PIXUL™ gDNA Shearing Kit Manual
Catalog No. 53131(version A1)

Active Motif North America
1914 Palomar Oaks Way, Suite 150
Carlsbad, California 92008, USAToll free:877 222 9543
Telephone:
760 431 1263
Fax:
760 431 1351
Active Motif Europe
Waterloo Atrium
Drève Richelle 167 – boîte 4
BE-1410 Waterloo, Belgium
UK Free Phone:		
0800 169 31 47
France Free Phone:
0800 90 99 79
Germany Free Phone: 0800 181 99 10
Telephone:		+32 (0)2 653 0001
Fax:		
+32 (0)2 653 0050
Active Motif Japan
Azuma Bldg, 7th Floor
2-21 Ageba-Cho, Shinjuku-Ku
Tokyo, 162-0824, Japan
Telephone:+81 3 5225 3638
Fax:
+81 3 5261 8733
Active Motif China
787 Kangqiao Road
Building 10, Suite 202, Pudong District
Shanghai, 201315, China
Telephone:(86)-21-20926090
Hotline:400-018-8123
Copyright 2020 Active Motif, Inc.
www.activemotif.com

TABLE OF CONTENTS

Page

Overview . .  .  .  .  .  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Kit Components and Storage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Reagents for gDNA Shearing  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Additional Materials Required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Protocol . .  .  .  .  .  .  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Technical Services  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Information in this manual is subject to change without notice and does not constitute a commitment on thepart of Active Motif, Inc. It is supplied on an “as is” basis without any warranty of any kind, either explicit orimplied. Information may be changed or updated in this manual at any time.
This documentation may not be copied, transferred, reproduced, disclosed, or duplicated, in whole or in part,without the prior written consent of Active Motif, Inc. This documentation is proprietary information andprotected by the copyright laws of the United States and international treaties.
PIXUL™ is sold under an exclusive license to patents owned by Matchstick Technologies Inc. and University ofWashington, specifically Matula, T.J.; Bomsztyk, K.; Darlington, G.P., Maxwell, A.D.; MacConaghy, B.E., Reed, J.
“Ultrasound system for shearing cellular material”. US Patent US10809166. European Patent EP3169451.
The manufacturer of this documentation is Active Motif, Inc.
© 2020 Active Motif, Inc., 1914 Palomar Oaks Way, Suite 150; Carlsbad, CA 92008. All rights reserved.
All trademarks, trade names, service marks or logos referenced herein belong to their respective companies.
For Research Use Only. Not for use in diagnostic procedures.

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Overview
Highly consistent shearing of genomic DNA (gDNA) to an appropriate size for conversion intofunctional next-generation sequencing (NGS) libraries is integral to high quality and comparable
next-generation sequencing data. Manual shearing with a probe sonicator or shearing with aninconsistent high-throughput sonicator can lead to sample-to-sample variability.
The PIXUL gDNA Shearing Kit delivers highly consistent average fragment lengths and low standard
deviations across entire plates time after time. PIXUL sonication is compatible with a wide rangeof purified gDNA (500 ng - 20 µg) or cells (100,000 - 1,000,000) with no changes in sonication
efficiency or processing time.

PIXUL Advantages• Process 1 - 96 samples in parallel• Extremely consistent sonication• Up to 12 different sonication conditions per run
product
PIXUL™ gDNA Shearing Kit

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1formatcatalog no.

1 X 96 reactions

53131

Kit Components and Storage
The kit contains sufficient reagents to sonicate 96 wells in one PIXUL run. The reagents in this kit
have multiple storage temperatures. Please store components according to the storage conditions
below. All reagents are guaranteed stable for 6 months from date of receipt when stored properly.
Reagents

Quantity

Storage

1 mL

RTRNase A

2 X 45 µL-20°C

Proteinase K

600 µL-20°C

Low EDTA TE

5.6 mLRTSPRI Beads

13 mL

4°C

PIXUL™ 96-well plate with sealer

1 unit

RTCell Shearing Buffer

Additional Materials Required• 100% Ethanol• Nuclease-free water• 1X PBS• PIXUL™ Multi-Sample Sonicator (Cat. No. 53130)• Microcentrifuge tubes• PCR tube strips (300 µL well volume capacity)• Centrifuge to spin 96-well plate• Thermal cycler or other 37°C incubator• 96-well plate magnet or bar magnet• Single channel and multi-channel pipettors and tips
• Hemocytometer and light microscope

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PIXUL gDNA Shearing Kit Protocol
IMPORTANT:PIXUL sonication requires using PIXUL 96-well round bottom plates. These plates
are available as Active Motif Catalog No. 53139, and these are the same plateas Corning Catalog No. 3799. Using any other plates will result in inefficientsonication, may damage the instrument, and will void the instrument warranty.

Sample Preparation•

If sonicating purified gDNA in water, add concentrated Tris-HCl pH 8.0 to a final
concentration of 10 mM Tris-HCl.

•

If sonicating cells growing directly in the PIXUL 96-well plate, aspirate media, wash with 1X
PBS, and add 100 µL Cell Shearing Buffer per well.

•If sonicating cells grown in a different plate or dish, resuspend the desired number of cells in
100 µL Cell Shearing Buffer per well and add to wells in the PIXUL 96-well plate.

PIXUL Sonication of gDNA1.

Add 100 µL of purified genomic DNA or cells in Cell Shearing Buffer to wells in the PIXUL
96-well plate and seal the plate with a PIXUL plate seal.
Note:

All wells lacking sample in the columns being sonicated MUST be filled with
100 µL liquid (water, coupling buffer, etc.) prior to starting the run.

2.

Turn on and run the instrument as specified in the PIXUL Multi-Sample Sonicator User
Manual or Quick Guide.

3.

We recommend using the following parameter specifications as a starting point, andadjusting Process Time to optimize for your specific sample and application:
Sonication Parameter

Setting

Pulse [N]50

PRF [kHz]

1.00

Process Time [min]36:00

Burst Rate [Hz]

20.00

Note:

The instrument software will not allow settings that could damage thetransducers. The upper limits are a maximum Pulse of 50 or a maximum
PRF of 1.00. We recommend a minimum Burst Rate of 20.00. Varying
the Process Time is typically the only parameter that needs adjusting.

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DNA Purification using SPRI Beads
Take SPRI Beads out of 4°C and warm to room temperature by simply placing the vial of SPRI
beads on the benchtop. Prepare fresh 80% ethanol (4.8 mL 100% ethanol + 1.2 mL nuclease-freewater).
1. Add 0.5 µL RNase A to each well and incubate for 30 minutes at 37°C.
2. Add 5 µL Proteinase K to each well and incubate for 30 minutes at 55°C.
3. Add 120 µL (1.2 volumes) of SPRI Beads to each well. Pipette the bead-lysate mixture 10 times
to mix and incubate for 5 minutes at room temperature.
4. Place plate on a magnet for 5 minutes to collect beads, and then aspirate supernatant.
5. Keeping the plate on the magnet, add 180 µL of 80% ethanol and incubate for 30 seconds atroom temperature.
6.

Aspirate the supernatant and perform a second wash with 180 µL of 80% ethanol.

7.

Completely aspirate the supernatant and air dry the beads until they are no longer shiny (2-5minutes).

8.

Remove the plate from the magnet and elute DNA by adding 50 µL of Low EDTA TE.

9.

Pipette the beads 10 times and incubate for 3 minutes at room temperature.

10. Place tube or plate back on the magnet for 5 minutes to collect beads.
11.
12.

Carefully remove eluted DNA in the supernatant and transfer to a new tube or plate.
Analyze gDNA yield using a spectrophotometric (Nanodrop) or fluorometric (Qubit) methodof your choice and analyze fragmentation efficiency using either agarose gel electrophoresis,Agilent TapeStation, or Agilent Fragment Analyzer. For most applications, we recommend
shearing DNA to 200 - 600 bp. This gDNA is suitable and ready for library preparation.

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4Technical Services
If you need assistance at any time, please call Active Motif Technical Service at one of thenumbers listed below.
Active Motif North America
1914 Palomar Oaks Way, Suite 150
Carlsbad, CA 92008, USA
E-mail: tech_service@activemotif.com
Active Motif Europe
Waterloo Atrium
Drève Richelle 167 – boîte 4
BE-1410 Waterloo, Belgium
E-mail: eurotech@activemotif.com
Direct: +32 (0)2 653 0001
Active Motif Japan
Azuma Bldg, 7th Floor
2-21 Ageba-Cho, Shinjuku-Ku
Tokyo, 162-0824, Japan
Active Motif China
787 Kangqiao Road
Building 10, Suite 202
Pudong District
Shanghai, 201315, China

Toll Free: 877 222 9543
Direct: 760 431 1263
Fax: 760 431 1351

Germany Free Phone: 0800 181 99 10France Free Phone: 0800 90 99 79
UK Free Phone: 0800 169 31 47
Fax: +32 (0)2 653 0050

Direct: +81 3 5225 3638
Fax: +81 3 5261 8733
E-mail: japantech@activemotif.com

Direct: (86)-21-20926090
Hotline: 400-018-8123
E-mail: techchina@activemotif.com

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