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Automated size selection is a superior alternative to manual gel extraction, allowing scientists to save time and money and improve the efficiency of sequencing runs and analysis.

Many scientists use agarose gels as a manual step to size-select their libraries prior to sequencing.

This is a laborious and time-intensive activity, fraught with known problems. Manual gel extraction is operator-dependent, resulting in significant variability between the DNA sizing step performed by any two people.

Excellent tools for automated size selection of DNA

Pippin instruments are the best alternative to excising DNA from agarose gels or purifying with kits. They are aimed to facilitate library construction for the most popular NGS platforms. Independent studies show that automated size selection with Pippin is more precise, reproducible, and higher throughput than is possible with manual gels.

We offer the Pippin Prep from Sage Science for reproducible collections of smaller fragments, up to 8 kb. The BluePippin within the Pippin family facilitates the collection of larger fractions, up to 50 kb. For higher throughput workfl­ows and with a lower cost per sample we propose Pippin HT.


How the System Works

Pippin gel cassettes are pre-cast with agarose and are disposable. Sizing is determined by the detection of DNA markers run in one dedicated lane.

Sample capacity depending on cassette type and electrophoresis protocol.

Each sample lane is physically separate, and DNA is separated along a gel column until the programmed fragment range reaches the branch point.

By switching the active electrode, DNA is diverted into a membrane-bound buffer chamber.

When the size range has been collected, the active electrode is switched back to the separation channel, and the sample can be removed with a standard pipette.

Key application areas

  • Library construction for paired-end sequencing
  • Library construction for mate-pair sequencing
  • Template preparation for clonal amplification of DNA on beads
  • Library construction for Chromatin Immunoprecipitation (ChIP) techniques
  • Isolation of miRNA libraries from adapter dimer and larger cDNAs
  • RNA-seq
  • Automated collection of PCR bands or restriction fragments

Benefits of the Pippin DNA size selection system

  • Saves time and effort compared to manual gel purification
  • Sample-to-sample reproducibility
  • Provides narrow fragment size distributions
  • Minimal low molecular weight contamination reduces wasted reads
  • Individual sample channels allow for multiplexing without sample cross-contamination