Agilent eBook - 19

Best Practices with an Agilent Parallel CE System
Results and discussion

DQN and GQN

18,000

Agilent designed the DNA quality number (DQN) and the
genomic quality number (GQN) for use in ProSize data
analysis software to allow for easy analysis of sheared
DNA and genomic DNA (gDNA) quality, respectively.
The user defines a size threshold they deem appropriate
for their specific application. ProSize then calculates
a DQN or GQN value based on the fraction of the total
measured concentration of the sample that lies above
the specified size threshold. The DQN and GQN scores
samples on a scale of 0 to 10. 0 indicates that none
of the sample exceeds the threshold and 10 indicates
100 % of the sample lies above the threshold value.
DNA size can vary due to numerous factors, such as:
origin of organism, extraction methods, tissue type,
and sample handling. Therefore, the ability to define the
size threshold gives the user the advantage of defining
quality DNA for their specific application.

16,000

GQN is used specifically for genomic DNA samples
separated on the 5200 Fragment Analyzer system with
the Agilent Genomic DNA 50 kb kit (p/n DNF-467-0500)
and Agilent HS Genomic DNA 50 kb kit (p/n DNF-4680500) and on the Femto Pulse system with the Agilent
Genomic DNA 165 kb kit1. The DQN is used for all other
DNA sample types and was created for samples that
use a reagent kit with both a lower and upper marker.
As seen in Figure 1, sheared gDNA samples from
PacBio of varying sizes were separated on the

| GENengnews.com

14,000
12,000

8,000
6,000
4,000

Average smear size (bp)

165,500

42,000
50,000

17,700
23,000

1,300

10,000

2,000
1

RFU

10,000

Size (bp)

GQN Set at 30 kb

12,147

23,339

1.5

45,304

6.4

57,789

7.1

73,267

7.8

94,045

7.8

109,968

8.2

164,292

8.8

Figure 1. Sheared gDNA from PacBio separated on the Agilent Femto Pulse system with the Agilent Genomic DNA 165 kb kit.
(A) Separations on the electropherogram (B) Average smear size, and GQN30 kb, n = 2, LM = lower marker.

http://www.GENengnews.com

Agilent eBook

Table of Contents for the Digital Edition of Agilent eBook

Agilent eBook - 1
Agilent eBook - 2
Agilent eBook - 3
Agilent eBook - 4
Agilent eBook - 5
Agilent eBook - 6
Agilent eBook - 7
Agilent eBook - 8
Agilent eBook - 9
Agilent eBook - 10
Agilent eBook - 11
Agilent eBook - 12
Agilent eBook - 13
Agilent eBook - 14
Agilent eBook - 15
Agilent eBook - 16
Agilent eBook - 17
Agilent eBook - 18
Agilent eBook - 19
Agilent eBook - 20
Agilent eBook - 21
Agilent eBook - 22
Agilent eBook - 23
Agilent eBook - 24
Agilent eBook - 25
https://www.nxtbookmedia.com