Catalog No. : SAG-BLU0001

 BluePippin Size Selection System

BluePippin Size Selection System


DNA Size Selection for Next-Gen Sequencing, with Pulsed-Field (100bp – 50kb)

Collect HMW DNA with High-Pass Filtering

The BluePippin has the DNA capabilities of the Pippin Prep, plus the extra benefit of pulsed-field electrophoresis for resolving and collecting high molecular weight DNA.  For long-range genomic applications, high-pass filtering allows users to collect all fragments above a size threshold set by the user.

Target sizes or ranges of sizes are entered in software, and fractions are collected in buffer. Up to 5 samples/gel cassette may be run, with no possibility of cross-contamination.

Benefits of the BluePippin System

  • Saves time and effort compared to manual gel purification
  • Sample-to-sample reproducibility streamlines research
  • Higher sample quality improves downstream analysis

Key Downstream Technologies

  • Mate-pair sequencing
  • Single molecule sequencing
  • Bar-coded linked reads
ItemSize Application Price
BluePippin Size Selection System

1 Package

Next Gen Sequencing Automated Electrophoresis Please Inquire


The BluePippin instrument includes a monitor, keyboard, and mouse. A CPU is built in; an external PC is not required.

Blue Pippin Specs

Electrophoresis voltage
25V, 100V or 150V constant, 100V pulsed field
Optical detection
470 nm excitation, 525 nm emission
Power requirements
100-240 VAC, 2.5 A, 50-60 Hz
15 lbs / 7 kg
7h x 11w x 21d (in) | 18h x 28w x 53 d (cm)

Cassette Kits

Kits include 10 ea. disposable pre-cast gel cassettes.  All necessary standards and reagents are included with the purchase.

Pre-Cast Agarose Gel Cassettes for DNA Size Selection

Gel cassettes for DNA selections are available in four agarose concentrations to provide a full range of size selection options between 100bp up to 50kb.  For smaller fragment sizes, internal standards may be used for higher accuracy and increased sample capacity (from 4 to 5 samples/cassette).  Higher molecular weight fragments require a dedicated lane to run a calibration marker.  Run times are as little as 30 minutes,  To resolve very large DNA fragments, pulsed-field runs may last several hours.

View the BluePippin cassette reference chart (in Documents section) to explore the DNA size selection options and run times.

Gel Cassette Types and Target Ranges

  • 3% agarose, 100-250bp
  • 2% agarose, 100-600bp
  • 1.5% agarose, 250bp – 1.5kb
  • 0.75% agarose, 1-50kb

Downstream Technologies

  • miRNA isolation
  • DNA sequencing, RNA-seq, genotyping
  • DNA sequencing, ChIP-seq
  • Mate-pair, single molecule

Sage Pippin: Say Goodbye to Manual Gels


Pippin Family Brochure


BluePippin cassette reference chart

BluePippin Installation Guide

BluePippin User Manual v.6_31

BluePippin IQ/OQ Document

Automated Size Selection of NEBNext Small RNA Libraries with the Sage Pippin Prep

"ChIP-Seq Libary Prep" Westerling, T., Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute.

"Size selection of long-chain fragments (8kb) in Nextera Mate Pair library preparation", Dr. Yoshitoshi Ogura and Dr. Yasuhiro Gotoh of Division of Microbiology, Department of Infectious Diseases, School of Medicine, Faculty of Medicine, University of Miyazaki, Japan (Nippon Genetics)

"The effect of size selection of PacBio long-fragment libraries (≧7 kb) (comparison of size distribution and sequencing results)", Dr. Yasuhito Arai of Division of Cancer Genomics, National Cancer Center Institute, Japan (Nippon Genetics)

"Long-fragment library preparation for PacBio RSⅡ・P5-C3 chemistry", Okinawa Institute of Advanced Sciences, Japan (Nippon Genetics)

Case Studies

Case Study: "Tag Team: Scientists Use Pippin to Optimize Nextera Libraries", Zach Herbert, Dana Farber Core Facilities

Case Study: "New Take on RADseq Enables High-Throughput Variant Discovery", Hoekstra Lab, Harvard Univ.

Case Study: "Better Metagenomics Methods Offer Hope for Studies with Ultra-Low DNA", Sullivan Lab, Univ. Arizona

Case Study: "Precise Sizing and SMRT Sequencing Offer Unprecedented Read Length for Clinical Studies", Robert Sebra, Mt. Sinai

Cassette Guides

DNA Sequences of Internal Standards

High-Pass User Guide for BluePippin BUF7510 and BLF7510

High-Pass User Guide for SMRTbell templates

Quick Guide BDF1510 Marker R2

Quick Guide BDF2010 Marker V1

Quick Guide BDF3010 Marker Q2

Quick Guide BDQ3010 Marker Q3

Quick Guide BEF2010 Marker M1

Quick Guide BHZ7510 Marker Z1

Quick Guide BLF7510 Marker S1

Quick Guide BMF7510 Marker T1

Quick Guide BUF7510 Marker U1

DNA Control Kit Guides

CHP7504 Marker Guide for High-Pass >6-10kb and >15-20kb Protocols

Guide CIS1504, Control DNA, Internal Standard K or R2

Guide CIS2004, Control DNA, Internal Standard L or V1

Guide CIS3004, Control DNA, Internal Standard F or Q2

Guide CON7604, Control DNA, External Marker T1

Guide CON7504, Control DNA, External Marker D or S1


Software update:

Pippin v6.31 / v6.40 Software Release Notes | Released:08/07/18

Software Update Instructions


  •  BluePippin Size Selection System
  •  BluePippin Size Selection System
Please Inquire

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