pre-cast gel cassettes, DNA is automatically collected in buffer according to software input size ranges. Gel cassettes use an internal DNA size standard run in a dedicated sample lane to determine the timing of size-selected collections

BluePippin Size Selection Parameters

Gel cassettes for DNA selections are available in four agarose concentrations to provide a full range of size selection options between 90bp and 50kb. Protein size selection provides similar resolution to acrylamide gels. See the BluePippin cassette kit reference chart to explore the DNA size selection options.

% Agarose Gel Cassette Target Fragment Range (bp or kb)

3% agarose


2% agarose


1.5% agarose


0.75% agarose


Sample Preparation

To ensure successful results, the sample must be of sufficient purity and appropriate concentration. We recommend using only purified products. Quality of the sample is very important for accurate fragmentation; high salt concentration and particulates are known to adversely affect results. Please see protocol section for guidelines and examples of extraction/purification methods.

Selecting the appropriate fragmentation parameters is sample concentration dependent. So it is important to determine sample concentration prior to submission. We recommend using a spectrometer, such as the Nanodrop, or a fluormetrics, such as Qubit. For an additional service fee, we can assess the quantity of the sample using the Qubit. Please contact us for additional services.

For each sample to be analyzed, please provide a minimum of 500ng and up to 10ug of sample in a clearly labeled 1.5ml tube. Bring sample volume to 30ul in 1x Tris EDTA buffer. All tubes must be labeled on the side with PI Name, Date (MM/DD/YYYY), Concentration, and unique Sample Name.

Please follow all instructions as detailed in the Sample Preparation Guidelines. To avoid sample-processing delays, ensure your tubes/plates are clearly labeled with your initials, date, and sample number.

Contact us to schedule delivery of your samples to our Genomics Core Facility.

Genomics Core Facility
Galvin Life Science Center Room 019
Phone: (574) 631-1902


After service completion, the size-selected sample is returned in a sterile 1.7mL microcentrifuge tube and documentation of parameters is provided.

For an additional fee, we can assess the size distribution using the Agilent 2100 Bioanalyzer and the sample concentration by Qubit Quantification. For addtional services, contact us.