®
NGEx ®
Next Generation Extraction technology
Application Note: FFPE DNA/RNA Purification Kit (48 reactions)
ExScale® Next Generation Extraction technology (NGEx®)
Automated and sequential isolation of DNA and RNA from
FFPE tissue
Introduction
Automated purification of DNA and RNA from the same specimen is essential for a number of reasons. First, it is necessary for the
reliable comparison of genomic and transcriptomic data. Second, it minimizes consumption of precious biospecimens and third,
it significantly reduces turnaround time and labour costs compared to isolating each separately.
Using NGEx® technology, ExScale can sequentially isolate both DNA and RNA from a single FFPE tissue specimen using magnetic
bead-based extraction technology. This is of particular importance when dealing with FFPE tumor specimens as material is often
limited (e.g. biopsies) and tumors display high regional heterogeneity, meaning that comparing genomic and transcriptomic data
from two separate sections may provide misleading results.
Features and Benefits
Conclusion
ExScale offers nucleic acid purification kits and software that
can isolate both DNA and RNA from the same FFPE tissue
specimen. The system is fully automated and easy-to-use.
The pre-filled cartridges and the user-friendly instrument start
panel makes the procedure extremely versatile in a multiuser
environment.
The ExScale FFPE DNA/RNA Purification kit provides a highly
efficient automated method for extraction of DNA and RNA
from FFPE tissue.
• Fully automated on Magtration® system magLEAD 12GC
• CE marked for IVD
• Reduction of manual handling errors
• Maximum output with minimal sample consumption
• Releases and separates DNA/RNA without compromising integrity
• User and environmentally-friendly chemicals and processes
Figure 1. The Magtration® system magLEAD 12GC instrument
(Precision System Science Co., Ltd) can process 1-12 samples
simultaneously.
The extraction protocol is fully automated using a liquid handling
robotic workstation that can handle 1-12 samples simultaneously
with a user-friendly interface. All steps, including tissue deparaffinization using a non-toxic agent, are performed inside the
instrument, resulting in minimal hands-on time for the user.
Total run time is between 3 hr 10 min (easy-to-lyse tissue) or 4
hr 30 min (fibrous or muscular tissue). The magLEAD 12GC is
an easy-to-use instrument for a multiuser environment, which
decreases the risks for human errors. Built in UV light and prefilled cartridges reduce risk of sample contamination.
Figure 2. Prefilled cartridges reduce hands-on time and manual
handling errors
© 2017 ExScale Biospecimen Solutions. All rights reserved. Application Note: ES-K110210FP-C and ES-S110210FP-C. Document number: 23000-00013v1
NGEx ®
®
Next Generation Extraction technology
Results
Skin
3000
2500
2000
2000
1500
2000
1500
1000
1000
500
0
0
RNA
500
0
DNA
RNA
4000000
3000000
10
R 0.971
5
log2 RPM Replicate 1
Read length
histogram
5000000
15
15
10
6000000
127 bp
Mode
log2 RPM up_175_4
112 bp
Median
Average read length
5
5
112 bp
Mean
RNA
15
B
log2 RPM up_175_4
A
DNA
10
500
DNA
Read count
Figure 3
Average yields of DNA and RNA
from various tissue types using the
ExScale FFPE DNA/RNA purification
kit and software. Yields assessed
using Qubit® dsDNA and RNA BR
assay kits (ThermoFisher Scientific).
2500
1500
1000
Lung
3500
3000
0
0
Average yield (ng)
Kidney
2500
RR 0.971
0.971
2000000
0
1000000
0
0
50
100
150
200
0
5
5
5
10
15
log2 RPM up_175_3
10
15
10up_175_3
log2 RPM
15
log2 RPM Replicate 2
Read length
A
0
0
Figure 4.
Next generation RNA sequencing
performed using the Ion
AmpliSeqTM Transcriptome Human
Gene Expression kit.
Data analysis was performed using
the Torrent SuiteTM Software. A)
RNA extraction using the FFPE
serial DNA and RNA Purification kit
resulted in long sequence reads
with a median read length of 109
indicating good quality RNA. B)
Scatter plot of log2 RPM (read per
gene per million mapped reads)
gene counts from the RefSeq gene
set indicating high correlation
between the two technical
replicates with a Pearson correlation
coefficient (R) of >0,97.
B
Figure 5.
Bioanalyzer profile of RNA from
FFPE rectal (A) and hepatocellular
carcinoma (B) samples extracted
using ExScale FFPE Purification kits
and software. DV200 values are
39% and 58% respectively.
Ordering information
Product
Description
Article no.
ExScale FFPE DNA/RNA
Purification Kit and Software*
Prefilled reagent cartridges, deparaffinization
agent and plasticware for 48 extractions
ES-K110210FP-C and ESP-S110210FP-C
*CE marked according to IVD 98/79/EC for use on Magtration® system magLEAD 12GC (Precision System Science Co., Ltd).
ExScale Biospecimen Solutions
Dag Hammarskjölds väg 26
Majoren, Uppsala Science Park
753 37 Uppsala
Sweden
Email: [email protected]
© 2017 ExScale Biospecimen Solutions. All rights reserved. Application Note: ES-K110210FP-C and ES-S110210FP-C. Document number: 23000-00013v1
Production: www.hsop.se
For more information, see our website exscalebio.com