RainDance RainDrop Sense User manual

RainDrop®Sense
Operator’s Manual

Patent,Trademarks, & Copyrights
Patent
www.raindancetechnologies.com/patents
Trademarks
RainDance Technologies, ThunderStorm, RainDrop, ThunderBolts, RainDrop Analyst II, and
RainDrop Plus and logos thereof are trademarks of RainDance Technologies, Inc. All other
brands may be trademarks of their respective holders.
Copyrights
© 2018 RainDance Technologies, Inc. All rights reserved. RainDance Technologies, Inc. owns
the copyright to the RainDance software.
Reproduction Disclaimer
You may make a reasonable number of copies of this manual for internal use only and only for
use in connection with the RainDrop Sense Instrument. All such copies shall contain the copy-
right info set forth on Page ii of this manual and this reproduction disclaimer. Except as explicitly
provided by this section, neither this manual nor any part of it may be reproduced, photocopied,
or electronically transmitted in any way without the advanced written permission of RainDance.
Contact
RainDance Technologies, Inc.
749 Middlesex Turnpike
Billerica, MA 01821
Fax: [phone] (support)
Web: www.raindancetech.com/support
Email: [email protected]
For Research Use Only. Not for use in diagnostic procedures.

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RainDrop Sense Operator’s Manual
Table of Contents
Chapter 1: Foreword 1-1
About this Manual ............................................................................................. 1-2
Intended Use..................................................................................................... 1-2
Data Entry and Collection ................................................................................. 1-2
Design Change Disclaimer................................................................................ 1-3
Reproduction Disclaimer ................................................................................... 1-3
RainDance Support........................................................................................... 1-3
Microsoft Windows Familiarity........................................................................... 1-4
Notes, Warnings, and Cautions ........................................................................ 1-4
Notes ........................................................................................................... 1-4
Warnings...................................................................................................... 1-4
Cautions....................................................................................................... 1-5
Biohazard Safety Warnings ......................................................................... 1-5
Laser Safety Warnings ................................................................................ 1-6
Safety Information............................................................................................. 1-7
Electrical Safety Warnings........................................................................... 1-7
Mechanical Safety ....................................................................................... 1-8
Gas Pressure Safety.................................................................................... 1-8
Product Labels .................................................................................................. 1-8
Safety Interlock ................................................................................................. 1-8
Packing and Transport ...................................................................................... 1-8
Chapter 2: Introduction 2-1
System Overview .............................................................................................. 2-2
RainDrop System Major Components............................................................... 2-2
RainDrop Sense Major Components ................................................................ 2-3
RainDrop Sense Layout.................................................................................... 2-4
RainDrop Sense Barcode Reader ............................................................... 2-5
RainDrop Sense Chip .................................................................................. 2-6
Handling the Sense Chip............................................................................. 2-6
RainDrop Sense Chip Compression Plate................................................... 2-7
Specifications.................................................................................................... 2-8
Chapter 3: Installation and Setup 3-1
Space Requirements......................................................................................... 3-2
Gas Connectivity.......................................................................................... 3-2
Connecting RainDrop Sense and Instrument Controller ................................... 3-3
Connecting Cables to the RainDrop Sense Instrument ............................... 3-3
Connecting Cables to the Instrument Controller.......................................... 3-4
Gas Pressure Quality ........................................................................................ 3-6
Starting Up the RainDrop Sense Instrument..................................................... 3-6
Relocating RainDrop ......................................................................................... 3-7

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RainDrop Sense Operator’s Manual
Chapter 4: Launching the Instrument Control Software (ICS) 4-1
Introduction ....................................................................................................... 4-2
The Microsoft Windows 7 Login ........................................................................ 4-2
Starting the ICS Application .............................................................................. 4-2
ICS Login Levels.......................................................................................... 4-3
Changing the ICS Password........................................................................ 4-5
The ICS Account Types............................................................................... 4-6
ICS Initialization ........................................................................................... 4-7
Status Indicators ............................................................................................. 4-10
Using Tabs in the ICS ..................................................................................... 4-10
Navigating Through the Tabs .................................................................... 4-12
Canceling a Process.................................................................................. 4-12
Completing a Process................................................................................ 4-13
Using Scan Buttons ................................................................................... 4-13
Alarms, Log, and Status Tabs......................................................................... 4-14
Chapter 5: Performing a Sense Run 5-1
Introduction ....................................................................................................... 5-2
Gathering Supplies............................................................................................ 5-2
Starting a Sense Run........................................................................................ 5-3
Completing the ICS Setup................................................................................. 5-9
Checking the Status Indicators .................................................................... 5-9
Completing the Run Data Tab......................................................................... 5-11
Completing the Run Info Tab..................................................................... 5-14
Completing the Run Tabs Using the Import Function................................ 5-15
Using Email Notification............................................................................. 5-15
Performing the Run......................................................................................... 5-17
Canceling a Run.............................................................................................. 5-18
Handling Data ................................................................................................. 5-19
Exporting Data........................................................................................... 5-20
Moving Data Files...................................................................................... 5-21
Chapter 6: Managing the System 6-1
Introduction ....................................................................................................... 6-2
Managing Users................................................................................................ 6-2
Adding a New User...................................................................................... 6-3
Editing a User .............................................................................................. 6-5
Deleting a User............................................................................................ 6-7
Resetting Password or Unlocking an Account............................................. 6-7
Viewing Past Runs ............................................................................................ 6-8
Viewing Runs............................................................................................... 6-8

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RainDrop Sense Operator’s Manual
Chapter 7: Support, Customer Maintenance, and Troubleshooting 7-1
RainDance Support........................................................................................... 7-2
RainDance Planned Maintenance..................................................................... 7-2
Customer Maintenance ..................................................................................... 7-2
Restarting the IC Workstation...................................................................... 7-2
Cleaning the RainDrop Sense ..................................................................... 7-2
Refilling the Oil Reservoir.................................................................................. 7-3
Service and Diagnostic Requirements .............................................................. 7-6
Powering Off the System .................................................................................. 7-6
Powering On or Restarting the System............................................................. 7-6
Restoring the System After a Failure ................................................................ 7-6
Support Agreement Information ........................................................................ 7-6
Moving the System............................................................................................ 7-7
Storing the System............................................................................................ 7-7
Reinstalling/Updating ICS Application............................................................... 7-7
Error Messages................................................................................................. 7-7
Troubleshooting ................................................................................................ 7-8
Chapter 8: Waste Management 8-1
Introduction and Disclaimer............................................................................... 8-2
Classification of Waste...................................................................................... 8-2
Anticipated Typical Waste Stream Composition ............................................... 8-3
Recommended Waste Stream Disposal ........................................................... 8-4
Chapter 9: Customer Care Information 9-1
General Care Information.................................................................................. 9-2
Consumables .................................................................................................... 9-2
Chapter 10: Regulatory Information 10-1
Sense Instrument Declaration of Conformity .................................................. 10-2
Chapter 11: Symbol Glossary 11-1
Appendix A: RainDrop® Consumables and Equipment A-1

Chapter 1: CHAPTER 1
LCN 50-04344 Rev. D 1-1
1
Chapter 1:
Foreword
This chapter covers the following topics:
About this Manual page 1-1
Intended Use page 1-2
Data Entry and Collection page 1-2
Design Change Disclaimer page 1-2
Reproduction Disclaimer page 1-3
RainDance Support page 1-3
Microsoft Windows Familiarity page 1-3
Notes, Warnings, and Cautions page 1-3
Notes page 1-4
Warnings page 1-4
Cautions page 1-5
Biohazard Safety Warnings page 1-5
Laser Safety Warnings page 1-6
Safety Information page 1-7
Electrical Safety Warnings page 1-7
Mechanical Safety page 1-8
Gas Pressure Safety page 1-8
Product Labels page 1-8
Safety Interlock page 1-8
Packing and Transport page 1-8
About this Manual
This manual is designed to serve the operators of the RainDance Technologies®, Inc.
(hereafter called “RainDance”) RainDrop® Sense instrument. All material operating
instructions, product illustrations, screen graphics, troubleshooting, error messages, and
other relevant information are contained in this manual. It is the operator's responsibility to
ensure that all safety instructions in this manual are strictly applied.
Where there is any conflict between the RainDance Software End User License Agreement
included in the software, and the terms and conditions of sale, the order of precedence shall

RainDrop Sense Operator’s Manual
LCN 50-04344 Rev. D 1-2
be as follows: (1) the RainDance Software End User License Agreement and (2) the terms
and conditions.
Intended Use
For Research Use Only. Not for use in Diagnostic Procedures.
RainDance Technologies RainDrop Sense is the detection instrument that enables
identification and counting of target molecules in each picoliter droplet following PCR
amplification. Together the RainDance Source and RainDrop Sense instruments make up the
RainDrop Digital PCR System delivering quantitative results.
Data Entry and Collection
RainDance requires that you do not enter health information identifiable to a particular
person, or other information that is subject to regulatory or contractual protection, into any
RainDance instrument. Such information is not protected from disclosure to service or other
personnel and, as noted below, may be included in information provided to RainDance for
purposes of servicing or evaluating the performance of your instrument.
Further, by requesting service of your RainDance instrument, you give RainDance consent to
access and use data stored in your RainDance instrument. RainDance uses the data to
troubleshoot and service the instrument in response to your service requests. RainDance
also may aggregate data collected from your instrument in response to service requests with
similar data from other customers and may use the aggregated data to improve instrument
performance.
Your instrument from RainDance is enabled with an automatic email functionality that allows
RainDance to receive performance data from the instrument from time to time without your
knowledge. You may choose to disable that functionality. Disabling that functionality prevents
the instrument from sending such data to RainDance. The data collected with this automatic
email functionality consists of the number of samples processed, the success rate of the
samples processed, data specific to the performance of your instrument, and data that is
entered by your operators. RainDance collects this data solely so that it may better
understand and improve instrument performance. By allowing the functionality to remain
enabled, you give RainDance permission to use the automatic email functionality.
Design Change Disclaimer
Due to design changes and product improvements, information in this manual is
subject to change without notice. RainDance reserves the right to change the product
design, including illustrations, screen shots, and diagrams, at any time without notice to
anyone, which may subsequently affect the contents of this manual.

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RainDance assumes no responsibility for any errors that may appear in this manual.
RainDance will make every commercially reasonable effort to ensure that this manual
is up-to-date and corresponds with the shipped RainDrop Sense Instrument.
The depictions of the workstation screens in this manual are representative only.
Depending on the hardware and software versions of the system, minor differences
may appear between the actual displays and those shown in this manual.
Reproduction Disclaimer
You may make a reasonable number of copies of this manual for internal use only and only
for use in connection with the RainDrop Sense Instrument. Except as provided by the
previous sentence, neither this manual nor any part of it may be reproduced, photocopied, or
electronically transmitted in any way without the advanced written permission of RainDance.
RainDance Support
If you have any difficulty running the RainDance Source instrument, contact your RainDance
Support representative. Chapter 7 of this manual includes a list of problems and possible
solutions. The information given is general. Some applications may require additional
procedures or equipment modification. Contact RainDance Support via email:
[email protected], Monday through Friday, excluding holidays.
Microsoft Windows Familiarity
The supplied Instrument Control Software (ICS) is designed for the Microsoft®
Windows® Embedded 7 operating system and uses the standard Windows interface.
This manual assumes that you are familiar with these standard techniques: clicking the
mouse, highlighting an item, right-clicking, dragging, using the keyboard, interacting
with dialog boxes, keyboard commands, selection techniques, and other Windows
basics.
If you require assistance with these aspects of the software user interface, refer to the
Microsoft Windows documentation.
Notes, Warnings, and Cautions
The symbols described in this section are used throughout this document to draw your
attention to specific situations involving safety and proper use of the equipment. Symbols
found on the instruments are listed in Chapter 11: “Symbol Glossary.”

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LCN 50-04344 Rev. D 1-4
Notes
Notes are set apart from the body of the document with either the word Note or Important.
They are meant to draw your attention to reminders and information that is important to
successful operation of the RainDrop Sense Instrument.
Note: A Note indicates a useful piece of information.
Important: An Important note is similar to a regular Note, except that it is meant to
communicate greater weight to the issue at hand.
Warnings
Warnings are represented by a red triangle with an exclamation point inside of it. Warnings
are reserved for situations that indicate the possibility of personal injury if the instructions are
not followed.
Warning: A Warning indicates a potentially hazardous situation that, if not avoided,
could result in serious personal injury or death to you or others. Warnings are set
within boxed rules and indented.

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LCN 50-04344 Rev. D 1-5
Cautions
Cautions are represented by a blue triangle with an exclamation point inside of it. They
indicate that you must follow a particular procedure in order to correctly operate the RainDrop
Sense Instrument and to avoid any possible damage to the equipment or loss of
consumables.
Caution: Do not operate the System in a manner other than specified in this
manual. Doing so could damage the instrument or produce erroneous results.
Caution: RainDance service representatives are trained in the safe operation of the
RainDrop Sense Instrument, including accessing those areas reserved for trained
service representatives.
Biohazard Safety Warnings
A biohazard warning indicates that the user must use precautions, for example, gloves, when
handling biological samples, to prevent any infections or hazards that can be caused by
them.
Warning: Follow your laboratory's procedures and regulations when handling
biohazardous materials.
Warning: RainDance suggests that users be professional and conscientious and
take the appropriate safety measures when preparing, handling, and disposing of
any biohazardous samples or waste.
Warning: When working with biohazardous samples, or waste, always follow
standard universal safety procedures (lab coats, safety glasses, gloves, mask,
etc.).
In addition, users should take precautions in accordance with local, state, and national
requirements.

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Laser Safety Warnings
The RainDrop Sense, classified as a Class 2 System, contains a Class 3B laser and Class 2
barcode laser. Avoid direct exposure to the Class 3B laser radiation when the unit is open
and interlocks are defeated. Only a qualified service person should remove the cover or
attempt to service this device, due to possible eye injury.
A laser warning indicates that the user must use precautions when operating the instrument
to avoid injury from the lasers.
Warning: A Class 3B laser is hazardous if the eye is exposed directly, but diffuse
reflections such as those from paper or other matte surfaces are not harmful. The
AEL for continuous lasers in the wavelength range from 315 nm to far infrared is
0.5 W. For pulsed lasers between 400 and 700 nm, the AEL is 30 mW. Other
limits apply to other wavelengths and to ultrashort lasers. Protective eye wear is
typically required where direct viewing of a class 3B laser beam may occur. Class-
3B lasers must be equipped with a key switch and a safety interlock.
In addition, users should take precautions in accordance with local, state, and national
requirements.
Figure 1-1: Laser Safety Warnings

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LCN 50-04344 Rev. D 1-7
Safety Information
Electrical Safety Warnings
Warning: This equipment is operated with hazardous voltages that can shock,
burn, or cause death. To reduce the possibility of electrical shock, do not remove
any fixed panels. Ensure that all service to the system is performed only by qualified
RainDance service personnel.
Warning: Remove the wall plug before servicing the equipment. Never pull cords
to remove the power cord from the outlet. Grasp the power cord plug and pull it
from the outlet to disconnect it.
Warning: Do not operate the equipment with a damaged power cord.
Warning: Ensure that there is easy and adequate clearance to the power cord so
that it can be disconnected in the event of a problem.
Warning: Position the power cord so that it cannot be tripped over, walked on,
rolled over, crimped, bent, pinched, or accidentally pulled from the wall outlet.
Warning: Connect the equipment only to a grounded outlet.
Warning: This instrument is not disconnected from the AC power source (mains)
as long as it is still connected to the wall outlet, even if the instrument is turned off.
The primary means of disconnecting the instrument is to remove the plug from the
wall outlet. Do not locate the instrument such that access to this plug is difficult.

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Mechanical Safety
Warning: The RainDrop Sense instrument weighs approximately 65 lbs (29 kg). To
avoid injury and damage to the instruments, do not move it without assistance from
RainDance Technologies.
Warning: The potential for serious injury to hands or fingers exists as a result of
rotating or clamping motion. Watch your hands and fingers when opening and
closing the cover. Keep your hands away from moving parts.
To move the instrument to another location, contact RainDance Support.
Gas Pressure Safety
Do not exceed a maximum input pressure of 120 psi at the instrument.
Product Labels
Figure 1-2 shows the RainDrop Sense product label.
Figure 1-2: RainDrop Sense Product Label
Safety Interlock
The RainDrop Sense is equipped with an automatic safety interlock, which prevents it from
operating unless its door is properly closed.
Packing andTransport
RainDance provides initial shipping and installation. If you are considering moving the
RainDrop Sense instrument within your laboratory, refer to Chapter 3 for the space
requirements. Do not move the instrument without assistance from RainDance Technologies.

Chapter 1: CHAPTER 2
LCN 50-04344 Rev. D 2-1
2
Chapter 2:
Introduction
This chapter covers the following topics:
RainDrop® System Overview page 2-2
RainDrop System Major Components page 2-2
RainDrop Sense Major Components page 2-3
RainDrop Sense Layout page 2-4
RainDrop Carrier and Drive Oils page 2-4
RainDrop Sense Barcode Reader page 2-5
RainDrop Sense Chip page 2-6
Handling the Sense Chip page 2-6
RainDrop Sense Chip Compression Plate page 2-7
Specifications page 2-8

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LCN 50-04344 Rev. D 2-2
RainDrop®System Overview
The RainDance RainDrop® System comprises two instruments: the RainDance Source and
the RainDrop Sense.
RainDrop System Major Components
RainDance Source Instrument
RainDrop Sense Instrument
Two Instrument Control (IC) Workstations (computers), one for each instrument
Two Instrument Control (IC) Monitors, one for each instrument
Instrument Control Cables and Peripherals
IC Workstation Power Cables
IC Monitor Power Cables
IC Keyboards
IC Mouses
IC USB Cables
Instrument Control Software (ICS)
RainDrop Analyst II™ Software
Figure 2-1: RainDrop System Major Components

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RainDrop Sense Major Components
Figure 2-2 shows the major components of RainDrop Sense instrument.
Instrument control workstation monitor RainDrop Sense instrument
Figure 2-2: RainDrop Sense Major Components

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RainDrop Sense Layout
Figure 2-3 shows the RainDrop Sense layout and oil reservoir fill ports.
Chip alignment pins
Tube strip nest
Objective lens
Carrier oil
reservoir fill port
Carrier oil low
indicator light
Drive oil reservoir
fill port
Drive oil low
indicator light
Figure 2-3: RainDrop Sense Layout
RainDrop Carrier and Drive Oils
Aqueous samples are encapsulated within each droplet on the Source instrument,
surrounded by an immiscible carrier oil. The droplets are stabilized with surfactants allowing
for robust manipulation both on and off the chip. Precise control of carrier and drive oil flow
rates on the Sense instrument allows for control of droplet spacing. Use only RainDance-
supplied oils to avoid damage to the RainDrop System. The carrier oil and drive oil ports can
be filled with the oil provided in the Carrier Oil Syringe.

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RainDrop Sense Barcode Reader
The barcode reader is used to scan barcodes that identify the various components used in
the RainDrop Sense (see Figure 2-4). The following lists the components to be scanned:
RainDrop Sense Chip(s)
RainDrop Carrier Oil
Tube Strips (May have a user-generated barcode. Scanning tube strips is optional.)
Items bearing a user-generated barcode for sample tracking (within the limits of
supported barcode formats)
Figure 2-4: RainDrop Sense Barcode Reader
Scanning Barcodes
Scan items as follows:
1. Click Scan in the ICS software. The red scanner light pulses for 10 seconds.
2. Hold the barcode on the item in front of the barcode reader. When the scanner reads
the barcode, it automatically fills in the barcode information. The ICS accepts a
barcode in the 2D Data Matrix format, which allows up to 96 characters of text. You
may hear a subtle beep tone from the instrument when the barcode is accepted. If the
scanner does not read the barcode, the ICS software displays a message and allows
you to enter the barcode manually.

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RainDrop Sense Chip
The RainDrop Sense Chip is placed into the instrument on top of the PCR tube strip. As part
of the Sense process, the chip punctures the tube strip caps and transfers the emulsified
sample through its lanes where the Sense instrument identifies and counts the droplets.
Microfluidic chip
Droplet detection
region of interest (ROI)
Fluid lanes
Chip alignment hole
Chip alignment holeWaste collection area
Oil input gaskets
Figure 2-5: RainDrop Sense Chip
Handling the Sense Chip
Handle the Sense Chip as follows:
Grasp the chip by its sides.
Do not touch the clear microfluidic chip and its droplet detection region of interest.
Save the bag the chip comes in for later disposal of the chip.

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RainDrop Sense Chip Compression Plate
The RainDrop Sense Compression Plate is needed for smooth operation of the RainDrop
Sense Instrument. Position the plate over the Sense chip prior to start of the run. When the
plate is properly positioned, its RainDance logo should be facing you, the plate should be flat,
and it should not be movable left to right or front to back.
Figure 2-6: RainDrop Sense Chip Compression Plate