Agilent eBook - 18

Quality Metrics for Nucleic
Acids with the Agilent Fragment
Analyzer and Femto Pulse Systems


Chava Pocernich and Steve Siembieda,
Agilent Technologies, Inc.

Assessment of nucleic acid integrity is essential to the success of many downstream
applications. The Agilent 5200 Fragment Analyzer system and the Agilent Femto
Pulse system offer quick and easy user‑friendly metrics for evaluating DNA, RNA, and
genomic DNA quality and integrity. The versatility of these quality metrics allows them
to be applied to various DNA and RNA samples from different organisms, extraction
methods, and tissue types, including extremely degraded formalin‑fixed, paraffin‑
embedded (FFPE) samples.
To assess the quality and integrity of DNA and RNA, four quality metrics are used
for the Agilent 5200 Fragment Analyzer system: DQN, GQN, RQN, and DV200 . These
metrics have been published in numerous articles and incorporated in protocols and
literature by Illumina, PacBio, and Bionano Genomics.



The experiments in this study were performed using a 5200 Fragment Analyzer
system and can be replicated with comparable results on Agilent 5300 and 5400
Fragment Analyzer systems. An Agilent Femto Pulse system was also used, with an
Agilent Genomic DNA 165 kb kit (p/n FP-1002-0275) and an Agilent HS RNA kit (15 nt)
(p/n DNF-472).

Additional Content
Detect low-concentration
samples down to the single
cell with the unprecedented
sensitivity and precision of the
Agilent Femto Pulse system.


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