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: [e-mail]

For Research Use Only. Not for use in diagnostic procedures.

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

LCN 50-04344 Rev. D iii

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

LCN 50-04344 Rev. D iv

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

LCN 50-04344 Rev. D v

Chapter 1:

CHAPTER 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

1

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

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.

®

Sense instrument. All material operating

Where there is any conflict between the RainDance Software End User L

included in the software, and the terms and conditions of sale, the order of precedence shall

LCN 50-04344 Rev. D 1-1

icense Agreement

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.

RainDrop Sense Operator’s Manual

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.

LCN 50-04344 Rev. D 1-2

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.

solutions. The information given is general. Some applications may require additional

procedures or equipment modification. Contact RainDance Support via email:

[e-mail], Monday through Friday, excluding holidays.

Chapter 7 of this manual includes a list of problems and possible

RainDrop Sense Operator’s Manual

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.”

LCN 50-04344 Rev. D 1-3

Notes

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.

RainDrop Sense Operator’s Manual

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.

Warnings

Note: A

Important: An

communicate greater weight to the issue at hand.

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.

Note indicates a useful piece of information.

Important note is similar to a regular Note, except that it is meant to

LCN 50-04344 Rev. D 1-4

Cautions

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.

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.).

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.

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.

RainDrop Sense Operator’s Manual

In addition, users should take precautions in accordance with local, state, and national

requirements.

LCN 50-04344 Rev. D 1-5

Laser Safety Warnings

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. Class­3B lasers must be equipped with a key switch and a safety interlock.

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.

RainDrop Sense Operator’s Manual

A laser warning indicates that the user must use precautions whe

to avoid injury from the lasers.

In addition, users should take precautions in accordance with local, state, and national

requirements.

n operating the instrument

LCN 50-04344 Rev. D 1-6

Figure 1-1: Laser Safety Warnings

Safety Information

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.

Electrical Safety Warnings

RainDrop Sense Operator’s Manual

LCN 50-04344 Rev. D 1-7

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.

RainDrop Sense Operator’s Manual

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 and Transport

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

LCN 50-04344 Rev. D 1-8

RainDance Technologies.

Chapter 1:

CHAPTER 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

2

Handling the Sense Chip page 2-6

RainDrop Sense Chip Compression Plate page 2-7

Specifications page 2-8

LCN 50-04344 Rev. D 2-1

RainDrop Sense Operator’s Manual

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

LCN 50-04344 Rev. D 2-2

RainDrop Sense Operator’s Manual

Instrument control workstation monitor RainDrop Sense instrument

RainDrop Sense Major Components

Figure 2-2 shows the major components of RainDrop Sense instrument.

Figure 2-2: RainDrop Sense Major Components

LCN 50-04344 Rev. D 2-3

RainDrop Sense Layout

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 shows the RainDrop Sense layout and oil reservoir fill ports.

RainDrop Sense Operator’s Manual

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 RainDance­supplied 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.

LCN 50-04344 Rev. D 2-4

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)

RainDrop Sense Operator’s Manual

Figure 2-4: RainDrop Sense Barcode Reader

Scanning Barcodes

Scan items as follows:

1. Click Sc

2. Hold

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.

LCN 50-04344 Rev. D 2-5

an in the ICS software. The red scanner light pulses for 10 seconds.

the barcode on the item in front of the barcode reader. When the scanner reads

RainDrop Sense Chip

Microfluidic chip

Droplet detection
region of interest (ROI)

Fluid lanes

Chip alignment hole

Chip alignment holeWaste collection area

Oil input gaskets

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.

RainDrop Sense Operator’s Manual

Handling the Sense Chip

Figure 2-5: RainDrop 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.

LCN 50-04344 Rev. D 2-6

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.

RainDrop Sense Operator’s Manual

Figure 2-6: RainDrop Sense Chip Compression Plate

LCN 50-04344 Rev. D 2-7

Specifications

Table 2-1 shows the specifications for the RainDrop Sense instrument. Table 2-2 shows the

specifications for the Instrument Control (IC) Workstation.

Table 2-1: RainDrop Sense Hardware Specifications

Requirement or
Spec

ification Description

RainDrop Sense Operator’s Manual

Width

Depth 17 inches (43.2 cm)

Height

Weight ~65 lbs (~29 kg)

Power Source (Electrical) Voltage: 100 to 240 VAC, 35 W max

Clearance 2 inches (5 cm) in rear

Fuses 2 fuses, 2 Amperes Medium Acting

Cable Connections USB: 1 USB 3.0 and 1 USB 2.0

Required compressed gas
input pressure range at the
instrument

Capacity 8 lanes per chip

Maximum Sample
Throughput per 8 hour shift

11 inches (27.9 cm)

15 inches (38.1 cm)

1 standard grounded outlet, within 6 ft (2 m) of the
instrument

90-120 PSI (0.62 MPa – 0.82 MPa)

24 samples per shift in Standard Mode
56 samples per shift in Fast Mode

Detection Time ~8 lanes in 4 hours for Standard Mode (for 25 µL

sample)
~8 lanes in < 2 hours for Fast Mode (for 25 µL sample)

Droplet Identification Precise control of relative pressure and oil flow rate

creates ideal spacing of the thermal cycled emulsion to
allow for proper droplet identification and analysis.

Droplet Processing Droplets are processed on a chip that has no moving

parts or valves. Samples have minimal contact with
either walls or air. In addition, one-time-only chip use
prevents sample cross-contamination.

LCN 50-04344 Rev. D 2-8

RainDrop Sense Operator’s Manual

Table 2-2: Instrument Control (IC) Workstation Specifications

Requirement or Specification

Instrument Control (IC) Workstation

Power Voltage: 100-240 VAC

Dimensions Width: 1.36 inches (3.45 cm)

Weight

Clearance 2 inches (5 cm) in rear

Network Connection

Description

Intel Computer: 19 V, 65 W
Standard grounded outlet within 6 ft (2 m) of the
instrument

Depth: 4.41 inches (11.20 cm)
Height: 4.59 inches (11.66 cm)

1.4 lb (520 g)

TCP/IP connectivity (i.e., Internet) using a standard
Ethernet connector. Instruments must be placed near
an active Ethernet port so the computers can be
networked. The Instrument Control Software has the
ability to email notifications to customers if it is
networked. In addition, RainDance has software that
allows us, with customer permission, to access the
computers to look at log files to assist in
troubleshooting and to assess instrument performance.
Without Internet access, support is compromised.

Instrument Control (IC) Monitor

Power Voltage: 100 to 240 VAC

View Sonic Monitor: 22 W max, 20 W typical
grounded outlet within 6 ft (2 m) of the instrument

Dimensions Width: 16.4 inches (41.62 cm)

Depth: 7.8 inches (19.91 cm)
Height: 15.8 inches (40.22 cm)

Weight

Clearance 0.5 inches (1.2 cm) in all directions

6.6 lb (3.0 kg)

LCN 50-04344 Rev. D 2-9

Table 2-3: Operating Environmental Requirements

RainDrop Sense Operator’s Manual

Requirement or Specification

Laboratory Ambient
Temperature Range

Ambient Temperature
F

luctuation

Relative Humidity 5-85% RH, non-condensing

Atmospheric Pressure

Safety Compliance IEC 61010-1:2010, the international safety standard for

Data Backup RainDance suggests using a standard backup

Description

15-30°C

<0.3°C per minute

101-81 kPa (1010-810 mbar) or sea level to 1800 m

laboratory equipment, including USA (UL), Canadian
(CSA), and European (CENELEC/EN) differences

dure for any computer system.

proce

LCN 50-04344 Rev. D 2-10

Chapter 1:

CHAPTER 3

Chapter 3:

Installation and Setup

This chapter covers the following topics:

Space Requirements page 3-2

Connecting RainDrop Sense and Instrument Controller page 3-3

Connecting Cables to the RainDrop Sense Instrument page 3-3

Connecting Cables to the Instrument Controller page 3-4

Gas Pressure Quality page 3-7

Starting Up the RainDrop Sense Instrument page 3-8

Relocating RainDrop page 3-9

3

Important: Only train

RainDrop

®

Sense instrument from its packaging and install it.

ed and certified RainDance Service Representatives may remove the

LCN 50-04344 Rev. D 3-1

Space Requirements

Caution: The RainDrop Sense instrument is sensitive to vibration and should be
placed on a bench top that is free from vibration.

The RainDrop® Sense instrument is designed to be placed on a standard laboratory bench.
The Instrument Controller (IC) Workstation can be located on either the left or right side of the
instrument.

Table 3-1: RainDrop Sense Dimensions (Including the IC Workstation)

Minimum Height (door open) 28 inches (71.1 cm)

RainDrop Sense Operator’s Manual

Minimum Depth

Bench Loading Weight 73 lb (26.4 kg)

Minimum Width 29 inches (74 cm)

Note: Refer to

Gas Connectivity

Gas source should be located in proximity to the instrument because the gas supply
connection is located on the back of the instrument. Use 4mm OD polyurethane tubing with
an in-line shutoff valve. See Appendix A for information on suppliers.

19 inches (48.3 cm)

the Pre-Site Guide for any additional installation details.

LCN 50-04344 Rev. D 3-2

RainDrop Sense Operator’s Manual

Power switch

AC power
cable

Gas pressure

USB connections

Connecting RainDrop Sense and Instrument Controller

Before powering on the RainDrop Sense instrument and its IC Workstation, make sure all
cables are properly connected as described in “Connecting Cables to the RainDrop Sense

Instrument” on page 3-3 and “Connecting Cables to the Instrument Controller” on page 3-4.

Connecting Cables to the RainDrop Sense Instrument

The RainDrop Sense instrument has three cable connections (AC Power Cable and two
USB) and a gas pressure connection as shown in Figure 3-1.

Figure 3-1: Cable Connections on RainDrop Sense

LCN 50-04344 Rev. D 3-3

RainDrop Sense Operator’s Manual

To plug cables into the back of the Sense instrument:

1. Plug one end of the AC Power Cable into the Power Cable Connection and the other

end into a standard grounded wall outlet.

Important: The Detachable Main AC Power Cable for North America or other
countries with 120 VAC 50/60 Hz supply voltage provided for the RainDrop Sense
instrument is a 3-wire cord, 18 AWG, 10 A, 125 VAC. Never substitute a Detachable
Main AC Power Cable with a lower current or voltage rating.

2. Plug the two USB Cables into the USB Connections on the Sense instrument as

shown in

Figure 3-1.

Connecting Cables to the Instrument Controller

The RainDrop IC Workstation has USB connections used for:

The mouse
The keyboard

The RainDrop Sense instrument

Both the Source and Sense instruments connect to their IC Workstations via USB
connections.

Figure 3-2 illustrates the USB cable connections on the IC Workstation.

Note: It is important that all the USB cables on the instruments are connected to USB ports
on the workstations. Failure to connect the USB cable correctly can result in a loss of
communication with the RainDrop instrument. In addition, the USB connections on your
workstation may differ from those shown in

Figure 3-2.

LCN 50-04344 Rev. D 3-4

RainDrop Sense Operator’s Manual

USB port that connects to
the left output from the
Sense

USB port that connects to
the right output from the
Sense

HDMI port that connects to
the monitor

The left USB/output connects to the USB port furthest from the gas inlet and the right USB/output

Figure 3-2: Cable Connections to the IC Workstation

connects to the other available USB port.

LCN 50-04344 Rev. D 3-5

RainDrop Sense Operator’s Manual

USB receiver

LCN 50-04344 Rev. D 3-6

Figure 3-3: USB Receiver

1. With the IC Workstation turned off, plug the USB receiver for the keyboard and mouse

into the IC Workstation.

2. Plu

3. Plu

g the right USB output from the Sense instrument into the right USB in Figure 3-2.
g the left USB output from the Sense instrument into left USB in Figure 3-2.

Gas Pressure Quality

You may use compressed argon or nitrogen. Ensure that the compressed gas system you
use meets the following standards.

RainDrop Sense Operator’s Manual

The input pressure must be regulated to a value, at the system, within the
120 psi.

In addition, the quality must meet the ISO/DIS8573 compressed gas qu
Class 2 for instrument quality gas, as follows:

Table 3-2:

Oil (ppm) 0.1

Water (dew point)

Dirt (µ) 1.0

GasPressure Quality

-40°F

ality standard,

range of 90-

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RainDrop Sense Operator’s Manual

Starting Up the RainDrop Sense Instrument

Use the following startup sequence for the RainDrop Sense instrument:

1. With the

have been connected properly as described in “Connecting Cables to the RainDrop

Sense Instrument” on page 3-3 and “Connecting Cables to the Instrument Controller”
on page 3-4.

2. T

urn on the IC Workstation (on the top of the workstation).

3. Lo

g on to the Windows 7 operating system using the RDT account.

Note: Logg

User name = RDT

No password

4. T

urn on the RainDrop Sense instrument (located on the back of the instrument).

5. W

ait 1 minute for the RainDrop Sense instrument to perform internal initialization. As
the instrument initializes, the lights on the panel illuminate to indicate its status (see

Figure 3-4).

RainDrop Sense and IC Workstation turned off, ensure that all the cables

ing on using any other account results in ICS failures.

Figure 3-4: RainDance LED Lights

6. Launch the Instrument Control Software (ICS) application as described in Chapter 4.

Table 3-3 lists the LED lights that indicate the status of the instrument.

Table 3-3: LED Lights Within the RainDance Logo

LED Name and Illumination Pattern Meaning

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RainDrop Sense Operator’s Manual

Caution: The RainDrop Sense instrument weighs approximately 65 lbs (29 kg). To
avoid injuries and damage to the instrument, do not move it without assistance from
RainDance Technologies. If you want to move your instrument either within your
laboratory or to another location, contact RainDance Technologies.

Table 3-3: LED Lights Within the RainDance Logo

Main Power LED (Solid) Instrument is powered on.

All LEDs except Main Power are rotating

and off.

on

All LEDs are flashing simultaneously. Instrument has detected an error.

All LEDs are on.

All LEDs except Main Power are off. Instrument is disconnected from the ICS.

Relocating RainDrop

Instrument is operating normally.

Instrument is connected to the ICS.

LCN 50-04344 Rev. D 3-9

Chapter 1:

CHAPTER 4

Chapter 4:

Launching the Instrument Control Software (ICS)

This chapter covers the following topics:

Introduction page 4-2

The Microsoft Windows 7 Login page 4-2

Starting the ICS Application page 4-2

ICS Login Levels page 4-3

Changing the ICS Password page 4-5

4

The ICS Account Types page 4-6

ICS Initialization page 4-7

Status Indicators page 4-10

Using Tabs in the ICS page 4-11

Navigating Through the Tabs page 4-12

Canceling a Process page 4-12

Completing a Process page 4-13

Using Scan Buttons page 4-13

Alarms, Log, and Status Tabs page 4-14

LCN 50-04344 Rev. D 4-1

Introduction

The Instrument Control Software (ICS) application controls the operation of the RainDrop®
Sense.

The Microsoft Windows 7 Login

The Instrument Control Workstation is configured with a single Microsoft Windows 7
Operating System login. Do not edit this account or add additional accounts. Failure to
comply will result in ICS failures. The default login is an administrative account. The system
differentiates between upper and lower case characters.

RainDrop Sense Operator’s Manual

Note: Do not

use the RainDance Support Windows Logon. This will result in ICS failure.

Starting the ICS Application

The startup sequence works as follows:

1. Power on

Power on the IC Controller and log in to Windows.
Power on the RainDrop Sense. Wait one minute.

2. Click the ICS icon on

Note: You can also start the ICS application by selecting Windows 7 Start Program Menu,

and then selecting Start > All Programs > RainDance Technologies > Launch ICS.exe.

each component of the RainDrop Sense in the following sequence:

your desktop:

Note: The
designated application and software uses.

LCN 50-04344 Rev. D 4-2

IC Workstation must be dedicated to ICS Operation. Use it only for RainDance

RainDrop Sense Operator’s Manual

The Login window opens (see Figure 4-1).

Figure 4-1: Login Window

3. Enter your Login information in the appropriate fields. Enter the Username followed by
the Password and then click Login. See ICS Login Levels for more information.

Note: Microsoft

application, both usernames and passwords are case sensitive.

ICS Login Levels

The ICS application supports two levels of access to the ICS program: User and
Administrator. The ICS application is configured with two default login IDs: one for User and
one for Administrator. RainDance recommends that you change the default password on
each of these accounts after initial use.

Table 4-1: ICS Default User and Administrator Login Information

Requirement or Specification Description

User Login Username User

User Login Password

Administrator Login User Name Admin

Administrator Login Password admin

Windows 7 usernames are not case sensitive, but passwords are. In the ICS

user

LCN 50-04344 Rev. D 4-3

Caution: After three failed attempts to login with the wrong password, the ICS
application locks the account. You will not be able to login to your account. If this
happens, you must contact someone in your facility with an Administrator account
who can either unlock or reset your password. For details, see “Resetting Password

or Unlocking an Account” on page 6-7.

Figure 4-2 shows the message for a failed login.

RainDrop Sense Operator’s Manual

Figure 4-2: Invalid Username Message

LCN 50-04344 Rev. D 4-4

Changing the ICS Password

This section describes how to change an ICS password. RainDance recommends that you
change the default User and Administrator passwords after initial use.

RainDrop Sense Operator’s Manual

1. Select Chan

(Figure 4-3).

2. Enter the old password in the Old Password field, the new password in the New
Password field, and the new password again in the Verify Password field. Click Save

when you are done to save the new password. Click Cancel to dismiss the dialog
without saving your changes.

ge Password from the Home menu. The Change Password dialog opens

Figure 4-3: Change Password Window

LCN 50-04344 Rev. D 4-5

The ICS Account Types

Your account type defines the features you have access to (User and Administrator) within
the ICS application.

Table 4-2: ICS Account Type

RainDrop Sense Operator’s Manual

Feature User

Change Passwords X X

Export Instrument Files X

View Runs X X

Maintenance Actions

Add New Users X

Edit Users

Reset Passwords X

Unlock Passwords

Start Runs X X

Stop Runs X X

The pull-down menu selections differ depending on your access righ
different for a User and an Administrator account.

Administrator

X

X

X

X

ts; they are slightly

LCN 50-04344 Rev. D 4-6

ICS Initialization

When you login to the instrument, the Initialization screen appears (see Figure 4-4).

RainDrop Sense Operator’s Manual

Figure 4-4: Initialization Screen

From the Initialization screen, click Start Initialization to initialize the system. A progress bar
shows the progress of the initialization.

Figure 4-5: Initialization Progress Bar

LCN 50-04344 Rev. D 4-7

RainDrop Sense Operator’s Manual

If initialization fails, the following message appears:

Figure 4-6: Initialization Failure Message

Click OK and contact RainDance Support. See “RainDance Support” on page 1-3.

This error is often the result of starting ICS right after you turn on
recommends the following steps:

1. Exit the

2. T

urn the instrument off.

3. T

urn the instrument back on.

4. W

ait 1 minute.

5. Start t

ICS.

he ICS.

If the message appears again, restart the ICS.

the instrument. RainDance

LCN 50-04344 Rev. D 4-8

RainDrop Sense Operator’s Manual

If initialization is successful, the ICS home page is displayed (see Figure 4-7).

Note: All

menu items are inactive until the initialization is finished.

Figure 4-7: Home Page

From the home page, you can Setup a Run (see Chapter )

You can perform additional tasks by ma

View Runs (see Chapter 6)

Maintenance Actions (see Chapter 7)

Add New Users (Administrator only) (see Chapter 6)
Edit Users (Administrator only) (see Chapter 6)

king selections from the drop down menus:

LCN 50-04344 Rev. D 4-9

Status Indicators

A common set of status indicators appears throughout the system indicating the status of an
item or process being performed. In general, the green check mark (
everything is working as expected and you can proceed. The orange exclamation point (!)
indicator is a warning that means that you can continue, but that some optional fields are
blank. The red X indicator means there is a problem that needs to be resolved before you can
continue.

RainDrop Sense Operator’s Manual

?

) indicator means that

Table 4-3 shows the status indicators a

Table 4-3: Status Icons

Icon

Meaning

Ready – If all icons are green check marks, the system is ready to start a

run.

Warning (Run Will Proceed) – If there is one or more orange
exclamation point icons on the tabs, the run can start. These represent
optional information.

Error (Run Will Not Proceed) – If there is one or more red X icons on the
tabs, there is an issue that may prevent the run from being performed.

nd describes their meanings.

LCN 50-04344 Rev. D 4-10

Using Tabs in the ICS

There are two tabs in the ICS that appear after you click Setup a Run: Run Data and Run
Info. To perform a run, you will need to complete some of the fields on each tab.

RainDrop Sense Operator’s Manual

To ensure that all of the steps are completed correctly, RainDrop
the right side of the tabs to indicate the state of each of the required items. As you complete
each step in the process the status icon for that step is updated. This section provides
general information on what appears on the tabs and how to complete these processes.

Details on how to complete each of these pro
descriptions assume you are familiar with how to use the tabs described h

Figure 4-8 shows an example of the Sense interface.

process are shown on the left side of the screen:

Run Data

Run Info

cesses is provided in Chapter . Those

The tabs required to complete the

provides a System Status on

ere.

Figure 4-8: Sense Tabs

Only one tab is visible at a time. The selected (or active) tab has a white background and the
inactive tab has a transparent background (Run Data is the active tab in Figure 4-8).

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RainDrop Sense Operator’s Manual

To prepare for a run on the Sense instrument, you must complete the following fields in the
Sense ICS:

Run Data Tab:

Run Name

Sense Chip barcode lot and serial number
At least one selected lane (indicated by a green check mark)

In addition, before you can proceed with the run on the Sense instrument, you

must have clicked the Insert PCR Tube button to indicate that you have inserted
the closed tube strip into the instrument.

Select Standard or Fast Mode detection.

Run Info Tab:

Carrier Oil field and Drive Oil field and only if the instrument is out of one of those

oils

As you complete each tab, the software updates the System Status fo
green check mark is displayed, the item is ready to go. If an orange exclamation point is
displayed, it means that optional fields are blank. If a red X is displayed, there are errors or
missing data required for the run (see Table 4-3).

For a description of the meaning of the Status Indicators used on
system, see “Status Indicators” on page 4-10.

Navigating Through the Tabs

You can switch back and forth between the two tabs at will. Click the tab name to move to a
tab.

Canceling a Process

The Run Data tab has a red Cancel button in the lower left corner (Figure 4-8). If you click
Cancel while a

run is active, the application asks you to confirm that you want to cancel.

r various items. If the

the tabs and throughout the

Figure 4-9: Cancel Confirmation

When you click Yes, the information you entered when you started the process is deleted, the
run is canceled and you are returned to the RainDrop main screen.

LCN 50-04344 Rev. D 4-12

Completing a Process

When you have completed each step to prepare for a run, review the System Status
indicators. Ideally, all the status indicators will be green check marks, although you can still
continue with orange exclamation points since they indicate only that optional fields are
blank. The process cannot be started if there is even one red X (error indications) on any of
the tabs.

RainDrop Sense Operator’s Manual

When you are satisfied that the steps for the process are complete
bottom right side of the Run Data tab. This starts the process on the RainDrop Sense
instrument.

Using Scan Buttons

The ICS allows you to scan barcodes to enter information into various text fields. There are
two types of Scan buttons available in the system as shown in Table 4-4.

Table 4-4: Scan Buttons

Button Description Use

, click Start Run on the

Figure 4-10: Start Run Button

Manual Scan Button The instrument requires that you

manually enter a barcode.

Scan Button The system allows you to scan any

type of barcode.

Clicking either type of scan butt
to scan the barcode.

If you scan the wrong type of barcode, an error message appears. ICS will not a
invalid barcode.

LCN 50-04344 Rev. D 4-13

on activates the barcode reader on the system and allows you

ccept an

Alarms, Log, and Status Tabs

The Alarms, Log, and Status tabs are displayed on the bottom of the screen (see Figure 4-

11). Each of these tabs is described below.

Figure 4-11: Example of Screen Showing Alarms, Log, and Status Tab at Bottom

The Alarms tab is displayed by default. Click Log or Status to display that tab.

Alarms Tab – This tab lists instrument errors that exist in the system. If an error

appears, the system is in a warning or error state. Different errors occur during the
setup of the instrument. If an error does not clear when you close the door and click
Start Run, check “Troubleshooting” on page 7-8. If the issue is still not resolved,
contact supp

Log Tab – This tab is used for service purposes. It is used to check on the system

automation.

Status Tab – This tab is used for service purposes. It is used to determine the status of

the instrument at different points during operation.

[e-mail] for assistance.

RainDrop Sense Operator’s Manual

LCN 50-04344 Rev. D 4-14

Chapter 1:

CHAPTER 5

Chapter 5:

Performing a Sense Run

This chapter covers the following topics:

Introduction page 5-2

Gathering Supplies page 5-2

Starting a Sense Run page 5-3

Completing the ICS Setup page 5-10

Checking the Status Indicators page 5-10

Completing the Run Data Tab page 5-12

Completing the Run Info Tab page 5-15

5

Completing the Run Tabs Using the Import Function page 5-16

Using Email Notification page 5-16

Performing the Run page 5-18

Canceling a Run page 5-20

Handling Data page 5-21

Exporting Data page 5-22

Moving Data Files page 5-23

LCN 50-04344 Rev. D 5-1

Introduction

Perform the operations described in this chapter on the RainDrop® Sense instrument. This

procedure requires a number of consumables (available from RainDance Technologies
other manufacturers).

Note: For the list of required consumables, see “RainDrop® Consumables and Equipment”

on page A-1.

This chapter describes how to start a run on the RainDrop Sense instrument. Some of the
steps involve preparing the physical components of the system and some of them take place
within the RainDrop ICS.

For detailed information the ICS software, see Chapter 4 and Chapter 6.

Note: Extraneous clusters have been noted in 50ul samples run in the FAST mode on the
Sense instrument. For the highest quality data we recommend limiting sample volumes to
25ul if the samples are to be run in the FAST mode on the Sense instrument.

RainDrop Sense Operator’s Manual

®

and

Gathering Supplies

To start a run on the RainDrop Sense instrument, have the following equipment and supplies
available:

Gloves, nitrile or latex
Sense Chip, P/N 30-06086

Sense Chip Compression Plate, P/N 30-06423

Drive Oil, shipped in syringes, P/N 30-07117

PCR tube strip containing emulsion generated on the RainDance Source instrument

and following thermal cycling.

For Standard Mode detection, standard PCR Tube Strip Caps (P/N 40-06087)

For Fast Mode detection, High Speed Caps (P/N 40-08286)

LCN 50-04344 Rev. D 5-2

Starting a Sense Run

This procedure assumes you have prepared your sample and that you have assembled all
the necessary equipment and supplies. It also assumes that you have completed thermal
cycling the sample. It shows you how to start a run on the RainDrop Sense instrument.

unch the ICS software for the Sense instrument and log in.

1. La

RainDrop Sense Operator’s Manual

Figure 5-1: Login Screen

2. Click Start Initialization.

Figure 5-2: Initialization Screen

When you click Start Initialization, the system automatically prepares the instrument
for normal operation. It sets valves and pressures and turns the laser in the barcode
reader off. In addition, it homes the motion control subsystem. Initialization takes
approximately four minutes.

LCN 50-04344 Rev. D 5-3

RainDrop Sense Operator’s Manual

Note: If initialization fails, the ICS returns to the Initialization screen after about
fifteen minutes. Contact RainDance Support for assistance. See “RainDance Support”

on page 1-3.

3. Click Se

tup a Run.

Figure 5-3: Instrument Status and Setup a Run Screen

LCN 50-04344 Rev. D 5-4

4. Select the Run Info tab.

RainDrop Sense Operator’s Manual

Figure 5-4: Run Info Tab

5. On the Run Info tab, click Open Door. The door on the Sense instrument unlocks

allowing you to lift it to the upright, open position.

6. If ru

nning in Fast Mode, use High Speed Caps. Following thermal cycling, carefully
remove the domed caps (Axygen) and replace with High Speed Caps. Rock the caps
back and forth to seat properly, then press into place. Ensure the cap is secured and
the strip is tightly covered.

A properly covered PCR tube strip has:

A flat cap all the way across

Its tab oriented to the left (over number 1 on the tube strip)

An improperly covered PCR tube strip has:

A bump or buckle

A loosely fitting cap

Its tab to right (over number 8 on the tube strip)

LCN 50-04344 Rev. D 5-5

A bump in the cap

7. Lift the door to the fully open position.

.

RainDrop Sense Operator’s Manual

Figure 5-5: Improperly Covered PCR Tube Strip

LCN 50-04344 Rev. D 5-6

RainDrop Sense Operator’s Manual

Figure 5-6: Sense Door in Fully Open Position

LCN 50-04344 Rev. D 5-7

RainDrop Sense Operator’s Manual

8. Insert a tube strip into the tube strip nest (see Figure 2-3). Orient the tabbed end to the

left.

Figure 5-7: Insert a Tube Strip

9. Remove a Sense Chip from its packaging; for more information on the chip, see see

“RainDrop Sense Chip” on page 2-6. Handle the Sense Chip as follows:

With gloved hands, 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.

Do not touch the objective lens.

10. Scan the

chip by clicking Scan in the ICS software. The red scanner light pulses for

10 seconds. Hold the Sense Chip in front of the barcode reader. If 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 Sense instrument. 



If the scanner does not read the barcode, the ICS software displays a

message and

allows you to enter the barcode manually. To do so, click the Manual button and
enter the barcode numbers from the label of the chip. In manual format, the ICS
accepts 99 characters of text.

11. In

sert the chip into the Sense instrument. Orient the Sense Chip over the alignment
pins and ensure that the pins are coming through the alignment holes on the chip. Do
not insert it at an angle. The instrument is designed so that the Sense Chip punctures
the caps of the tube strip. Do not apply pressure to the chip after inserting it. It is
important that the instrument is able to make a seal and then puncture the tube caps.
The Sense instrument will not allow you to proceed until the chip is oriented properly.

LCN 50-04344 Rev. D 5-8

RainDrop Sense Operator’s Manual

Figure 5-8: Inserting a Sense Chip

12. Locate the Chip Compression Plate; for more information on the plate, see see

“RainDrop Sense Chip Compression Plate” on page 2-7.

13. Place t

When the plate is properly positioned, its RainDance logo should be

he Chip Compression Plate over the Sense chip as shown in Figure 5-9.

facing you, the

plate should be flat, and it should not be movable left to right or front to back.

Figure 5-9: Placing the Chip Compression Plate

After you insert the Chip Compression Plate, you are done setting up the physical

components.

14. Clo

se the door on the Sense instrument.

LCN 50-04344 Rev. D 5-9

Completing the ICS Setup

Before starting a run on the Sense instrument, you must complete a number of setup steps.
The steps ensure that the instrument is ready for operation and provide data about the run.
They include:

Check the status of various components.

Complete the Run Data.

Complete the Run Info.

Checking the Status Indicators

Status indicators tell you about the readiness of the instrument.

RainDrop Sense Operator’s Manual

Figure 5-10: System Statuses

Observe the status indicators in the software.

Table 5-1: System Status Indicators

Indicator

Pressure
Ready

Carrier Oil

Drive Oil Indicates the status of the drive oil reservoir. When there is sufficient oil to

Meaning

Indicates the status of the instrument gas pressure. When the pressure is
sufficient, the ready indicator is displayed.

Indicates the status of the carrier oil reservoir. When there is sufficient oil
to complete a run, the ready indicator is displayed. A valid carrier oil lot
number is required for the green check mark to be displayed.

complete a run, the ready indicator is displayed. A valid drive oil lot
number is required for the green check mark to be displayed.

LCN 50-04344 Rev. D 5-10

Table 5-1: System Status Indicators

RainDrop Sense Operator’s Manual

Chip
Inserted

Indicates the presence of the Sense Chip. When the Sense Chip is
present and inserted properly, the ready indicator is displayed.



Note: You must scan the chip prior to use; otherwise, the instrument will
not detect it. If you have scanned the chip before inserting it and it is still
not detected, wiggle the chip and try again.

Door Closed Indicates the status of the instrument door. When the door is properly

closed, the ready indicator is displayed.

System
Ready

Indicates the overall status of the instrument. When all the requirements
of the instrument are present and ready for a run, the ready indicator is
displayed.

In addition to satisfying the Status Indicators, in order to start a run you must also have:

Scanned or input the barcode number from a Sense Chip
Clicked Insert Tube Strip to affirm that you have inserted the tube strip

LCN 50-04344 Rev. D 5-11

Completing the Run Data Tab

The Run Data tab opens after you click Start Run on the startup screen and contains the
details about the contents of the run. You can enter this information manually or you can
import it from a file you saved on the Source instrument.

RainDrop Sense Operator’s Manual

Figure 5-11: Run Data Tab

Only the following fields on the Run Data tab are required for the run to proceed:

Run Name
Sense Chip barcode lot and serial number

At least one selected lane (indicated by a green check mark)

Your lab procedures determine how much of the optional information
specific situation.

In addition, before you can proceed with the run, you must have
button to indicate that you have inserted the closed tube strip into the instrument.

is necessary for your

clicked the Insert PCR Tube

LCN 50-04344 Rev. D 5-12

Table 5-2: Run Data Fields

RainDrop Sense Operator’s Manual

Field Name

Run Name The name of the run. Run name is required and can contain up to 20

Lanes A - H

Lane
Description

Sense Chip Lot
& Serial
Number

Meaning

characters. This is required.

The identifiers for each tube (or lane) on the chip. These fields are not
required. The lane letter identifiers are hard-coded and cannot be
edited.

The text description that you enter. This is not required.

The identifiers for each Sense Chip.
completed when you scan the chip and is required.

This information is automatically

Run Filenames

When the ICS saves data at the end of a run, it uses the information you enter in the fields in
the above table to name the file. It creates one file per lane in a folder named for the Run ID,
as follows:

The filename for one lane of a run looks like this:

<Run ID>-<Lane Letter>-<Lane Description>.fcs

For example: 1302181535-A-ExampleDescription.fcs

The Run ID is the numeric run number from the upper right corner of
appears on both the Run Data tab and the Run Info tab. See “Handling Data” on page 5-21
for more information.

the ICS screen. It

Entering the Run Data

Enter the run data as follows:

1. T

ype the name of the run into the Run Name field.

2. All lan

3. If n

es are selected by default. Deselect any lanes you are not using. At least one

lane must be selected in order for the run to proceed.

ecessary, enter lane information in one of the following ways:

Type the name for the lane manually. When you enter the name manually, the field

limits entry to 99 characters.

LCN 50-04344 Rev. D 5-13

RainDrop Sense Operator’s Manual

Scan the barcode from a printout. To do so, place the printout in front of the

barcode reader and click Scan next to the correct lane. When you enter the name
using the scanner, the field limits entry to 96 characters.

Import the lane information as described in see “Completing the Run Tabs Using

the Import Function” on page 5-16.

4. Select the number of droplets you want from the Droplet drop-down.

5. Click Insert PCR Tube to confirm that you have inserted the tube strip into the

instrument.

Note: The Sense Chip field should already display the information you scanned earlier in see

“Starting a Sense Run” on page 5-3.

LCN 50-04344 Rev. D 5-14

Completing the Run Info Tab

The fields on the Run Info tab contain information about the run. The only fields on this tab
that are required are the Carrier Oil and Drive Oil fields and only if the instrument is out of one
of these types of oil.

RainDrop Sense Operator’s Manual

Figure 5-12: Run Info Tab

Your lab procedures determine how much of the information is necessary for your specific
situation. Enter the run information as follows:

Table 5-3: Run Info Fields

Field Name

Operator The name of the person performing the run.

PCR Tube ID

Run
Comments

LCN 50-04344 Rev. D 5-15

Meaning

The identifier of the sample to be run.

Any detailed descriptive information you want stored with the run
information.

RainDrop Sense Operator’s Manual

Completing the Run Tabs Using the Import Function

To complete the run tabs using the import function:

1. Click Import at the top of the Run Data tab. The import works only with XML files

generated by the Source instrument. The page displays a list of runs.

2. Locate the file to import and click on it.

3. ICS imports only the following fields:

On the Run Data tab:

Run Name

Lane information

On the Run Info tab:

Operator

PCR Tube ID

Run Comments

4. Complete any other of the optional fields, as needed.

Using Email Notification

The RainDrop Sense instrument is located in a lab space which may be a distance from your
desk or usual work area. Email Notification allows you to receive messages when a run is
finished, so that you do not have to continually check the instrument. Select Send Run
Emails on the Run Info tab. If email addresses have been entered by an Administrator, they
appear in the Email Notification field. You can leave these addresses as is, edit them, or add
to them. Notifications are sent to those addresses.

Note: Email notification does not support text messaging.

Setting Up Email Notification (Administrator)

Setup Email Notification as needed. You do not have to edit these settings for each run. You
can establish email settings and then not change them unless you need to change who is
notified at the end of a run.

To enter email addresses:

1. Select Setup Email from the Actions menu. The Email dialog opens.

2. Enter email addresses in the Email Notification field, separated by semi-colons.

These email addresses will appear on the Run Info tab by default.

3. Select Send Run Emails, if you want this to be the default action.

LCN 50-04344 Rev. D 5-16

RainDrop Sense Operator’s Manual

4. Click Save to save the new addresses. Click Close to dismiss the dialog.

Email Messages

Email messages contain the following information:

Table 5-4: Email Message Data

Field Name What is reported

RainDance ID

Run Name The name the user entered in the Run Name field prior to

Description

Start Time The date and time the run was started

End Time

Sample Info For each sample, it lists: Lane, Sample Description, Droplets,

Total Samples The number of samples attempted

Samples
Succe

Samples Failed The number of samples that generated an error, including any

Errors All errors encountered during the run

ssful

The serial number of the instrument

beginning the run. If the user does not enter a Run Name, this
lists a name provided by the RainDrop Sense instrument.

The comments entered by the user at run time, if any

The date and time the run ended

CV (coefficient of variance), Read Length, and Status

The number of samples that successfully ran without errors

samples not processed because the run was stopped because
of a prior/fatal error

LCN 50-04344 Rev. D 5-17

Performing the Run

After you have entered the required run data, you are ready to begin the run.

RainDrop Sense Operator’s Manual

1. Click the Start Run bu

progress as shown in the following image.

tton. The screen displays information about the Sense run in

Figure 5-13: Sense Run Screen

The center of the screen displays information about which sample is being processed.
The right side of the screen displays information about the progress of the run.

2. Whe

3. Lift the

4. T

LCN 50-04344 Rev. D 5-18

n the sample is done, the door unlocks automatically.

door to its full open position.

o minimize the potential for contaminating the lab environment with the amplicon,
return the used chip to the bag it came in and discard it in a solid waste disposal
container.

The ICS displays the Run Complete screen.

RainDrop Sense Operator’s Manual

Figure 5-14: Sense Run Complete Screen

5. Click View Run Report to review the run data.

6. Click Sa

ve and Close. ICS saves the data from the run in a file in FCS format, which

can be read by the RainDrop Analyst software.

Note:

As stated above, the instrument door unlocks after the run is complete. If you

accidentally close the door and still need access, click Open Door to open it.

LCN 50-04344 Rev. D 5-19

Canceling a Run

If you want to stop a run after you have started filling out the Run Data tab, but before clicking
Start Run, click Cancel. This brings you back to the Instrument Status and Setup a Run
Screen (see

If you want to stop a run after clicking Start Run, click the Abort button. This brings you to the
Run Completion screen.

Figure 5-3) and blanks out any data you have entered for this run.

RainDrop Sense Operator’s Manual

LCN 50-04344 Rev. D 5-20

Handling Data

The data from Sense runs is collected on the hard drive of the ICS Workstation. Files are
stored in folders on the D drive named for their runs within a RainDance folder as follows:

D:\RainDance\RunLogs\<RunID>

The <RunID> is displayed in the upper right corner of the ICS screen on both the Run Data
tab and the Run Info tab.

The Run ID is built on the date and time as follows: YYMMDDHHMM. In the above image, the
number 1302181529 represents 3:29 pm on February 18, 2013. The Sense ICS creates the
folder when you click Start Run.

Upon completing the run, the Sense ICS creates one FCS file per lane within the Run ID
folder. The filename for one lane of a run looks like this:

<RunID>-<Lane Letter>-<Lane Description>.fcs

For example: 1302181529-A-ExampleDescription.fcs

RainDrop Sense Operator’s Manual

The lane letter and lane description come from data you enter on the Run Data tab. See

“Completing the Run Data Tab” on page 5-12 for more information.

LCN 50-04344 Rev. D 5-21

Exporting Data

The Export Data function allows you to search for previous runs and to save that run data to
either the same or a new location. This allows you to move your FCS files from one location
to another to make them available for use by other applications such as analysis software. To
export data:

1. La

RainDrop Sense Operator’s Manual

unch the ICS as you normally do. See “Starting the ICS Application” on page 4-2.

2. Click Export Data.

The Export Data screen opens.

Figure 5-15: Export Data Screen

3. Use the Start Date and End Date fields to specify a range for the data. Click Update
List to tell ICS to display only data that fall between the dates you enter.

4. Select o
runs or Ctrl+Click to select non-contiguous runs.

5. T

ype the name of an Export Directory or click Browse to locate a folder for the

export.

6. Click Ex
the message.

LCN 50-04344 Rev. D 5-22

ne or more runs by clicking on them. Use Shift+Click to select contiguous

port. When the export is done, ICS displays a message. Click OK to dismiss

Moving Data Files

The data files created by the Sense instrument from just one run can easily exceed several
gigabytes. You can use the Export process described above to locate your FCS files in a
location that is accessible by your analysis software. In addition, RainDance offers the
following instructions for moving your files when disk space becomes an issue on the ICS
Workstation. Keep in mind that the network configuration at your location is unique. You may
need to seek assistance from your in-house IT department to learn their recommendations.

Because RainDrop files are large, RainDance has several recommendations for managing
your data files.

Never attempt to move files while a run is in process.
Move files at a time when network activity is at a minimum so that file transfer is as

efficient as possible.

Consider developing a file management protocol. The disk drive on the ICS is large,

but not infinite. You may need to save files to an external storage device and remove
some from the internal hard drive from time to time. Consult with your internal IT
department to develop a strategy for managing large amounts of data.

RainDrop Sense Operator’s Manual

To copy files using a flash drive:

1. Insert the flash drive into a USB port on the ICS Workstation.

2. Launch Windows Explorer and navigate to the D drive.

3. Open the RainDance folder on the D drive.

4. Open the Run folder whose data you want to copy.

5. Click the Type column to sort the data files by type. The only files you need to move to

the computer running RainDrop Analyst II are the FCS files. They should appear at the
top of the sorted list.

6. Select only the FCS files. Click and drag them to the flash drive icon within Windows
Explorer.

7. When Windows Explorer is done copying the files to the flash drive, bring the drive to
the computer running RainDrop Analyst.

To copy files over a network:

1. Launch Windows Explorer and navigate to the D drive.

LCN 50-04344 Rev. D 5-23

RainDrop Sense Operator’s Manual

2. Open the RainDance folder on the D drive.

3. Open the Run folder whose data you want to copy.

4. Click the Type column to sort the data files by type. The only files you need to move to

the computer running RainDrop Analyst II are the FCS files. They should appear at the
top of the sorted list.

5. Select only the FCS files. Right-click on the collection of files.

6. From the pop-up menu, select Copy.

7. Navigate to the network drive where you want to copy the files.

8. Locate the folder where you want to move the FCS files. Right-click and from the pop-
up menu, select Paste.

LCN 50-04344 Rev. D 5-24

Chapter 1:

CHAPTER 6

Chapter 6:

Managing the System

This chapter covers the following topics:

Introduction page 6-2

Managing Users page 6-2

Adding a New User page 6-3

Editing a User page 6-5

Deleting a User page 6-7

Resetting Password or Unlocking an Account page 6-7

Viewing Past Runs page 6-8

6

Viewing Runs page 6-8

LCN 50-04344 Rev. D 6-1

Introduction

You must have a username and password before you can login to the ICS application. There
are two types of user accounts: Administrator and User. Chapter 4 provides detailed
information on logins and account types.

RainDrop Sense Operator’s Manual

Important:

This chapter describes several soft

Managing Users

Viewing Past Runs

To manage users, you must be logged in with Administrator privileges.

Managing Users

The ICS software lets you manage user accounts from the Actions menu (see Figure 6-1).

ware management functions. These include:

Figure 6-1: Actions Menu

LCN 50-04344 Rev. D 6-2

Adding a New User

To add a new user:

RainDrop Sense Operator’s Manual

1. From the Ac
The Add New User dialog

tions menu, select Add New User (see Figure 6-1).

opens (see Figure 6-2).

Figure 6-2: Add New User Dialog

2. Enter the information for the new user as required (see Table 6-1) and click Add to
save it or Cancel to dismiss the dialo

LCN 50-04344 Rev. D 6-3

g without saving your entries.

Table 6-1: Add New User Dialog

RainDrop Sense Operator’s Manual

Field or Table Element

User Name Specifies the name you use to login. Case sensitive.

Password

First Name, Last Name Specifies the user's first and last names. Required.

Email Address

Address Specifies the user's address. Required.

Contact Number

Privilege Specifies the user's Privilege level (Admin or User)

Add, Cancel buttons Adds the user information, or cancels the process. If

Description

Required.

Specifies the password; any alphanumeric combination
is acceptable. Case sensitive. Required.

Specifies the user's email address. Required.

Specifies the user’s phone number. Required.

selected from a drop-down menu. Required.

added

successfully, a confirmation window displays.

LCN 50-04344 Rev. D 6-4

Editing a User

The Edit Users dialog allows a user with administrator privileges to edit the information for an
existing user or remove an existing user from the database. An administrator can also add a
new user from this dialog.

RainDrop Sense Operator’s Manual

1. From the Ac
opens (see Figure 6-3).

tions menu, select Edit Users (see Figure 6-1). The Edit Users dialog

Figure 6-3: Edit Users Dialog Box

LCN 50-04344 Rev. D 6-5

RainDrop Sense Operator’s Manual

2. To edit the data for an existing user, click Edit in the row for that user. The Edit User
Information dialog opens for the selected user (see Figure 6-4).

Figure 6-4: Edit User Dialog Box

3. Editing user information is essentially the same as adding new user information. Edit

the user information as required (see Table 6-1) and th

en click Save. Click Cancel

button to dismiss the dialog without saving any changes.

LCN 50-04344 Rev. D 6-6

RainDrop Sense Operator’s Manual

Deleting a User

To delete a user:

1. Select Edit Users from the Actions menu (see Figure 6-1). The Edit Users dialog
opens as in Figure 6-3.

2. Click Remove in the same row as the user to be deleted. The system asks you to
confirm that you want to delete the user. Click Yes to confirm or No to cancel the
deletion.

Resetting Password or Unlocking an Account

After three failed attempts to login with the wrong password, the ICS application locks the
account and you are not able to login. If this happens, you must contact someone in your
facility with Administrator privileges who can either reset or unlock your password.

To reset an account:

1. Select the Reset Password check box in the Edit User dialog (see Figure 6-4). This
changes the user's password to the default password, abc123.

2. To save the changes to the account, click Save. The application displays a message
confirming that the changes have been saved.

To unlock an account:

1. Select the Unlock Account check box in the Edit User dialog (see Figure 6-4). This
allows the user to login again with his/her original password.

2. To save the changes to the account, click Save.The application displays a message
confirming that the changes have been saved.

LCN 50-04344 Rev. D 6-7

Viewing Past Runs

This section describes how to view previous runs. It also describes how to generate and view
reports and how to export run results.

Viewing Runs

Certain run parameters are saved by the ICS application. The ICS application lets you search
for and view past run parameters by entering a specific Start Date and an End Date
(inclusive) on which the run was completed.

To view a run report:

RainDrop Sense Operator’s Manual

1. Select V

iew Runs from the Actions menu (see Figure 6-1). The View Run Report

window opens (see Figure 6-5).

Figure 6-5: View Run Report Window

2. Enter a date range to locate the run of interest and click Search. The default start and

end dates are today’s date, so if you want to see the run you just completed, you can
just click Search without changing the date.

All runs that match the selected date range appear in a list below the white title b

LCN 50-04344 Rev. D 6-8

ar.

RainDrop Sense Operator’s Manual

3. Clicking or selecting a row in the list of runs opens the report for that run. This may
take 2-5 seconds.

Figure 6-6: Example of a Sense Run Report

Reports are divided into three sections. The first section contains:

Run Name
Operator

RainDance ID (machine name)

Tube Strip

The second section contains a summary of how the run performed. It

Channel Pass/Fail

Sample Information

The last section lists the following:

Start Time
End Time

Chip Lot

Chip Serial Number
Carrier Oil Lot

Drive Oil Lot

Run Comments

includes:

LCN 50-04344 Rev. D 6-9

RainDrop Sense Operator’s Manual

4. From the menu bar (see Figure 6-7) you can print the report or export it to various
formats, such as a PDF file or an Excel file.

Figure 6-7: Report Menu

5. When you are done viewing the report, close it by clicking on the Close box in the

upper right corner of the screen. You return to the View Runs window so you can view
additional reports if necessary.

LCN 50-04344 Rev. D 6-10

Chapter 1:

CHAPTER 7

Chapter 7:

Support, Customer Maintenance, and Troubleshooting

This chapter covers the following topics:

RainDance Support page 7-2

RainDance Planned Maintenance page 7-2

Customer Maintenance page 7-2

Restarting the IC Workstation page 7-2

Cleaning the RainDrop Sense page 7-2

7

Refilling the Oil Reservoir page 7-3

Service and Diagnostic Requirements page 7-6

Powering Off the System page 7-6

Powering On or Restarting the System page 7-6

Restoring the System After a Failure page 7-6

Support Agreement Information page 7-7

Moving the System page 7-7

Storing the System page 7-7

Reinstalling/Updating ICS Application page 7-7

Error Messages page 7-7

Troubleshooting page 7-8

LCN 50-04343 Rev. D 7-1

Maintenance refers to non-technical procedures you must perform to keep the system

working properly. Service refers to tasks that are intended to be performed only by a qualified

RainDance-authorized service representative. The RainDrop® System comprises two
instruments: RainDance Source and RainDrop Sense. The sections in this chapter describe
them separately only when each instrument requires different maintenance or service.

RainDance Support

RainDrop Sense Operator’s Manual

RainDance Technologies

Some troubleshooting information is provided within this chapter (see

“Troubleshooting” on page 7-8.). Additional self-service technical and troubleshooting

information is available at www.raindancetech.com/support.

To request technical assistance from RainDance support personnel, send an email to

[e-mail].

®

provides full support for their products.

RainDance Planned Maintenance

A Planned Maintenance (PM) schedule and tasks are designed to be performed by
RainDance Support personnel. A number of PMs are conducted as part of the service
contract agreement. Contact RainDance Support for a recommended PM schedule.

Customer Maintenance

This section lists the steps you should follow for proper maintenance of the RainDrop Sense
system.

Restarting the IC Workstation

Good operating practice for any Windows operating system includes restarting the operating
system on a weekly basis. To perform a shutdown, select the Start icon the lower left corner
of the screen and select Shut down. When the system has completed its power off routine,
reboot the Windows 7 operating system on the IC Workstation as described in

or Restarting the System” on page 7-6.

“Powering On

Cleaning the RainDrop Sense

There is no extraordinary routine maintenance required for the RainDrop instruments. Clean
the chip dock of spills and residues as follows:

Always use protective gloves.

Use only a soft, lint-free towel to clean the chip dock; wet with either isopropanol or

HFE-7100.

For DNA decontamination, RainDance recommends using HFE-7100 or DNA-

ExitusPlus.

LCN 50-04343 Rev. D 7-2

Keep cleaning fluids away from the objective lens.

Caution: Use caution while cleaning the chip dock, specifically in the area of the
lenses of each instrument.

Caution: Never refill an oil reservoir unless the red light is illuminated. Failure to
comply can result in an internal overflow and potential damage to the instrument.

DO NOT submerge the system in liquid or pour or spray liquid onto the system.

Clean the IC workstation monitor window as described in its manufacturer's

documentation.

All technical maintenance or service must be performed by RainDance Support

personnel.

Refilling the Oil Reservoir

The oil reservoir on the RainDrop Sense instrument must be refilled from time to time. You
will know that it is time to refill the reservoir when the oil light on the front of the instrument
glows red.

RainDrop Sense Operator’s Manual

Carrier oil reservoir

fill port

Carrier oil low

indicator light

Drive oil reservoir

fill port

Drive oil low

indicator light

Figure 7-1: RainDrop Sense Oil Reservoir Fill Ports

LCN 50-04343 Rev. D 7-3

To refill the oil reservoir:

RainDrop Sense Operator’s Manual

1. Obtain

2. Sca

a pre-measured syringe of oil (P/N 30-07117).

n the barcode on the oil syringe. Refer to “Scanning Barcodes” on page 2-5 for

more information on how to scan.

3. Remove t

4. Pla

ce a gloved finger over the end of the syringe to ensure that it does not squirt oil

he cap from the tip of the syringe.

while you are moving it.

Figure 7-2: Gloved Finger over Syringe

5. Unscrew the cap that covers the oil reservoir fill port and place it in a safe place.

LCN 50-04343 Rev. D 7-4

RainDrop Sense Operator’s Manual

Caution: Do not overtighten the syringe onto the fill port.

6. Place the tip of the syringe over the fill port and begin to turn the entire syringe

clockwise. The syringe screws onto the fill port to create a tight fit.

Figure 7-3: Syringe Connected to the Fill Port

7. Continue to turn the syringe until it fits snugly.

8. Press the end of the syringe and inject its contents until the syringe is empty.

9. Unscrew

the empty syringe and discard it in a lab-approved solid waste stream. When

you are done refilling the reservoir, the oil low indicator light turns off.

10. Replace

the cover on the fill port. Do not overtighten.

LCN 50-04343 Rev. D 7-5

RainDrop Sense Operator’s Manual

Service and Diagnostic Requirements

The system checks its status at start-up automatically. The ICS application prevents

runs when it detects a system failure or not ready condition.

The hardware is designed to facilitate field replacement of subsystems and/or

subsystem components as required.

There are no user serviceable parts inside the RainDrop instrument. For safety

reasons, those components have limited access.

All technical maintenance or service is provided by RainDance Support.

Powering Off the System

Follow this sequence to turn the system off:

1. Exit the ICS application. Wait 10 seconds.

2. Power off the instrument by turning off the switch on the rear of the instrument.

3. Power off the IC Workstation by selecting the Start icon and then selecting Shut
down.

4. Press the Power button on the monitor to turn it off.

Powering On or Restarting the System

Refer to “Starting the ICS Application” on page 4-2.

Restoring the System After a Failure

In most cases, the RainDrop instruments automatically reset after a failure. You can start
subsequent runs without manual intervention.

LCN 50-04343 Rev. D 7-6

Note: Never start another run until the root cause of the failure is identified and resolved.

Warning: The RainDrop Sense instrument weighs approximately 65 lbs (29 kg). To

avoid injury and damage to the instruments, do not move them without assistance
from RainDance Technologies.

Support Agreement Information

For detailed information on Support Agreements, go to 

www.raindancetech.com/support and click

on the Support Agreement link.

Moving the System

To move the instrument to another location, contact RainDance Support.

RainDrop Sense Operator’s Manual

Storing the System

For short term storage (less than 30 days) of the instruments:

Remove any RainDrop Chips and PCR tube strips from the instruments.

Leave the Carrier Oil and Drive Oil from the last run in the instruments.

Close the door.
Power off the instruments.

For long term storage of the instruments contact RainDance Support.

Reinstalling/Updating ICS Application

The ICS application is installed and tested during installation. You are not required to perform
any installation or maintenance of ICS. Any new version of ICS that is user-installable
includes instructions for installation. If the ICS application files lose their integrity for any
reason (for example, they get accidentally moved or deleted), you can re-install the ICS
application after contacting RainDance.

Error Messages

For current error messages and actions, refer to www.raindancetech.com/support.

LCN 50-04343 Rev. D 7-7

Troubleshooting

The following table lists some problems that you may observe while working with the
RainDrop Sense instrument. The table is divided into three columns as follows:

Observed Problem

Possible Cause

Corrective Actions and Comments

Table 7-1: Troubleshooting the RainDrop Sense Instrument

Observed Problem Possible Cause

RainDrop Sense Operator’s Manual

Corrective Actions and
Comments

There is a red X on the

Instrument Status and Setup
a Run screen.

The ready indicator next to the
Chip Inserted System Status
displays a red X even after I
insert a chip.

The gas pressure is not
connected or is not
adequate.

The instrument does not
detect a properly inserted
chip. The chip is not
inserted properly, may not
be seated well, or is not
aligned with the chip
alignment pins.

Ensure that the gas
pressure cable is
connected properly and
that the gas pressure is
sufficient. Click Start Run.
A dialog box opens listing
the reason(s) the run
cannot start. If you
continue to have problems,
check the Alarms Tab first;
see

Alarms, Log, and
Status Tabs on page 4-14.

Then contact RainDance
Support. See

Support on page 1-3.

The chip sensor will not
detect the chip if there is
an error in the barcode
name. If you have entered
the barcode try scanning
the chip, then placing it in
the instrument. Shut down
the software and
instrument, then restart the
instrument, wait 1 minute,
and restart the software
and scan the barcode
again, then place it in the
instrument. If the chip is
still not recognized, try
another chip and contact
RainDance support. See

RainDance Support on
page 1-3.

RainDance

LCN 50-04343 Rev. D 7-8

Table 7-1: Troubleshooting the RainDrop Sense Instrument

RainDrop Sense Operator’s Manual

The ICS does not display
droplets during a run or
displays an unstable pattern of
droplets.

One of the lanes fails, displays
erratic droplet formation, or
uneven droplet spacing.

There is a white sheen on the
tube strip when I remove it from
the instrument and there is
liquid in the tube strip nest and
the emulsion is not in the tube
as expected.

You have under-filled one
or more sample wells. This
means that there is less
than 25 µL in the
problematic well. The lane
will fail.

Sample may be improperly
sheared, may have too
much DNA, or may have
contaminants such as
fibers that interfere with
droplet formation. Refer to
the RainDrop Assay dPCR
Guidelines for information
in preparing the sample.

Inspect the tube strip to
see if there is a hole in the
bottom of one of the tubes.
This is a rare, but known,
manufacturing defect and
the sample may have
leaked out of the tube.

The run may time out after
50 minutes or it may finish
properly.

The sample in that lane is
lost. Deselect the
corresponding lane on the
Sense run.

The sample is lost. Make
sure the DNA is properly
sheared. Try diluting the
sample and generating
droplets. Filter materials
through a 0.2 micron filter
to remove debris and
contaminants.

Visually inspect tube strips
before using them.

The sample is lost in tube
strip nest and is
unrecoverable. In addition,
you must contact
RainDance Support (see

RainDance Support on
page 1-3) to clean the

instrument to ensure that
the tube strip sensor is
working properly.

The ICS displays unstable
droplet generation, a lower than
expected number of droplets,
or the lane fails.

LCN 50-04343 Rev. D 7-9

The sample was
improperly pipetted and
either is mixed with too
much air or is a bead on
the side wall of the sample
input well.

Sample may be lost. When
you pipette sample, ensure
that you place the tip at the
bottom of the well to avoid
leaving the sample on the
wall of the sample input
well.

Table 7-1: Troubleshooting the RainDrop Sense Instrument

RainDrop Sense Operator’s Manual

One of the lanes does not
display any droplets. In
addition, the run may stop
prematurely if emulsion is not
detected.

The ICS displays a message
telling me that the chip I
inserted has been used before.

The ICS displays a message
telling me that the barcode for
samples is invalid.

Emulsion is not detected
because the emulsion
sensor is tripped. This may
be due to one of the
following:

--the tube strip is dirty

--the tube strip contains
writing in the conical area

--the tube strip was
partially filled prior to your
using it

--there is a static problem
that pulls the emulsion
down the side of the tube

--tube strip is not installed
properly

You are attempting to run a
chip that has already been
run.

You are attempting to use
a barcode format (for
samples) that is not
supported by the barcode
reader.

The sample is lost. In
some cases, you may be
able to recover the sample.
Contact RainDance
Support (see

Support on page 1-3) for

more information.

You must use a new chip
for each run.

You must use a supported
barcode format or
manually enter the
barcode information for
samples. The ICS accepts
a barcode in the 2D Data
Matrix format, which allows
up to 96 characters of text.

RainDance

I am not receiving emails, even
though I have entered an email
address.

You have entered an
invalid email address. The
system does not detect
undelivered emails.

There may be a
connectivity issue with
your network.

If you are not receiving
email messages at the end
of the run, check the email
addresses you have
entered for accuracy.

Check with your IT
department to be sure you
are properly connected.

When setting up a run,
ensure that the Send Run
Emails check box is
selected.

Click the Send Test Email
button to see if you have
solved the problem.

LCN 50-04343 Rev. D 7-10

Table 7-1: Troubleshooting the RainDrop Sense Instrument

RainDrop Sense Operator’s Manual

I tried to fill the oil reservoir
before the oil light came on.

There is dirt, debris, or oil
residue on the instrument.

The sample has evaporated.
The sample volume in one or
more wells is reduced or totally
gone. The droplet count is
lower than expected.

The tube strip or the tube strip
cap was deformed during
thermal cycling and resulted in
a leak into the PCR tube strip
nest of the Sense.

It is possible to overfill the
oil reservoir and to spill oil
into internal areas of the
instrument. You may not
notice it, even when you
have done this.

The instrument has not
been properly cleaned.

The tube strip cap was not
seated properly or the tube
strip was not covered
within 30 minutes of
Source run completion.

For this reason, do not
refill the oil reservoir until
the oil light comes on.

Clean the instrument
according to the
instructions in

RainDrop Sense on page
7-2.

Ensure that the tube strip
cap is seated properly. It
should be even along the
entire length of the tube
strip. An extra cap is
supplied in each kit; if you
find one that does not fit
properly, discard it and use
another.

Do not reuse tube strip
caps. Caps are pierced by
the Sense instrument as
part of the process.
Pierced tube strip caps
allow evaporation and
introduce the potential for
cross contamination.

Cleaning the

Clean the PCR tube strip
nest on the Sense
instrument. Use the
recommended cleaning
protocol. See

RainDrop Sense on page
7-2.

One lane or the entire run has
failed.

LCN 50-04343 Rev. D 7-11

There may be dirt, debris,
scratches, or smudges on
the imaging region of
interest on the Sense Chip.

Handle chip as
recommended in

the Sense Chip on page 2-

6.

Keep the chip dock clean
as described in

the RainDrop Sense on
page 7-2.

Cleaning the

Handling

Cleaning

Table 7-1: Troubleshooting the RainDrop Sense Instrument

RainDrop Sense Operator’s Manual

The Alarms tab or Log tab
displays an error message. The
ICS displays an error message
in a dialog box.

The ready indicator next to the
Chip Inserted System Status
displays a red X even after I
insert a chip.

A known error has
occurred. The ICS may
suggest a way for you to
deal with the error.

The instrument does not
detect a properly inserted
chip. The chip is not
inserted properly, may not
be seated well, or is not
aligned with the chip
alignment pins.

Follow the instructions
provided by the error
message. If no instructions
are provided, verify that the
instrument has power and
verify that all cable
connections are secure.
See

Connecting RainDrop
Sense and Instrument
Controller on page 3-3.

Contact RainDance
Support if the problem is
not resolved. See

RainDance Support on
page 1-3.

The chip sensor will not
detect the chip if there is
an error in the barcode
name. If you have entered
the barcode try scanning
the chip then placing it in
the instrument. Shut down
the software and
instrument, then restart the
instrument, wait 1 minute,
and restart the software
and scan the barcode
again, then place it in the
instrument. If the chip is
still not recognized, try
another chip and contact
RainDance support. See

RainDance Support on
page 1-3.

There is a large leak from the
PCR tube.

The ICS reports a minimal
number of droplets being read.
In addition, you may receive an
email notification that includes
failure information.

LCN 50-04343 Rev. D 7-12

You are using an incorrect
PCR tube strip, meaning
that it is not an Axygen
tube strip.

There is no sample in one
or more lanes. The assay
may be too dim for non­amplified droplets to be
detected.

The sample is lost.

The lane or lanes will fail or
timeout after 30 minutes.
Multiplex your assay or
reorder with a different
quencher.

Table 7-1: Troubleshooting the RainDrop Sense Instrument

RainDrop Sense Operator’s Manual

Some of the expected lanes
were not processed. The
sample remains in the Sense
Chip sample wells.

The data does not appear
where I expect it. The expected
results appear in another lane
or are not detectable at all.

You did not select the
lanes on the Run Data tab
of the ICS (see

the Run Info Tab on page -

15) that represent the

lanes on the Sense Chip
that contain sample.

You may have confused
the lane name with the
physical position of the
sample in the tube strip.

Completing

The sample may be
recoverable, but you
cannot reuse the chip.
Contact RainDance
Support (see

Support on page 1-3) for

help recovering the
sample. In addition, there
is a risk of contaminating
the work area with
amplicon. See

the RainDrop Sense on
page 7-2.

The run proceeds as
normal. Make a note of
which samples have been
switched and address this
issue in downstream
analysis. Use a
multichannel pipettor in the
future to reduce the risk of
mixing up samples.

RainDance

Cleaning

The Sense ICS displays a
lower or higher than expected
droplet count.

The ICS displays a message
telling me that the chip I
inserted has been used before.

The ICS displays a message
telling me that the barcode for
samples is invalid.

You have selected a
droplet count, but the
Sense Instrument is not
delivering what you
requested.

You are attempting to run a
chip that has already been
run.

You are attempting to use
a barcode format (for
samples) that is not
supported by the barcode
reader.

The run proceeds as
normal. It is not always
possible to achieve an
exact number of droplets.

The system is designed to
produce a number of
droplets higher than what
you select to account for
filtering losses.

You must use a new chip
for each run.

You must use a supported
barcode format or
manually enter the
barcode information for
samples. The ICS accepts
a barcode in the 2D Data
Matrix format, which allows
up to 96 characters of text.

LCN 50-04343 Rev. D 7-13

Table 7-1: Troubleshooting the RainDrop Sense Instrument

RainDrop Sense Operator’s Manual

I am not receiving emails, even
though I have entered an email
address.

I am not receiving a text
message at the end of a run
even though I have entered my
phone number into the email
field.

You have entered an
invalid email address. The
system does not detect
undelivered emails.

There may be a
connectivity issue with
your network.

The RainDrop Sense
instrument does not
support text messages.

If you are not receiving
email messages at the end
of the run, check the email
addresses you have
entered for accuracy.

Check with your IT
department to be sure you
are properly connected.

When setting up a run,
ensure that the Send Run
Emails check box is
selected.

Click the Send Test Email
button to see if you have
solved the problem.

You must use a valid email
address for email
notification.

I tried to fill the oil reservoir
before the oil light came on.

There is dirt, debris, or oil
residue on the instrument.

It is possible to overfill the
oil reservoir and to spill oil
into internal areas of the
instrument. You may not
notice it, even when you
have done this.

The instrument has not
been properly cleaned.

For this reason, do not
refill the oil reservoir until
the oil light comes on.

Clean the instrument
according to the
instructions in

RainDrop Sense on page
7-2.

Cleaning the

LCN 50-04343 Rev. D 7-14

Table 7-1: Troubleshooting the RainDrop Sense Instrument

RainDrop Sense Operator’s Manual

The sample has evaporated.
The sample volume in one or
more wells is reduced or totally
gone. The droplet count is
lower than expected.

The tube strip or the tube strip
cap was deformed during
thermal cycling and resulted in
a leak into the PCR tube strip
nest of the Sense.

The tube strip cap was not
seated properly or the tube
strip was not covered
within 30 minutes of
Source run completion.

Ensure that the tube strip
cap is seated properly. It
should be even along the
entire length of the tube
strip. An extra cap is
supplied in each kit; if you
find one that does not fit
properly, discard it and use
another.

Do not reuse tube strip
caps. Caps are pierced by
the Sense instrument as
part of the process.
Pierced tube strip caps
allow evaporation and
introduce the potential for
cross contamination.

Clean the PCR tube strip
nest on the Sense
instrument. Use the
recommended cleaning
protocol. See

RainDrop Sense on page
7-2.

Cleaning the

The Alarms tab or Log tab
displays an error message. The
ICS displays an error message
in a dialog box.

A known error has
occurred. The ICS may
suggest a way for you to
deal with the error.

Follow the instructions
provided by the error
message. If no instructions
are provided, verify that the
instrument has power and
verify that all cable
connections are secure.
See

Connecting RainDrop
Sense and Instrument
Controller on page 3-3.

Contact RainDance
Support if the problem is
not resolved. See

RainDance Support on
page 1-3.

LCN 50-04343 Rev. D 7-15

Chapter 1:

CHAPTER 8

Chapter 8:

Waste Management

This chapter covers the following topics:

Introduction and Disclaimer page 8-2

Classification of Waste page 8-2

Anticipated Typical Waste Stream Composition page 8-3

Recommended Waste Stream Disposal page 8-4

8

LCN 50-04344 Rev. D 8-1

Introduction and Disclaimer

The waste stream from the RainDrop® platform includes fluorocarbon oil-emulsified aqueous
samples and wetted solid materials (PCR tubes, chips, etc.). The following guidelines are
intended to assist the customer in communicating with Environmental Health and Safety staff
and/or commercial waste disposal service providers. The following guidelines are not
definitive. The Customer is solely responsible for complying with applicable laws and
regulations with respect to waste management and disposal.

Important: The Customer must dispose of all waste in accordance with all applicable
environmental laws and regulations.

Classification of Waste

Depending on applicable environmental laws and regulations, the waste stream may

be treated as hazardous chemical waste.

Depending on applicable environmental laws and regulations, the waste stream may

not be classified as mixed hazardous waste.

RainDrop Sense Operator’s Manual

Important: If the DNA sample is classified as infectious by the institution that operates
the RainDrop, it is not considered the normal waste stream. Refer to the institution's
EH&S regulations.

The customer may be required to certify to the chemical waste disposal service

provider that the normal waste stream is non-infectious.

Consult applicable laws and regulations to determine if fluorinated materials present in

the waste stream are regulated.

Customers should consult with local authorities to determine specific state and local

requirements.

LCN 50-04344 Rev. D 8-2

RainDrop Sense Operator’s Manual

Anticipated Typical Waste Stream Composition

During normal workflow operation, for every 96 samples run on the RainDrop Sense system,
approximately 570 grams (20.11 oz) of waste is generated. The following approximate
composition of the waste stream is expected if all consumables and waste reagents are
combined into a single waste stream:

Table 8-1: Solids Appearing in Waste Stream

Sense Waste

Material

Fluorocarbon oil (from Carrier and Drive Oil) 15.3

Amount (wt %)

Fluorosurfactant (from Carrier and

Water 0.8

DNA, polymerase, DNTPs, buffer salts

Commercial polymers (for example,
poly(etheretherketone), polyethylene, polycarbonate,
polypropylene, COC)

Figure 8-1 and Figure 8-2 show images of solid waste.

Drive Oil) 0.4

Trace

83.4

Figure 8-1: Syringe

LCN 50-04344 Rev. D 8-3

RainDrop Sense Operator’s Manual

Figure 8-2: Spent Sense Chip with Tube Strip Attached

Recommended Waste Stream Disposal

Depending on applicable environmental laws and regulations, the waste stream, which

contains fluorinated chemicals, should be incinerated in an industrial or commercial
facility in the presence of a combustible material.

Combustion products will include hydrofluoric acid.

The incineration facility must be capable of handling halogenated – particularly

fluorinated – materials.

Depending on applicable environmental laws and regulations, the non-infectious

aqueous samples and the solid materials (chips, tube strips, and caps, etc.) do not
need to be separated from the fluorinated oil.

Depending on applicable environmental laws and regulations, all components can be

collected in a single container, and the container can be incinerated as miscellaneous
lab debris.

Customers should consult with local authorities to determine specific state and local

requirements.

LCN 50-04344 Rev. D 8-4

Chapter 1:

CHAPTER 9

Chapter 9:

Customer Care Information

This chapter covers the following topics:

General Care Information page 9-2

Consumables page 9-2

9

LCN 50-04344 Rev. D 9-1