Samplix Xdrop User Manual

dPCR)

Droplet PCR (

Xdrop™ manual

User manual v. 1.0 released 26 Aug. 2019

Table of Contents

Chapter 1: XdropTM at a Glance page 03
Targeted enrichment overview

Xdrop™ instrument overview
Required items for Xdrop™ dPCR
Suggested Samplix products

Equipment and reagents for Xdrop™ supplied by the user

Chapter 2: dPCR – General Considerations page 09

dPCR assay design
Target sequence
Primer design guidelines
DNA sample preparation
Primer optimization

Chapter 3: dPCR Setup page 12

Preparations for dPCR
Setup of dPCR reaction
Positive control dPCR reaction
Prepare dPCR cartridge
Collect generated droplets

Chapter 4: Single DNA Molecule Detection and Sorting of Droplets page 20

Requirements for flow cytometer analyzer and cell sorter
Notes to operator
Preparation of droplets for flow cytometry
Flow cytometry analysis of dPCR droplets
Set up flow cytometry with Cell sorter control droplets
Sorting of PCR positive dPCR droplets

Contact:
Samplix ApS
Mileparken 28
DK – 2730 Herlev
www.samplix.com
Mail: [e-mail]

For research use only, not for use in diagnostic procedures.
Copyright 2019. Reproduction in any form, either print or electronic,
is prohibited without written permission of Samplix ApS

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Chapter 1: Xdrop™ at a Glance

Targeted enrichment overview

Congratulations with your new Xdrop™ instrument, which we expect will facilitate groundbreaking research.

The Xdrop™ technology introduces a new approach for genomic analysis as the technology enables targeted
enrichment of genomic regions in droplets. The Xdrop™ technology offers sensitive and unbiased PCR-free sample
enrichment and general amplification prior to downstream analysis e.g. next generation sequencing.

Using the Xdrop™ instrument, cartridges, and reagents, sample DNA is partitioned into millions of picolitre size highly
stable droplets. The Xdrop™ droplet PCR (dPCR) droplets are suitable for standard PCR cycling, flow cytometry analysis
and sorting.

In the first step of enrichment, the sample is diluted and partitioned into millions of double emulsion droplets using the
Xdrop™ instrument and the advanced microfluidics dPCR cartridge. Droplets containing the target DNA molecules are
identified by a 120-160 base pair targeted PCR specific to a sequence within or adjacent to the region of interest.
Positive droplets are identified by their fluorescence and physically separated from negative droplets by use of a
standard cell sorter. The result is an enrichment of long single molecules comprising tens of kilobases of DNA
information.

For downstream universal amplification of the single molecules, Samplix has developed a proprietary technology by
which the high molecular weight DNA molecules are partitioned into thousands of droplets for high fidelity multiple
displacement amplification in droplets (dMDA).

The Xdrop™ enrichment and amplification technology are compatible with downstream molecular biology techniques
such as short and long read DNA sequencing.

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Xdrop™ instrument overview

The Xdrop™ droplet generator is compatible with Samplix dPCR cartridges for production of dPCR droplets

and Samplix dMDA cartridges for the generation of droplets for amplification of DNA. When using dMDA

cartridges, always use the accompanying holder. The Xdrop™ droplet generator is used for generating both

dPCR and dMDA droplets.

The Xdrop™ droplet generator is composed of the following parts (see figure below):



Drawer – holds the dPCR or dMDA cartridge.



Touch screen – provides the means to control the droplet generator with gloved or un-gloved
hands.

 USB port on the back of the instrument – connects to a USB flash drive for troubleshooting, saving log files,

and for updating instrument firmware.



Status LED – Green when in standby and operating and yellow-green when opening and closing the
drawer.



Air vents on the back of the instrument – for ventilation.
A start button on the front of the instrument.




A hardware switch on the back of the instrument.

Specifications

Width: 25 cm / 9,8 inches
Height: 25 cm / 9,8 inches
Length: 48 cm / 18,9 inches
Weight 17 kg / 37,5 lbs.
Voltage requirements: 110 V-240 V

Support

To find technical support, contact the technical support team at [e-mail]

Warranty

The Xdrop™ instrument and associated accessories are covered by a standard Samplix ApS warranty. Contact your local
Samplix ApS office for the details of the warranty.

Safety

We strongly recommend that you follow the safety specifications listed in this section and throughout this manual.

Xdrop™ is produced to comply with Safety Requirements for Electrical Equipment for Measurement, Control, and
Laboratory Use (UL 61010-1) and complies with EU (CISPR 11, class A, group 1, 150 kHz – 30 MHz) EMC.

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Instrument safety warnings

The following warning labels refer directly to the safe use of the droplet generator.

Icon

Meaning

Warning about the risk of harm to body or equipment. Operating the Xdrop™

before reading this manual can constitute a personal injury hazard. Only

qualified laboratory personnel should operate this instrument.

Warning about the risk of harm to body or equipment from electrical shock.

Do not attempt to repair or remove the outer case of this instrument, power

supply, or other accessories. If you open these instruments, you put yourself

at risk for electrical shock and void your warranty. All repairs must be done

by an authorized repair service.

Never remove the outer case of an Xdrop™ instrument. This may cause

you to receive an electrical shock.

Warning about the risk of harm to hands and fingers. Always keep hands

and fingers away from the instrument when the drawer is in motion.

Intended use and intended users

The Xdrop™ instrument is intended for use by trained laboratory personnel in a clean laboratory environment for DNA
sample preparation from mixed DNA samples using droplet microfluidic technology.

Transportation and storage

Always transport the instrument in the original Samplix box. Before starting up the instrument, let it stay in room
temperature for at least 2 hours.

Maintenance and cleaning

If the instrument is shipped back to Samplix for maintenance, please make sure that the outer surfaces are cleaned
using a cloth and 70 % ethanol.

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Required items for Xdrop™ dPCR

Xdrop™ Instrument (Cat. No. IN00100)

dPCR cartridge (Cat. No. CA10100)
dPCR gasket (Cat. No. GA10100)
Storage film (Cat. No. FI00100)

dPCR kit (Cat. No. RE10100)

dPCR kit part 1 (store at -20°C)

dPCR mix (2x) ●
Droplet dye ●

dPCR kit part 2 (store at -20°C)

dPCR buffer (2x) ●

dPCR kit part 3 (store at room temperature)

dPCR oil ●

Suggested Samplix products

Cell sorter control kit (Cat. No. CO10100)

Cell sorter control kit part 1 (store at -20°C)

Droplet dye ●
dPCR buffer (2x) ●

Cell sorter control kit part 2 (store at 4°C)

Control droplets ○

Positive control primer kit (store at -20°C) (Cat. No. CO10200)

dPCR control primers ●
Enrichment validation primers ●
Positive control DNA ●

Primer test PCR kit (store at -20°C) (Cat. No. RE10200)

dPCR mix (2X) ●
qPCR dye (20x) ●