Agilent eBook - 23

Best Practices with an Agilent Parallel CE System

correlate strongly and can be used interchangeably.
We also have a couple of quality metrics for genomic
DNA (gDNA). The DNA Integrity Number (DIN) can be
found on the TapeStation, and the Genomic Quality
Number (GQN) on the Fragment Analyzer and Femto
Pulse systems. Similar to the RNA metrics, the DIN
automatically rates sample quality on a 1 to 10 scale,
with 1 being highly degraded and 10 being highly
intact gDNA. The GQN also uses a 1 to 10 scale, but is
based on a user-defined threshold. Once a threshold
is set, the GQN tells you the percent of the DNA that is
larger than that threshold, thereby allowing the user to
determine the size of gDNA that is considered to be of
good quality based upon individual needs and library

Pulse system streamlines the analysis of high molecular weight gDNA by automating pulsed-field separations with sizing through 165 kb in as little as 1.5 hours.
GEN: Why is proper sampling, handling, and mixing
important for accurate library QC?

KL: Proper sampling, handling, and mixing ensures that
the results of the quality control analysis are indicative
of the sample itself. First, it is important that you are
storing your own samples in appropriate conditions.
For example, the use of appropriate containers, such
as LoBind tubes, can help preserve sample integrity.

Agilent introduced the Fragment Analyzer system
to cover DNA, gDNA, and RNA quality control.

GEN: What are the key trends you are seeing in
next‑generation sequencing?



Photo by Tim Menzel

KL: Long-read sequencing is becoming more prevalent. With the increase in read length, it is important to
understand how intact the starting genomic DNA is
and to perform multiple quality control steps throughout library preparation to ensure that the integrity of
the high molecular weight DNA is maintained. Preparation of long-read libraries, such as PacBio, can be
time consuming due to these necessary quality control
steps which have traditionally been done using agarose
pulsed-field gel electrophoresis. The Agilent Femto

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