GS Junior Installation Manual v1.3 PDF

454 Life Sciences
r
GS Junior
Installation Manual
Version: 1.3 FOR INTERNAL USE ONLY
GS Junior Installation Manual USM-00099.04

Confidential and Proprietary Information – For Internal Use by Roche Only 1 / 61
Not for distribution to Customers
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Table of Contents
Preface ............................................................................................................................. 3
Revision History ......................................................................................................................................... 3
1 Unpacking and Physical Setup............................................................................ 3
1.1 Verification of delivered Items ............................................................................................................ 3
1.2 Unpacking, Inspection and Physical Setup ........................................................................................ 4
2 Attendant PC (Control Unit) Setup .................................................................... 11
2.1 Applying BIOS Settings .................................................................................................................... 11
2.2 Installing the Factory Image ............................................................................................................. 15
2.3 Password Validation ......................................................................................................................... 22
2.4 Installing the GS Junior Software ..................................................................................................... 23
Data Processing SW ................................................................................................................................ 26
Data Analysis SW ..................................................................................................................................... 27
2.5 Installing the Documentation Disk .................................................................................................... 27
2.6 Installing the Third Party Software Disk............................................................................................ 31
2.7 Installing SW Patches ....................................................................................................................... 32
3 Instrument Start-Up and Validation ................................................................... 33
3.1 Arranging Desktop Icons .................................................................................................................. 33
3.2 Instrument Start-Up .......................................................................................................................... 34
3.3 Instrument Upgrade ............................................................................Error! Bookmark not defined.
3.4 Instrument Validation ........................................................................................................................ 38
4 Teleservice Installation, Configuration and Setup ........................................... 42
4.1 Teleservice Installation ..................................................................................................................... 42
4.2 Teleservice Configuration ................................................................................................................. 43
4.3 Teleservice Activation ....................................................................................................................... 49
4.4 Teleservice Activation Test ............................................................................................................... 50
5 XLTF Testfragment-Run ..................................................................................... 53
5.1 Material Preparation ......................................................................................................................... 53
5.2 Set up Procedure .............................................................................................................................. 53
5.3 Results Verification ........................................................................................................................... 59
6 Installation Report............................................................................................... 61

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Preface
Revision History
Version Revision Date Revision Information
1.0 May 2010 First release
1.1 May 2010 - Axeda configuration – password handling revised
- minor additions and corrections
1.2 July 2010 - Monitor & PC setup procedure revised
- Install sequence for Teleservice changed
- minor additions and corrections
1.3 Aug 2010 Accounting for changes for SW patch 2.5p1
Download the GS Junior Installation Report from GRIPS, attached to this manual.
1 Unpacking and Physical Setup

1.1 Verification of delivered Items
Verify that all items listed below have been included in the installation kit.
Update section 1.1 of the Installation Report.
P/N Item Description Qty

05996627001 GS JUNIOR SOFTWARE (Set of 7 disks) 1
05581443001 BUFFER BOTTLE SIPPER (Long sipper tube) 1
05372593001 1000ML STERILE MEDIA BOTTLE 1
05889103001 BDD COUNTERWEIGHT AND ADAPTER KIT 1
05415756001 US Power CORD, 6' 7" 1
05373298001 ZEISS MOISTENED TISSUE Box 1
05582300001 Network CABLE, RJ45 CAT6 7FT 2
05954070001 SIPPER MAINTENANCE KIT 1
05882923001 FUSE, 4A 250 VAC, TIME LAG 2
05934419001 BDD, 21X45 PTP 1
05934427001 Bead Counter 1

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1.2 Unpacking, Inspection and Physical Setup
a. Inspect the condition of the box.
Note any significant damage in section 1.2 of the Installation Report.
b. Open the box as shown below to unpack the instrument
i. Remove the top half of the box to remove the top protection foam
1. 2.
ii. Remove the inner side carton, leaving the instrument accessible for pick up
3. 4.
iii. Remove the plastic from the instrument and place the instrument on a bench top
iv. Remove the camera dampening gasket from the camera door area

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c. Inspect specifically the following items:
Inspection Picture
Inspect the camera door for

proper movement and
closing.
Verify that the camera

faceplate did not incur any
damage during shipping.
Verify that the pump tubing

is routed properly and
installed free of kinks.
Verify the movement of the

sipper manifold.
Note any visible damage that may have incurred during shipping in section 1.3 of
the Installation Report.

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d. Install the buffer tray (the buffer tray is part of the Sipper Maintenance Kit)
e. Install the 10 short sipper tubes on the sipper manifold
1. 2.
Sipper tubes and filters are part of the Sipper Wear gloves when handling the sipper tubes
Maintenance Kit
Tip:
- when right-
handed, start on
left side installing
sippers (as in
picture);
- when left-
handed, start on
right side
3. 4.
Attach each sipper tube to a filter Install the assembly to the sipper manifold
5. 6.
WRONG! Do not hold on the filter CORRECT: Hold by the sipper when tightening white the connection
Note: Tighten the filter assembly to the sipper manifold as tight as possible.

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f. Install the long sipper tube on the sipper manifold
Note: Tighten the connection finger-tight.
Grabbing it by the blue filter, install the long sipper tube to the luer adapter.
g. Unpack the Attendant PC and monitor and inspect for any damage.
Update section 1.3 in the Installation Report.
Note: The instrument has been shipped with US standard power cords. Regional power
cords will have to be purchased separately where required.
h. Set up and connect all components as outlined below

i. Set up the monitor
Disconnect the VGA cable from the monitor

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Attach the DVI cable to the BizLink adapter cable
Connect the DVI and the power cable to the monitor and guide both cables through
the monitor cable support
ii. Set up the Junior instrument

Connect the power cable and the Ethernet cable to the instrument
Ensure that the power switch

is turned OFF
Note: Do not power up the Junior instrument yet.

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iii. Set up the Attendant PC
Connect the monitor cable to the PC
Connect the instrument cable to the PC
Ensure to connect the instrument

cable to the added network card
Connect the keyboard, mouse and power cable to the PC

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Connect the Ethernet cable for the public network to the PC
Ensure that the public network

cable is connected to the port
on the mainboard
Note: DHCP is set per default for the public network port
iv. Plug in all power cables to the wall receptacles.
Note: Do not power up the Junior instrument yet.

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2 Attendant PC (Control Unit) Setup
Select English as operating language.
2.1 Applying BIOS Settings

1. Power up the PC and at the boot prompt hit F10 to enter the BIOS mode
2. Select Advanced -> Processors and set Hyper-Threading to ENABLE

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Accept with F10
3. Select Advanced -> Power-On Options and set POST Messages to ENABLE

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Accept with F10
4. Select Advanced -> Device Options and turn Num-Lock to ON

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Accept with F10
5. Save Changes and Exit the BIOS

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2.2 Installing the Factory Image
1. Insert the Operating System disk and reboot the Control Unit
2. Press Enter at the following screen: (option 1 is already pre-selected)
The process will run for approx. 4 minutes while the installation package is confirming
software checksums.
3. Agree to continue – type y (for yes) – when following screen is displayed
The process will continue running for approx. 20 minutes while the hard drive imaging
operation executes.

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4. Remove the DVD at this point and press Enter at following screen to continue
The PC will now restart and login automatically.
5. Double click on the “RUN_THIS_IMMEDIATELY_AFTER_IMAGING_PC” icon and

acknowledge the pop-up below by clicking OK
6. Acknowledge the following informational pop-up windows (represented by the

screenshots) by clicking <OK>

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7. Follow the instructions to set a password for the adminrig user
8. Retype the adminrig password and click OK
9. A pop-up window will confirm successful completion

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10. Follow the instructions to set a password for the root user
11. Retype the root password and click OK

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12. A pop-up window will confirm successful completion
13. At the following screen, type in a new hostname for the instrument
Note: Use JR as the prefix, followed by the serial number as the hostname,
e.g. JR12345678
14. Confirm with OK two times

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15. Configure the time zone
Open the Time Zone tab and select your time zone from the list, confirm with OK
Note: An Internet connection is required for above procedure.
If no Internet connection is available, follow the workaround below:
a. Select the Network Time Protocol tab and uncheck the tickbox
Uncheck the tickbox

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b. Select the Date & Time tab and set date and time manually
Set date and time manually
16. Confirm with OK and the system will reboot automatically for the settings to take effect.
17. Remove the disk from the disk drive.
Note: If the CD drive does not eject the disk when pressing the Eject button, apply
following workaround:
a. Open a Terminal window: right-mouse-click, select Open Terminal
b. Type: cd / (Enter)
c. Then type: eject (Enter)
d. Close the Terminal window.

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2.3 Password Validation
1. Login as adminrig user
UN: adminrig
PW: enter the pwd that was set before
2. Open a Terminal window: right-mouse-click, select Open Terminal
3. Hit Enter after typing following command: su -
4. Enter the root password and hit Enter
5. Confirm that the console switches to the root user
6. Type in exit and hit Enter
7. Close the Terminal window

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8. Write down both passwords on the paper called ‘User Passwords’
Î The document is intended for end users and can be downloaded from GRIPS. It
is attached to the Installation Manual.
2.4 Installing the GS Junior Software

As adminrig user, follow the steps below:
Note: root access is required to install software. Have the root password handy.
Data Acquisition SW
1. Insert the Data Acquisition disk
2. Once the pop-up window opens, double-click on the setup.sh icon
3. Click on Run when following screen is displayed

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4. Click Next at the Welcome screen
5. Click Next
6. Enter the root password at following prompt

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7. The software is being installed. This might take a few minutes.
8. Click Finish at following screen

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9. Press Enter to close following screen
10. Close any other open windows and remove the disk from the disk drive.
Î see workaround on page 21 if Eject button does not eject the disk
Data Processing SW
1. Insert the Data Processing disk
2. Double-click on the setup.sh icon and follow the instructions on the screen
Note: The installation process is similar to the Data Acquisition installation
3. When the install has completed, remove the disk from the disk drive.

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Data Analysis SW
1. Insert the Data Analysis disk
2. Double-click on the setup.sh icon and follow the instructions on the screen
Note: The installation process is similar to the Data Acquisition installation
3. When the install has completed, remove the disk from the disk drive.
2.5 Installing the Documentation Disk

1. Insert the Data Documentation disk
2. Double-click on the setup.sh icon
Note: Follow the prompts in the installation wizard.

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3. Agree to install Adobe Flash Player when the wizard prompts you to. Click YES.
Attention: An Internet connection is required to install the Adobe Flash Player. If an

internet connection is not available, skip to section 2.6
4. Click OK on following screen
Note: Following message will appear if the PC is not connected to the internet::

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5. Select .rpm for Linux and agree to install
Select .rpm for
Click to proceed
6. You will be prompted to enter the root password at this point. Enter the password and click
OK to proceed. You will then see the following screen. Follow the prompts as shown

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7. Click Install anyway
8. Click OK
9. Click Finish


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2.6 Installing the Third Party Software Disk
1. Insert the Third Party Software disk
Note: The installation via setup icon is not supported with SW 2.5. The software needs to
be installed via terminal window.
2. Open a Terminal window and become root user Î refer to steps 2. -5. in section 2.3
3. Change the directory, by typing
cd /media/454_3rd_Apps_JR_1.0 (Enter)
4. Begin installation, by typing
sh setup.sh (Enter)
5. The installation will proceed to completion.

7. Reboot the computer.
Note: The Teleservice software will need to be installed at a later point in time. Proceed
according to the manual.

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2.7 Installing SW Patches

If applicable, install any software patches. Consult GRIPS for Service Bulletins with
relevant information.
Note the SW version (and patches) installed on the front page of the in the
Installation Report.

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3 Instrument Start-Up and Validation
Login as techuser
UN: techuser
PW: M@5+3rch13F
3.1 Arranging Desktop Icons

Arrange the techuser desktop icons into following groups
Adminrig user group
adminrig-terminal
GS De Novo Assembler
GS Amplicon Variant Analyzer
GS Junior System
GS Reference Mapper
GS Run Browser
Root user group
root-terminal
open-file-browser
Techuser group
Computer
Trash
techuser’s Home

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Techuser Desktop Overview
Techuser user group
Adminrig user group
Root user group
3.2 Instrument Start-Up

1. Double Click the GS Junior System icon on the Desktop to open the sequencer control
GUI.
2. Sign In as Administrator

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3. Switch on the instrument Î the power switch is at the back of the instrument.
4. Wait until the instrument becomes “Available” and the status LED turns solid yellow.
Double-check that the status LED on the instrument also turned solid yellow.
Note:
If the software in the electronics module needs to be upgraded, the GUI will not turn amber,
instead it will turn red. If it turns red perform the steps in the Upgrading Electronic Module
Section.
3.3 Electronics Module Upgrade (E-Box)

1. Click on Proceed to begin the E-Box upgrade.

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2. This will begin a process where the firmware file is copied from the GS Junior
Attendant PC to the GS Junior Sequencer.
3. When the file transfer is complete, the firmware upgrade will launch automatically
and the instrument GUI will change to the following screen:

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4. The firmware upgrade will take about 10 minutes. When the process completes, the
GS Junior instrument GUI status LED will light with a solid amber color and an
instrument self test will automatically execute. The OK button will turn solid blue.
5. Click “OK” to complete the E-Box upgrade.
Once the self test completes, the status indicator will become yellow, the “Start”
button will be active again and all sensor outputs will be respond normally.
6. Open an adminrig-terminal window
7. Change directory to
cd /opt/454/apps/gsSequencer/firmware (Enter)
8.
type following command into the adminrig-terminal
./setInstrumentTimezone (Enter)
9. Close the adminrig-terminal window.

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3.4 Instrument Validation
1. Verify proper functionality of the sensors displayed on the GUI
Specification Set Point

Camera Door Sensor Open / Closed
Ambient temperature when instrument idle
Heater Temperature
36.8°C (+/- 1.5°C) while running a script
Ambient temperature when instrument idle
Chiller Temperature
12°C (+/- 2°C) while running a script
CCD Temperature Target: -25°C (limits: -21°C to -27°C)
Note any deviances in section 2.1 in the Installation Report.
2. Run Instrument Self-Test

Î Remove the ‘Cover Manifold’ and the ‘Cover Valve PCB’ to get access to the valve
PCB (required to see the LED’s on the board).
Î refer to iSDoc for the above procedures
In the GS Sequencer software, click on with the mouse pointer on the instrument
hostname and then click on Recheck to run a self-test
1.
2.

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Check following output:
a) All 12 valves are cycled in at a 1 second interval. Listen for the click of the actuation
and release of each valve and the illumination of the corresponding valve status
LED.
Valve
Status
LEDs
b) The Primary Pump turns slightly forward and then backward, watch for the
movement.
Primary
Pump

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c) The Purge Pump turns slightly forward and then backward, watch for the movement.
Purge
Pump
d) The status LED displays the pattern Green, Yellow, Red, Yellow, Green, Yellow,
Red, Yellow… The pattern repeats for 30 seconds. Make sure all colors are
displayed.
Status
LED
The Self Test function also checks Chiller and Heater thermistors and operation,
Bubble sensor operation and E-Box temperature. These tests don’t require user
attention.
Warnings or errors will be displayed on the GUI if any of the test results are not positive.
Note any warnings or error messages in section 2.2 of the Installation Report.

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3. Reset the sipper tube counter Î refer to iSDoc ‘Clear Sipper Tube Counter’,
chapter Procedures / Service Software
Note the results in section 2.3 of the Installation Report
4. Reset the pump tubing counter Î refer to iSDoc ‘Clear Pump Tubing Counter’,
chapter Procedures / Service Software
5. Check the fans for proper operation Î refer to iSDoc ‘Checking Fans’
6. Perform a camera test Î refer to iSDoc ‘Camera Test’

7. Perform a main pump calibration Î refer to iSDoc ‘Main Pump Calibration’
While the pump calibration script is running, verify that chiller, heater and camera
are reaching target temperatures.
Update section 2.8 of the Installation Report
8. Run a prime volume verification test Î refer to iSDoc ‘Prime Volume Verification’
9. Run a maintenance wash

Note: The short sipper tubes MUST be replaced AFTER the maintenance wash.

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4 Teleservice Installation, Configuration and Setup
4.1 Teleservice Installation
1. Insert the Teleservice disk
Note: The installation via setup icon is not supported with SW 2.5. The software
needs to be installed via terminal window.
2. Open the root terminal
3. Then change directory by typing
cd /media/454_Axeda_JR_1.0 (Enter)
4. Begin the installation by typing:
sh setup.sh (Enter)
5. Once the Axeda Service installation is complete, the following icon will appear on
the desktop:
6. Remove the disk from the disk drive


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4.2 Teleservice Configuration
1. In the root terminal type
/opt/axeda/agent/AxedaAgentConfiguration (Enter)
2. Using the TAB key, select ‘Run an Action’ and hit Enter
3. As Login ID, type in : adminrig
Go to the line below using the arrow down key

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4. Enter adminrig in the ‘Password’ and the ‘Retype Password’ fields . Hit the TAB
key to go to Next and hit Enter
5. Under Customer Code, enter the name of the institution, and go to the next line

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6. Under Lab Code, enter a lab name. Then via TAB key, go to Next and hit Enter
Note: Customer Code and Lab code are mandatory fields. An error message will be
shown if no text is entered.
Note: Country Name and Country Code are preset and cannot be changed.

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7. Enter a valid address, city and zip code. Then via TAB key, go to Finish and hit
Enter
8. Select Quit and hit Enter
9. Ensure to still operate as root user, and type
service AxedaAgent start (Enter)
10. To confirm that the Axeda service is running, type the command below and check
for the output highlighted below
service AxedaAgent status (Enter)

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11. In the root-terminal window type:
gedit /etc/crontab (Enter)
Following file opens:
12. Manually add following two lines at the end of the file. Be careful to avoid any typing
mistakes.
# GS Jr pc settings backup snapshot

* */4 * * * /usr/sbin/pcConfigBackup.sh

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13. Save and exit the file
14. Close the root user terminal
Note: The Axeda Agent service needs to be restarted after every computer reboot.
As root user, type:
service AxedaAgent restart (Enter)
15. Set up the password for the x11vnc session as follows:
a. Open an adminrig-terminal window
b. Type following command to initiate the process:
x11vnc --storepasswd (Enter)
c. When prompted for the password, enter adminrig as the password, hit Enter
d. Re-type adminrig when prompted to verify, hit Enter
e. Then type y (for yes) when prompted as shown below, and hit Enter

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4.3 Teleservice Activation
Note: Teleservice requires a connection to the internet
1. Ensure that the PC is properly connected to the public network (internet)
Ensure that the public network

cable is connected to the port
on the mainboard
2. Ensure that the Junior Attendant PC is running and that the Axeda service
has been restarted since the last reboot Î details see section above
3. The Attendant PC will then automatically register itself on the Axeda server.
Note: This process takes approx. 10 minutes when the network connection
is established.

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4.4 Teleservice Activation Test
1. Logout as techuser and login as adminrig user
2. Double-click the Teleservice icon
Note: there is no noticeable action after double-clicking the icon, but services start
running in the background
3. Using your COE computer, login the Roche network and access the Axeda portal
https://sergate.dia.roche.com
Note: The Axeda serviceLink e-learning is a pre-requisite to get access to the

Axeda server.
4. Login using your COE login credentials

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5. Change the view of the browser by selecting ‘Models’ in the drop-down list
6. Expand the list GS Junior by clicking on the + sign
Alternatively, enter your S/N in the ‘Device’ field and click on Search

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7. Check whether your Junior S/N is listed as an active instrument
If your S/N is not showing up within 10 minutes, check whether your internet
connection is ok, reboot the PC and go through chapter 4.1 and 4.2 again, making
sure every step is completed.
Note the configuration details in section 3 of the Installation Report.
If the Roche network is not accessible at customer site for an immediate check, Level 1
Support (Indy, Penzberg, Shanghai, Tokyo) might be able to assist and check on the
Axeda server whether the instrument has become active.

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5 XLTF Testfragment-Run
5.1 Material Preparation
5.1.1 Reagents
05996554001 GS Junior Titanium Sequencing Kit
Material-# Subkit-Name Storage
05996562001 GS Junior Sequencing Reagents and Enzymes -20°C
05996597001 Sequencing Kit Packing Beads and Supplement CB +4°C
05996589001 Sequencing Kit Buffers Ambient
05996643001 GS Junior Control Bead Kit -20°C

05996619001 GS Junior Titanium PicoTiterPlate Kit Ambient
5.1.2 Tools
• Box with ice for temporary reagent storage
• Magnet Particle Separator
• Centrifuge for 2 ml tubes
• Centrifuge for Bead Deposition Device
• Vortex
• Rotator
• Pipettes (20µl - 1000µl) with according Tips
• Serological pipette
• 10 ml and 25 ml Serological Pipette tubes
• 50 ml conical tube
• Siliconized 1.7 ml tubes
• GS Junior Bead Deposition Device (BDD)
5.2 Set up Procedure

5.2.1 Reagent Preparation:
Material # 05996562001
Remove the sequencing kit reagents and enzymes kit from the freezer.
Remove the tray from the cardboard carton and peel the protective seal from the tray.
Remove the 2.0 ml reagent tubes and place on ice.
Discard the (6 ul) tube if control beads (Black Cap).
Remove the 50 mL conical tube of Substrate and set aside.
Fill tray with room temperature nanopure water until the water is just below the top of the
reagents cassette.
Place the conical tube of Substrate back into the tray.
Place the tray back into the cardboard box and leave at room protected from light.
When the tubes have thawed transfer to +4 C refrigerator.
Material # 05996597001
Remove from carton and place on ice.
Material # 05996589001
Remove Common Buffer from carton and leave at ambient.
Set aside carton at ambient for use later in the prewash steps.
Material # 05996643001
Remove from carton and place on ice.

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5.2.2 Instrument Preparation STEP A

Discarding Materials from Prior Run:
1. Remove used CB Sipper Tube – Change Gloves
2. Remove the used reagents cassette. Empty remaining reagents and discard cassette.
3. Remove the waste bottle from the right position. Empty the waste and discard the bottle.
4. Remove the Common Buffer bottle from the left position. Empty the Common Buffer.
5. Place the empty Common Buffer bottle in the waste position (Right Side).
6. Open the camera door and verify that there is a PTP plate and gasket in place.
Pre-Wash Prep
Material # 05996589001
Obtain the carton and with the remaining items and perform the following:
1. Remove CB Sipper tube from plastic and mount on the Sipper Manifold using clean gloves.
2. Remove pre-wash cassette from plastic.
3. Rinse the 10 tubes mounted in the pre-wash cassette with nanopure water 2 times.
4. Fill the 10 tubes mounted in the prewash cassette with pre-wash buffer. Fill until ~ 1 cm below
each tube top.
5. Mount the prewash cassette.
6. Place the Pre-Wash bottle into the open position on the left side.
7. Lower the manifold and close the instrument door.
Starting the Pre-Wash run

On the computer screen perform the following steps:
1. If required, clear any previous run messages by clicking OK.
2. If required, log into the instrument:
• Click on Operator located at the top left of the screen.
• Select a user name from the list and click “Sign In”.
3. Click on the start button located on the right of the instrument panel.
4. Choose “Sequencing” and then click on the <Next> tab.
5. Click <Proceed> to advance to the Pre-wash step.
6. The GS Junior Sequencer application window will open.
7. Click on <Proceed> to start the Pre-wash and Wait until the indicator light blinks Green before
continuing to the next step.
5.2.3 Site Preparation
Attention:
PPiase Beads and Packing Beads have both GREEN caps
Used Enzymes – Color Chart

Reagent Tube Qty Cap Color
Enzyme Beads 1 Brown
Control Beads 2 Black
Polymerase 1 White
Apyrase 1 Yellow
Polymerase Cofactor 1 Blue
PPiase Beads 1 Green
Packing Beads 1 Green
DTT 1 Orange

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BDD and Gasket Cleaning:
Material # 05996619001
Obtain the gaskets from the kit and the Bead Deposition Device.
Clean the components with Sparkleen solution or nanopure water and let them dry on a Paper
Towel.
If sparkleen is not available wash thoroughly with nanopure water. Change Gloves.
BB2
1. Obtain a 50 ml conical tube and Label it BB2.
2. Using 10 ml serological pipette, add 6.6 ml of Supplement CB to the 1100 ml bottle of the
Common Buffer.
Invert the bottle 10 times to mix.
3. Using a 50 ml serological pipette transfer 40 ml of the Common Buffer mixture to the 50 ml
conical tube.
4. Place on ice.
5. Spin the Apyrase in a microcentrifuge for 5 seconds at 10,000 rpm.
6. Using the 20 ul pipette, add 6.5 ul of Apyrase to the 50 ml conical tube.
Invert 10 times to mix and place on ice.
PicoTiterPlate
Material # 05233682001
1. Remove the PTP kit from the carton.
2. Grasp the PTP by the edges and gently lift to remove the PTP from the packaging.
3. Rest it on the tray.
4. Record the PTP serial number for later use.
5. Assemble the BDD as follows:
• Grasp the PTP by the edges and place the PTP on the BDD base so that the notches
on each are aligned.
• Obtain that BDD gasket and secure the gasket to the BDD using the alignment holes to
orient the gasket.
• Align the top cover of the BDD with the alignment dowels and gently rest the cover over
the assembly.
• Gently apply pressure to the BDD assembly and rotate the latches on either side of the
BDD until the latch clicks into the side groove of the BDD.
• Repeat the process for the other latch.
BDD and Centrifuge Informational Notes:

1. There are 2 holes at the top of the PTP. The larger one is the loading port, the smaller is a vent
hole.
2. When loading the PTP it is recommended to hold the PTP with the loading port resting on the
table and the vent port lifted to create a slight angle of the BDD.
3. If only 1 BDD is being centrifuged, then a counterweight must be used to balance the load in the
centrifuge.
4. All centrifugation will be performed with ambient conditions.
Buffer Layer:
1. Using a 1000 ul pipette, pipette 350 ul of BB2 into the larger hole at the top of the PTP.
2. Place the BDD in a centrifuge and spin for 5 minutes at 1620 rcf (4013 rpm for the Eppendorf
5430).
3. Remove the BDD from the centrifuge and leave resting at room temperature.
Control Bead Prep I:

1. Obtain the Control Beads (black cap) and pipette 50 ul from each tube into a single 1.7 ml tube.
2. Obtain the BB2. Pipette 500 ul of BB2 and add it to the 1.7 ml tube.
3. Place BB2 back on ice.
4. Gently vortex the 1.7 ml tube then incubate for 20 minutes (minimum) on a lab rotator at
ambient.

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Packing Bead Prep:

1. Obtain the Packing beads. (Green cap).
2. Repeat the following steps 3 times to wash the beads:
• Add 1 ml of BB2 to the packing bead tube.
• Gently vortex and then centrifuge at 9300 x g rcf (10,000 rpm) for 5 minutes.
• Rotate the tube so that the white pellet is at the top and remove as much of the fluid as
possible from the tube using the 1000 ul pipette.
3. After the third wash, add 200 ul of BB2 to the tube.
4. Vortex to mix and then place on ice.
Enzyme and PPiase Bead Prep:

In the following steps, it is important that new pipette tips be used for each step to prevent cross
contamination of the beads.
1. Obtain the Enzyme (Brown Cap) and PPiase (Green Cap) Packing beads.
2. Repeat the following steps 3 times to wash the beads:
• Add 1 ml of BB2 to each tube.
• Vortex each tube gently and then mount on a magnetic particle concentrator.
• Wait 30 second and then gently invert the magnetic particle concentrator a few times.
• Wait 30 seconds (or until supernatant is clear) then remove the fluid from the tubes.
• Remove the tubes from the magnetic particle concentrator.
3. Add 400 ul of BB2 to the Enzyme Beads ( Brown cap) tube and vortex. Return to the ice.
4. Add 410 ul of BB2 to the PPiase Beads (Green Cap) and vortex. Return to the ice.
Enzyme Pre and Post Layers:

In the following steps, it is important that new pipette tips be used for each step to prevent cross
contamination of the beads.
1. Obtain two 1.7 ml tubes. Label one Pre and the other Post,
2. To construct the Pre Layer perform the following:
• Add 300 ul of BB2 to the tube labeled Pre.
• Add 110 ul of Enzyme beads to the tube marked Pre.
• Vortex then place on ice.
3. To construct the post layer perform the following:
• Add 180 ul of BB2 to the tube labeled Post.
• Add 230 ul of Enzyme Beads to the tube marked post.
• Vortex then place on ice.
Control Bead Prep II:

1. Retrieve the control bead mixture from the rotator.
2. Spin the tube in a micro centrifuge for 10 seconds at 9300 x g rcf (10,000 rpm) for 10 seconds.
3. Remove 545 ul from the tube.
4. Obtain the Polymerase (white cap) and Polymerase Cofactor (blue cap) tubes in a micro
centrifuge for 5 seconds at 9300 x g rcf (10,000 rpm).
5. Add 40 ul of Polymerase (white cap) to the control bead mixture.
6. Add 20 ul of Polymerase Cofactor (blue cap) to the control bead mixture.
7. Add 65 ul of BB2 to the control bead mixture.
8. Vortex the control bead mixture for 5 seconds.
9. Incubate the control bead mixture on the lab rotator at room temp for 10 minutes (minimum).
10. Add 175 ul of washed and re-suspended Packing Beads (Green Cap) to the Control Bead
mixture.
11. Incubate the control bead mixture on the lab rotator at room temp for 5 minutes (minimum).
Load L1
1. Retrieve the BDD and pipette out as much BB2 as possible from the port hole of the BDD.

GS Junior r
2. Gently vortex the Enzyme Bead Pre-Layer (labeled Pre) for 5 seconds.
3. Load 350 ul of the Enzyme Bead Pre-Layer into the BDD.
4. Centrifuge the loaded PTP device in the BDD for 5 minutes at 1620 x g rcf (4013 rpm).
Prepare the Common Buffer

1. Retrieve the Common Buffer Bottle.
2. Obtain the tube of DTT and vortex vigorously for 5 seconds.
3. Add 1 ml of DTT to the Common Buffer Bottle.
4. Invert 10 times to mix.
5. Obtain the Substrate from the reagents tray.
6. Using a (50 ml) serological pipette transfer 44 ml of Substrate to the Common Buffer bottle.
7. Invert 10 times to mix.
8. Change gloves.
Load L2: Control Beads

1. Retrieve the BDD from the centrifuge.
2. Remove as much supernatant out of the BDD as possible through the port hole of the the BDD.
3. Remove the Control Bead mixture from the lab rotator.
4. Spin the mixture in a centrifuge for 5 seconds at 9300 x g rcf (10,000 rpm).
5. Gently pipette up and down the mixture five times to mix. Avoid spilling or creating bubbles.
6. Load 350 μl onto the PTP.
7. Centrifuge the loaded PTP device in the BDD for 10 minutes at 1620 x g rcf (4013 rpm for the
Eppendorf 5430).
5.2.4 Instrument Preparation STEP B

Priming the GS Junior Instrument
1. Open the instrument door and raise the sipper manifold.
2. Remove the Pre-wash cassette and Pre-wash bottle and discard.
3. Empty the waste bottle on the right and return it to the right position.
4. Change Gloves.
5. Invert the reagents cassette 20 times to mix the contents thoroughly.
6. Carefully remove the caps on all reagents tubes being sure not to pass over other tubes during
the process.
7. Mount the reagents cassette in the instrument.
8. Place the common buffer bottle on the left.
9. Slowly lower the sipper manifold, checking that the sipper tubes become inserted in the reagent
tubes and common buffer bottle.
10. On the instrument panel click on the < Proceed> key to start the instrument prime.

Load L3
1. Change Gloves.
4. Gently vortex the Enzyme Bead Post Layer (labeled Post) for 5 seconds to obtain a uniform
suspension.
Eppendorf 5430).
5.2.6 Instrument Preparation STEP C

GS Junior r
Preparing the GS Junior Instrument Cartridge
1. Lift the instrument door and open the camera door.
2. Remove the used PTP from the PTP cartridge.
3. Use a clean pipette tip to remove the used cartridge gasket.
4. Change Gloves.
5. Wet a Kimwipe with 50% ethanol and then use it to wipe the PTP cartridge.
6. Allow the cartridge to completely air dry.
7. Insert the washed seal.
8. Moisten a Kimwipe with 10% user-pre-pared solution of Tween-20 and wipe the surface of the
PTP cartridge with it.
9. Use a new Zeiss pre-moistened cleaning tissue to gently wipe the camera faceplate.
10. Allow the camera face to completely air dry.

Load L4
1. Change Gloves.
4. Gently vortex the PPiase (Green cap) suspension for 5 seconds to obtain a uniform suspension.
Eppendorf 5430).
5.2.8 The Sequencing Run

Loading PTP Device in the Instrument
1. Remove the PTP device from the BDD by performing the following.
• Rotate down the latches on either side of the BDD to unlock them.
• Carefully remove the top cover.
• Gently lift off and discard the bead loading gasket.
• Remove the PTP device by grasping the edges and lifting it.
2. Gently place the PTP device into the PTP cartridge frame face down and oriented so that the
notches line up.
3. Close the PTP frame making sure that the latch properly engages.
4. Carefully wipe the back of the PTP with a Kimwipe.
5. Close the Camera door and lower the instrument cover.
Setting the Instrument Parameters

1. Enter the barcode of the PicoTiterPlate Device that will be used in this run at the instrument
prompt and click on the <+> key to add it to the information table.
2. Enter any other kit lot numbers and material lot numbers that may pertain to this run and click
on the <+> Key to add the data to the information table.
3. Once done click on <Next>.
4. Enter a run name and select run group then click on <Next>.
5. Choose 200 cycle and click on <Next>.
6. Select “Full Processing for Shotgun or Paired End” and click on <Next>.
7. The Backup Run field will automatically be selected by default. Click on <Next> to continue.
8. Enter any comments about the run that you wish to add and click on <Next>.
9. Click on the <Proceed> button to start the run.

GS Junior r
5.3 Results Verification
1. Switch to the Data tab on the GS Sequencer GUI
2. Expand the instrument tree and select the fullProcessing D_ directory of your run
3. Click on ‘Browse’ to open the GS Run Browser
1.
2.
3.

GS Junior r
4. Open the Control DNA tab, select 400 Base Pairs and check the run results.
1.
3.
2.
3.
Note the run results in section 4 of the Installation Report.

GS Junior r
6 Installation Report
Complete the GS Junior Installation Report and send it via email to:
branford.454_sequencing_support@roche.com
Tip: On your COE machine, open the Address Book in MS Outlook and type in 454 s and
select the address shown below:
Handout the ‘User Passwords’ document to the customer.


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454 Life Sciences

GS Junior Installation Manual USM-00099.04

GS Junior Installation Manual USM-00099.04

1 Unpacking and Physical Setup

Update section 1.1 of the Installation Report.

P/N Item Description Qty

GS Junior Installation Manual USM-00099.04

GS Junior Installation Manual USM-00099.04

Inspect the camera door for

Verify that the camera

Verify that the pump tubing

Verify the movement of the

GS Junior Installation Manual USM-00099.04

e. Install the 10 short sipper tubes on the sipper manifold

GS Junior Installation Manual USM-00099.04

Note: Tighten the connection finger-tight.

Update section 1.3 in the Installation Report.

h. Set up and connect all components as outlined below

GS Junior Installation Manual USM-00099.04

Attach the DVI cable to the BizLink adapter cable

ii. Set up the Junior instrument

Ensure that the power switch

Note: Do not power up the Junior instrument yet.

GS Junior Installation Manual USM-00099.04

Connect the instrument cable to the PC

Ensure to connect the instrument

Connect the keyboard, mouse and power cable to the PC

GS Junior Installation Manual USM-00099.04

Ensure that the public network

iv. Plug in all power cables to the wall receptacles.

Note: Do not power up the Junior instrument yet.

GS Junior Installation Manual USM-00099.04

2.1 Applying BIOS Settings

2. Select Advanced -> Processors and set Hyper-Threading to ENABLE

GS Junior Installation Manual USM-00099.04

Accept with F10

GS Junior Installation Manual USM-00099.04

Accept with F10

4. Select Advanced -> Device Options and turn Num-Lock to ON

GS Junior Installation Manual USM-00099.04

Accept with F10

5. Save Changes and Exit the BIOS

GS Junior Installation Manual USM-00099.04

2. Press Enter at the following screen: (option 1 is already pre-selected)

3. Agree to continue – type y (for yes) – when following screen is displayed

GS Junior Installation Manual USM-00099.04

The PC will now restart and login automatically.

5. Double click on the “RUN_THIS_IMMEDIATELY_AFTER_IMAGING_PC” icon and

6. Acknowledge the following informational pop-up windows (represented by the

GS Junior Installation Manual USM-00099.04

8. Retype the adminrig password and click OK

9. A pop-up window will confirm successful completion

GS Junior Installation Manual USM-00099.04

11. Retype the root password and click OK

GS Junior Installation Manual USM-00099.04

14. Confirm with OK two times

GS Junior Installation Manual USM-00099.04

Note: An Internet connection is required for above procedure.

If no Internet connection is available, follow the workaround below:

Uncheck the tickbox

GS Junior Installation Manual USM-00099.04

Set date and time manually

17. Remove the disk from the disk drive.