SOP-M0281 Rev: 04, Title: Prep Station 5s Installation Procedure, InfoCard Type: Service, Effective Date: 01 Jul 2014

12:05 AM

SOP-M0281-04 Standard Operating Procedure

Prep Station 5s Installation
Title:
Procedure - RUO
Process Owner: Director of Instrument Service

Purpose: This document provides guidance on how to perform procedures necessary to

complete Prep Station Installation Record.

Intended Audience: NanoString installation and field personnel

Needed Material: NanoString Installation Software and Hardware Tools
Knowledge/Training: Familiarity with NPS service tool and nCounter software operation
Related Documents:
1. FRM-M0267 Prep Station 5s Installation Record
2. FRM-M0278 Prep Station 5s Installation and Operational Qualification Form
3. FRM-M0395 Installation Completion and Customer Acceptance Form
4. SOP-M0397 DU Prep Station Incoming Quality Control and Calibration Procedure
Prerequisite Materials
1. USB Keyboard
2. USB Mouse
3. Philips screwdriver
4. P10, P200, and P1000 pipettes and tips
5. nCounter Prep Station Installation Kit #999002

Definitions:
Term Definition
Blank Sample Cartridge A blank sample cartridge is a sample cartridge in which the glass
slide used in not functionalized and therefore is inappropriate for
use in an assay.
Deck The area within the robot accessible to the user which contains
reagents and devices for a single run
Electrode Fixture A movable, mechanical device that fastens to the sample cartridge
stage so that platinum electrodes are aligned within the wells of the
sample cartridge.
GUI Graphical User Interface
Heater Lid The lid covering the heater unit on the deck of the Prep Station
Module Any of the 16 uniquely identified objects in the nCounter
configuration file, config.PSS. Each of these objects could
correspond to a consumable (e.g. SHEATH to tip sheath) or a
section within a consumable (e.g. NanoDevice 0 to wells 1-6 in
Sample Cartridge).
MTP A 96 well plate (empty or filled); known also as Micro Titer Plate
nCounter Prep Station SW which through its GUI allows the user to process
samples as well as to perform simple routines such as those related
to hardware/software maintenance and trouble shooting
NPS Service Tool This SW is intended for use by NanoString engineers and field

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 SOP-M0281 Rev: 04, Title: Prep Station 5s Installation Procedure, InfoCard Type: Service, Effective Date: 01 Jul 2014 12:05 AM

SOP-M0281-04 Standard Operating Procedure

Prep Station 5s Installation
Title:
Procedure - RUO
Process Owner: Director of Instrument Service

Term Definition
personnel. Through its GUI, this SW allows the operator to
complete tasks such as calibrate, check calibration, check
functionality, manage configuration, and perform system
diagnostics
Sample Cartridge A laminated functionalized glass and acrylic device with
approximate dimensions of 25 x 85 x 9mm (LxWxH).
Sample Cartridge Stage The stage where sample cartridge is placed
Sample Tube 12-Well Strip Tube
Shock Sensors Shipping sensors found on an inner wall of the crate. They show if
the crate has experienced a significant shock during the shipment
(see direction on the sensors).
Shroud Green metal covering of the arm
Skin The outer covering of the Prep Station
SW Software
The Arm The mobile unit contained within the green shroud
Tilting Stage The unit consists of the sample cartridge stage as well as the
electrode fixture
Tip Holder The metal rack on which tips are loaded
Tip Sheath Custom 6-tip storage made for the Prep Station
Tip Sensor Shipping Sensor which are placed along two perpendicular side
walls of the crate and indicate if the crate has been tilted
excessively see:
http://www.uline.com/Product/ProductDetail.aspx?model=S-
866&pricode=wb142

General Considerations:
1. Initial every table after completion.
2. The power cord included in the accessories box is a standard 3-prong US power cord. For
installation in countries outside the US with other types of outlets, use the cable provided in
the installation kit.
3. Many labs have color coded power outlets. For example often red outlets indicate that the
power comes from a source with a backup generator. However there often exists a lag period
between a power outage and the backup generator re-establishing the power; such a source
while appropriate for fridges is not considered uninterrupted and therefore not suitable for the
Prep Station. Consult the facility personnel for the best power source available.

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sales rights are expressly reserved. Communication of this information to others is prohibited.
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 SOP-M0281 Rev: 04, Title: Prep Station 5s Installation Procedure, InfoCard Type: Service, Effective Date: 01 Jul 2014 12:05 AM

SOP-M0281-04 Standard Operating Procedure

Prep Station 5s Installation
Title:
Procedure - RUO
Process Owner: Director of Instrument Service

Procedure:
1. Signature Log
1.1 Full name, signature, title and initials of all individuals initialing the form need to be
entered along with date.
2. Approval
2.1 This section is completed by installation supervisor upon the review of the executed
installation checklist and the corresponding document. Completing this section
serves as objective evidence for successful installation and qualification of the
nCounter 5s Prep Station.
3. Instrument Identification
3.1 The serial number for each Prep Station is found on the backside of the unit near the
power input. Record this value in the “Instrument Identification” box after
unpacking the instrument. Initial and date once completed.
4. Site Information
4.1 Record the customer and site information in the form.
5. Crate Contents
5.1 Record the crate contents in the form.
5.2 Ensure the Trash, Liquid waste, tip rack, and power cord are present in the
companion box.
6. Instrument Condition
6.1 Thoroughly assess the crate condition for any dents or damage. Note any visible
damage to the crate on the form. If no damage is present, indicate ‘Pass’.
6.2 Observe the status of the tip and shock sensors. Indicate their status on the form.
6.3 While unpacking ensure these conditions are met and enter P in the corresponding
box of the “Instrument Condition” table. Enter F if the condition is categorized as
failure. Instruction for the course of action to be taken in each failure case is
outlined.
6.4 Any visible damage to the skin components is considered a failure and needs to be
fixed prior to instrument being signed off. However, if the damage is cosmetic and
minor (i.e. could be fixed on-site) in nature, proceed with the installation. At the end
of the installation if it is determined that the damage cannot be fixed with the parts
and tools included in the installation toolkit, arrangements need to be made for
replacement of the damaged component.
6.5 If the arm is not secured tightly with two locks, assess for any physical damage. Run
the range limit test and consider a Pass if it passes the test.
6.6 If the heater lid is secured with tape, ensure that no physical damage is done to the
lid and enter P in the corresponding box. Enter F if otherwise and comment.
6.7 If the electrodes are not aligned, complete align the electrodes using SOP-M0397 as
reference. Following completion of the routine if none of the electrodes are broken
enter P in the corresponding box. Otherwise enter F, do not proceed and contact
NanoString service personnel.
NanoString Technologies Company Confidential
All information contained herein is confidential and proprietary. All design, manufacturing, use, reproduction, &
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 SOP-M0281 Rev: 04, Title: Prep Station 5s Installation Procedure, InfoCard Type: Service, Effective Date: 01 Jul 2014 12:05 AM

SOP-M0281-04 Standard Operating Procedure

Prep Station 5s Installation
Title:
Procedure - RUO
Process Owner: Director of Instrument Service

6.8 Electrode fixture should lock securely with a blank cartridge placed on the stage.
6.9 Verify that the fuse setting matches the outlet specification. If not change the
orientation to match the site specification and enter P.
7. Unpacking and Setup
7.1 Remove the tape securing the door as well as the protective tape on the bottom inner
edge of the door and on the edge of the touch screen panel.
7.2 While accessing the Z-axis motor from the top of the shroud, raise the nozzle by
rotating the Z-axis motor until you can remove the packing material under the
nozzles.
7.3 Remove the packing material from the nozzle head.
7.4 Remove the locks. Store the locks and screws for subsequent shipment.
7.5 Remove tape and packing material which secures the heater lid and the tilting stage.
8. Instrument Start Up
8.1 Attach the power cord to the Prep Station.
8.2 Turn on the instrument. The on/off button is on the back of the instrument near the
power input.
8.3 Ensure that the LCD provides clear and stable (one that does not flicker) picture and
also that the text displayed is readable under ambient light.
8.4 Ensure that the touch screen is responsive and calibrated (i.e. the spot that is touched
is activated).
8.5 Ensure that the USB port to the right of the touch screen panel is functional by
plugging a USB drive and attempting and ensuring that USB is recognized.
9. Software Versions
9.1 The instrument should automatically boot into the maintenance account. Open an
explorer window.
9.2 Select the Start Menu\programs\nanostring\Dual Use Manager
9.3 Record the RUO software version as displayed on the screen in the form. It may also
be obtained through the Maintenance Menu, under Software\About. Compare with
the current released software version. Update as appropriate.
9.4 Select the image of the Prep Station to close the window.
9.5 Launch the service tool and select the about button.
9.6 Record the version of the service tool presented on the screen.
10. PC and Network Setup
10.1 Navigate to the Control Panel and select Date and Time
10.2 Set the date and time as needed
10.3 Close the Control panel
10.4 Under the Start Menu\Programs\NanoString\Dual Use Manager
10.5 Start a 12 sample run but leave the door open.
10.6 Ensure the alarm is audible.
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 SOP-M0281 Rev: 04, Title: Prep Station 5s Installation Procedure, InfoCard Type: Service, Effective Date: 01 Jul 2014 12:05 AM

SOP-M0281-04 Standard Operating Procedure

Prep Station 5s Installation
Title:
Procedure - RUO
Process Owner: Director of Instrument Service

10.7 Cancel the run and close the window by tapping on the image of the Prep Station.
10.8 If the customer requests, connect the instrument with an Ethernet cable to the local
network.
11. Sensor Test
11.1 Launch the service tool application
11.2 Select the Hide status button
11.3 Select the Home button
11.4 Click the “System Test” tab at the top of the service tool window.
11.5 Click the “Sensor Test” button
11.6 Follow the on-screen instructions.
11.7 Manually actuate the maintenance switch on the right side of the instrument.
11.8 At the conclusion of the test, a pie chart is displayed that indicates pass or fail for
each state of the door, heater lid, cartridge, and electrode fixture sensors by color
(Green = Pass, Red = Fail).
11.9 Record the results for these sensors in the Sensor Test table on the form.
12. Calibration Verification
12.1 NOTE: If any modules require adjustment to its teaching positions, follow the
instructions for adjusting the calibration contained within SOP-M0397. Enter any
modifications to the teaching positions in the appropriate boxes on the record. If the
original or adjusted position(s) meet the criteria described in the modules below,
enter ‘Pass’ in the appropriate box on the form. If a position cannot be identified
that meets the criteria, enter ‘Fail’.
12.2 Remove the dry consumables from the installation kit and set up the deck with Tips,
Sheaths, MTPs, Heater tubes, Sample tubes, and a Blank cartridge.
12.3 Tip Modules
12.3.1 Select the ‘Teaching Box’ tab.
12.3.2 Select “Home” from the “Module Name” dropdown menu and then click
the “Go” button. Once in the home position click the “ORG All” button.
12.3.3 Remove the waste bin from the deck.
12.3.4 Select “NEW_TIP1” from the “Module Name” dropdown menu and click
the “Go” button.
12.3.5 Click the “Collect Tips” button under “Commands.”
12.3.6 Select “Home” from the “Module Name” dropdown menu and click the
“Go” button. Once in the home position click the “ORG All” button.
12.3.7 Remove the tips from the tip rack.
12.3.8 Select “NEW_TIP1” from the “Module Name” dropdown menu and click
the “Go” button. Click the “ActionZ” button.
12.3.9 Ensure that the tips are centered in the holes on the tip rack.
12.3.10 If tips are centered, enter “No” under Adjusted and mark N/A under
Motors Adjusted.
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All information contained herein is confidential and proprietary. All design, manufacturing, use, reproduction, &
sales rights are expressly reserved. Communication of this information to others is prohibited.
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SOP-M0281 Rev: 04, Title: Prep Station 5s Installation Procedure, InfoCard Type: Service, Effective Date: 01 Jul 2014 12:05 AM

SOP-M0281-04 Standard Operating Procedure

Prep Station 5s Installation
Title:
Procedure - RUO
Process Owner: Director of Instrument Service

12.3.11 If the tips are not centered use SOP-M0397 as a guide to adjust the
calibration for all of the tip positions.
12.3.12 Once the position is calibrated enter “Yes” under Adjusted and record the
motor adjustments for New_Tip1 under Motors Adjusted.
12.3.13 Place the tips back in the tip rack.
12.3.14 Select “Home” from the “Module Name” dropdown menu and then click
the “Go” button. Once in the home position click the “ORG All” button.
12.4 Sheath Module
12.4.1 Select “Sheath” from the “Module Name” dropdown menu and click the
“Go” button. Click the “ActionZ” button.
12.4.2 Ensure that the tips are centered in the sheath.
12.4.3 If tips are centered, enter “No” under Adjusted and mark N/A under
Motors Adjusted.
12.4.4 If the tips are not centered, use SOP-M0397 as a guide to adjust the
calibration for the sheath positions.
12.4.5 Once the position is calibrated enter “Yes” under Adjusted and record
motor adjustments for Sheath under Motors Adjusted.
12.4.6 Select “Home” from the “Module Name” dropdown menu and then click
the “Go” button. Once in the home position click the “ORG All” button.
12.5 MTP Module
12.5.1 Select “MTP” from the “Module Name” dropdown menu and click the
“Go” button. Click the “ActionZ” button.
12.5.2 Ensure that the tips are centered in the MTP wells.
12.5.3 If tips are centered select the “amove Z 0” button.
12.5.4 If the tips are not centered use SOP-M0397 as a guide to adjust the
calibration for the MTP positions.
12.5.5 Once the position is calibrated enter “Yes” under Adjusted and record the
motor adjustments for MTP under Motors Adjusted.
12.5.6 Select the “Org Z” button. Note the value of the ActionZ on the ActionZ
button.
12.5.7 Select the “Search” button.
12.5.8 Do not confirm changing the “ActionZ” value unless the value is 30 steps
larger.
12.5.9 If the difference is less than 30 enter “No” under Adjusted and mark N/A
under Motors Adjusted.
12.5.10 If the difference is larger than 30 steps, confirm changing the “ActionZ”,
enter “Yes” under Adjusted and record the adjustment under Motors
Adjusted.
12.5.11 Select “Home” from the “Module Name” dropdown menu and then click
the “Go” button. Once in the home position click the “ORG All” button.

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sales rights are expressly reserved. Communication of this information to others is prohibited.
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SOP-M0281 Rev: 04, Title: Prep Station 5s Installation Procedure, InfoCard Type: Service, Effective Date: 01 Jul 2014 12:05 AM

SOP-M0281-04 Standard Operating Procedure

Prep Station 5s Installation
Title:
Procedure - RUO
Process Owner: Director of Instrument Service

12.6 NanoDevice Module

12.6.1 Select “NanoDevice” from the “Module Name” dropdown menu and click
the “Go” button. Click the “ActionZ” button.
12.6.2 Ensure that the tips are centered in the cartridge wells.
12.6.3 If tips are centered select the “amove Z 0” button.
12.6.4 If the tips are not centered use SOP-M0397 as a guide to adjust the
calibration for the NanoDevice positions.
12.6.5 Once the position is calibrated enter “Yes” under Adjusted and record the
motor adjustments for NanoDevice under Motors Adjusted.
12.6.6 Select the “Org Z” button. Note the value of the ActionZ on the ActionZ
button.
12.6.7 Select the “Search” button.
12.6.8 Do not confirm changing the “ActionZ” value unless the value is 30 steps
larger.
12.6.9 If the difference is less than 30 enter “No” under Adjusted and mark N/A
under Motors Adjusted.
12.6.10 If the difference is larger than 30 steps, confirm changing the “ActionZ”,
enter “Yes” under Adjusted and record the adjustment under Motors
Adjusted.
12.6.11 Select “NanoDevice” from the “Module Name” dropdown menu and
change index and item to 1.
12.6.12 Click the “Go” button.
12.6.13 Select the “Org Z” button
12.6.14 Select the “Search” button
12.6.15 Do not confirm changing the “ActionZ”
12.6.16 If the difference between the ActionZ values in 12.6.7 and 12.6.15 is
larger than 5 the standbyS position will need to be updated.
12.6.17 Use SOP-M0397 as a guide to adjust the standbyS position. Make a note
of any adjustments at the end of the record.
12.6.18 Select “Home” from the “Module Name” dropdown menu and then click
the “Go” button. Once in the home position click the “ORG All” button.
12.7 Heater Module
12.7.1 Select “Heater” from the “Module Name” dropdown menu and click the
“Go” button. Click the “ActionZ” button.
12.7.2 Ensure that the tips are centered in the heater tubes.
12.7.3 If tips are centered select the “amove Z 0” button.
12.7.4 If the tips are not centered use SOP-M0397 as a guide to adjust the
calibration for the Heater positions.
12.7.5 Once the position is calibrated enter “Yes” under Adjusted and record the
motor adjustments for Heater under Motors Adjusted.

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sales rights are expressly reserved. Communication of this information to others is prohibited.
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SOP-M0281 Rev: 04, Title: Prep Station 5s Installation Procedure, InfoCard Type: Service, Effective Date: 01 Jul 2014 12:05 AM

SOP-M0281-04 Standard Operating Procedure

Prep Station 5s Installation
Title:
Procedure - RUO
Process Owner: Director of Instrument Service

12.7.6 Select the “Org Z” button. Note the value of the ActionZ on the ActionZ
button.
12.7.7 Select the “Search” button.
12.7.8 Do not confirm changing the “ActionZ” value unless the value is 30 steps
larger.
12.7.9 If the difference is less than 30 enter “No” under Adjusted and mark N/A
under Motor Adjusted.
12.7.10 If the difference is larger than 30 steps, confirm changing the “ActionZ”,
enter “Yes” under Adjusted and record the adjustment under Motors
Adjusted.
12.7.11 Select “Home” from the “Module Name” dropdown menu and then click
the “Go” button. Once in the home position click the “ORG All” button.
12.8 Sample Module
12.8.1 Select “Sample” from the “Module Name” dropdown menu and click the
“Go” button. Click the “ActionZ” button.
12.8.2 Ensure that the tips are centered in the Sample tubes.
12.8.3 If tips are centered select the “amove Z 0” button.
12.8.4 If the tips are not centered use SOP-M0397 as a guide to adjust the
calibration for the Sample positions.
12.8.5 Once the position is calibrated enter “Yes” under Adjusted and record the
motor adjustments for Sample under Motors Adjusted.
12.8.6 Select the “Org Z” button. Note the value of the ActionZ on the ActionZ
button.
12.8.7 Select the “Search” button.
12.8.8 Do not confirm changing the “ActionZ” value unless the value is 30 steps
larger.
12.8.9 If the difference is less than 30 enter “No” under Adjusted and mark N/A
under Motors Adjusted.
12.8.10 If the difference is larger than 30 steps, confirm changing the “ActionZ”,
enter “Yes” under Adjusted and record the adjustment under Motors
Adjusted.
12.8.11 Select “NEW_TIP1” from the “Module Name” dropdown menu and click
the “Go” button.
12.8.12 Click the “Return Tips” button under “Commands.”
12.8.13 Select “Home” from the “Module Name” dropdown menu and then click
the “Go” button. Once in the home position click the “ORG All” button
12.9 Calibration Test
12.9.1 Using the Service Tool application, select the ‘System Test’ tab.
12.9.2 Execute the ‘Calibration Test’ and follow on-screen instructions.
12.9.3 Observe the execution of all of the steps of the test.

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 SOP-M0281 Rev: 04, Title: Prep Station 5s Installation Procedure, InfoCard Type: Service, Effective Date: 01 Jul 2014 12:05 AM

SOP-M0281-04 Standard Operating Procedure

Prep Station 5s Installation
Title:
Procedure - RUO
Process Owner: Director of Instrument Service


A Z-Unit crash or sheath movement during tip collection requires
adjustment of the sheath position and repeating of this test. Adjust the
teaching for the sheath module using SOP-M0397 as a guide and
repeat the calibration test.
 A Z-Unit crash at the cartridge requires adjustment of the NanoDevice
positions using SOP-M0397 as a guide and repeat the calibration test.
 A Z-Unit crash or consumable movement at any of the tip modules
requires adjustment of the corresponding tip module position using
SOP-M0397 as a guide and repeat the calibration test.
12.9.4 Enter any adjustments made after the calibration test into the additional
notes section of the record.
12.9.5 If the Calibration Test attempt completes on the first attempt, or if the
Calibration Test completes after adjustments have been performed, enter
‘Pass’ in the appropriate box on the form.
12.9.6 If adjustments to the positions are unable to produce a calibration test that
completes, enter ‘Fail’.
13. Deck Layout Validation Testing
NOTE: Prior to entering ‘Fail’ for any of the Deck Layout Validation Tests, repeat
testing must first be performed to confirm that the failure is not related to mispositioning
of the consumable. If a repeat failure is observed the X, Y, and Z positions for the
module must be verified using the Service Tool application and adjustments must be
made if necessary using SOP-M0397 as a guide. Any modifications to the taught
positions must be captured in the additional notes section of the record and the test must
be repeated. A ‘Fail’ entry must only be made after repeated attempts to adjust the
module have not yielded a passing result.
13.1 Launch Start Menu\Programs\NanoString\Dual Use Manager
13.2 Deck Layout Validation: Reverse MTP, Trash and Tip Rack Tests
13.2.1 Reverse the orientation of the following: both MTPs, the trash, and the tip
rack.
13.2.2 Initiate a 12 sample run using the GUI.
13.2.3 If the procedure stops at front MTP indicating that the front MTP is lidded
or not positioned properly, proceed to the next step. Otherwise, initiate
failure mitigation.
13.2.4 Reverse the front plate to the correct orientation and press “Resume.”
13.2.5 If the procedure stops at the back MTP, indicating that the back MTP is
lidded or not positioned properly (and if the previous step didn’t fail),
enter ‘Pass’. Otherwise initiate failure mitigation.
13.2.6 Reverse the back plate to correct orientation and press “Resume.”
13.2.7 If the procedure stops at the drain, indicating that the waste bin is rotated,
enter ‘Pass’. Otherwise initiate failure mitigation.
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SOP-M0281 Rev: 04, Title: Prep Station 5s Installation Procedure, InfoCard Type: Service, Effective Date: 01 Jul 2014 12:05 AM

SOP-M0281-04 Standard Operating Procedure

Prep Station 5s Installation
Title:
Procedure - RUO
Process Owner: Director of Instrument Service

13.2.8 Rotate the trash to its correct orientation and press “Resume.”
13.2.9 If the procedure stops at checking the tip rack orientation indicating that
the rack is rotated, enter ‘Pass’. Otherwise initiate failure mitigation.
13.2.10 Press “Abort” and confirm.
13.2.11 Reverse the orientation of the tip rack so that the grey tips are in the front.
13.3 Deck Layout Validation: Lidded MTP Test
13.3.1 Make sure that the MTPs are in their proper orientation and place lids on
both plates.
13.3.2 Initiate a 12 sample run using the GUI.
13.3.3 If the procedure stops at the front MTP check, indicating that the front
MTP is lidded or not positioned properly continue to the next step.
Otherwise enter failure.
13.3.4 Remove the front MTP lid and press “Resume”.
13.3.5 If the procedure stops again at the back MTP indicating that the back MTP
is lidded or not positioned properly and if the previous step didn’t fail,
enter ‘Pass’. Otherwise initiate failure mitigation.
13.3.6 Remove the back MTP lid.
13.3.7 Press “Abort” and confirm.
13.4 Deck Layout Validation: Absent Tips, Heater, MTP and Sample Tests
13.4.1 Remove the following: tip rack, the heater tubes, both MTPs and the
sample tubes.
13.4.2 Initiate a 12 sample run using the GUI.
13.4.3 If the procedure stops at tip check and indicates that the tips are missing,
enter ‘Pass’. Otherwise initiate failure mitigation.
13.4.4 Replace the tip rack and press “Resume.”
13.4.5 If the procedure stops at the heater tube check indicating that the front
heater tubes are missing, enter ‘Pass’. Otherwise initiate failure mitigation.
13.4.6 Replace the front heater tubes and press “Abort” and confirm.
13.4.7 Initiate a 12 sample run using the GUI.
13.4.8 If the procedure stops at the back heater tube check indicating that the
back heater tubes are missing, enter ‘Pass’. Otherwise initiate failure
mitigation.
13.4.9 Replace the back heater tubes and press “Resume.”
13.4.10 If the procedure stops at the front MTP check indicating that the front
MTP is missing, enter ‘Pass’.
13.4.11 Replace the front MTP and press “Resume.”
13.4.12 If the procedure stops at the back MTP check indicating that the back
MTP is missing, enter ‘Pass’. Otherwise initiate failure mitigation.
13.4.13 Replace the back MTP and press “Resume.”

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 SOP-M0281 Rev: 04, Title: Prep Station 5s Installation Procedure, InfoCard Type: Service, Effective Date: 01 Jul 2014 12:05 AM

SOP-M0281-04 Standard Operating Procedure

Prep Station 5s Installation
Title:
Procedure - RUO
Process Owner: Director of Instrument Service

13.4.14 If the procedure stops at the left sample tube check indicating that sample
tubes are not present, continue to the next step. Otherwise initiate failure
mitigation.
13.4.15 Press “Abort” and confirm.
14. Purification Spike Run
14.1 Purespike Dilution: Use the following to prepare a 6 point purification spike
dilution series with the concentrations 1 pM, 0.5 pM, 0.25 pM, 0.125 pM, 0.0625
pM, and 0.03125 pM ending with 100 µl of each concentration.
14.1.1 Retrieve 6 empty 1.5 ml tubes.
14.1.2 Label the tubes 1, 0.5, 0.25, 0.125, 0.0625, and 0.03125.
14.1.3 Dispense 249 µl of 5X SSPE 0.1% Tween 20 into the tube labeled “1.”
14.1.4 Dispense 100 µl of 5X SSPE 0.1% Tween 20 into the rest of the tubes.
14.1.5 Thaw the purification spikes found in the -20oC container, this may take
15 minutes.
14.1.6 Mix 1 µl of purification spikes into the tube labeled “1” gently. Avoid
vortexing the mixture, instead mix by pipetting the solution up and down.
For each transfer use a new pipette tip.
14.1.7 Take 100 µl out of tube 1 and transfer it to tube 0.5 and mix.
14.1.8 Take 100 µl out of tube 0.5 and transfer it to tube 0.25 and mix.
14.1.9 Take 100 µl out of tube 0.25 and transfer it to tube 0.125 and mix.
14.1.10 Take 100 µl out of tube 0.125 and transfer it to tube 0.0625 and mix.
14.1.11 Take 100 µl out of tube 0.0625 and transfer it to tube 0.03125 and mix.
14.2 Orient the 12-well strip tube to have sample 1 on the left.

14.3 Dispense 30 µl of the following mixtures to its corresponding sample tubes using a
new tip for each transfer.
14.3.1 Sample wells 1, 2, and 3: Tube 0.25
14.3.2 Sample wells 4, 5, and 6: Tube 0.125
14.3.3 Sample wells 7, 8, and 9: Tube 0.0625
14.3.4 Sample wells 10, 11, and 12: Tube 0.03125
Note: Tubes 1 and 0.5 are not processed.
14.4 Set the samples in the Prep Station sample holder so that tube 1 is on the left side.
14.5 Store the remaining purification spikes at -20 oC
14.6 Process the samples: Start a 12 sample run with the dilution series
14.7 Ensure that all other items are set properly for a 12 sample run: full rack of tips, two
sheaths, two spun reagent plates, sample cartridge, empty strip tubes in the heater
and sample modules. For detailed directions, follow those provided by the GUI.

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sales rights are expressly reserved. Communication of this information to others is prohibited.
Page 11 of 14

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SOP-M0281 Rev: 04, Title: Prep Station 5s Installation Procedure, InfoCard Type: Service, Effective Date: 01 Jul 2014 12:05 AM

SOP-M0281-04 Standard Operating Procedure

Prep Station 5s Installation
Title:
Procedure - RUO
Process Owner: Director of Instrument Service

14.8 Using the GUI select “start processing.” If you want to skip the detailed instructions
in the “Hybridized Samples” window select “finish,” followed by “select all,”
“finish,” “next” in the “Notifications Options” window and “Start.”
14.9 Ensure that the deck validation completes successfully.
14.10 Completion of Prep Station Processing: The Prep Station will complete the
processing of the sample after approximately 2.65 hours.
14.11 Remove the cartridge from the electrode fixture and seal the wells with the
adhesive film from the installation kit.
14.12 Download the log files for further assessment.
14.12.1Plug the USB drive into the USB port next to the touch screen.
14.12.2Select maintenance>Troubleshoot>DownloadLogs.
14.12.3Select the date.
14.12.4Select download.
14.13 Scan the cartridge on a Digital Analyzer
14.14 Set up a digital analyzer to scan at 280 FOVs using the rlf: n6_vnTrain48.rlf
14.15 Download the Log files from the digital analyzer when scan finishes.
14.16 Data Analysis
14.16.1 Using the most recent nCounter Report Tool, run type 0 (RCC summary)
and type 2 (Reporter Class Summary) report on the MTX files collected.
14.16.2 Open CAL-M0060.
14.16.3 Copy the RCC summary file into the RCC summary tab and the Class
summary file into the Class summary tab.
14.16.4 Record the results in the form.
Note: If there are any failures look into the calculation tabs to determine
cause. If the failure is related to poor pipetting make a note on the form
and remove the data point.
14.17 Temperature
14.17.1 Open the prep station logs
14.17.2 Open the Temperature folder
14.17.3 Open the CSV file with the time stamp that corresponds to the purespike
run.
14.17.4 Identify the maximum and minimum recorded temperatures and record in
the box on the record.
14.18 Voltage
14.18.1 Open the prep station logs
14.18.2 Open the Voltage folder
14.18.3 Open the CSV file with the time stamp that corresponds to the purespike
run.
14.18.4 Identify the maximum and minimum recorded voltage values and record
in the box on the record.

NanoString Technologies Company Confidential

All information contained herein is confidential and proprietary. All design, manufacturing, use, reproduction, &
sales rights are expressly reserved. Communication of this information to others is prohibited.
Page 12 of 14

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 SOP-M0281 Rev: 04, Title: Prep Station 5s Installation Procedure, InfoCard Type: Service, Effective Date: 01 Jul 2014 12:05 AM

SOP-M0281-04 Standard Operating Procedure

Prep Station 5s Installation
Title:
Procedure - RUO
Process Owner: Director of Instrument Service

14.19 Run Duration

14.19.1 Open the prep station logs
14.19.2 Open the Events folder
14.19.3 Open the Process.CSV file with the time stamp that corresponds to the
run.
14.19.4 Observe the start time and run complete time and calculate the run
duration.
14.19.5 Record the run duration in the form.
15. Hardware Check
15.1 Ensure that the shroud is tightly screwed in place.
15.2 Ensure that the side and back panel are tightly screwed in place.
15.3 Lubricate the O-rings
15.3.1 Using the GUI navigate to Maintenance>Hardware>Lubricate O-rings
15.3.2 Follow the directions of the GUI
15.3.3 With a gloved finger apply grease to the O-rings.
15.3.4 If there is any build up on the O-rings, clean them gently using a piece of
lens cleaning paper supplied in the installation kit.
15.3.5 Avoid putting excessive amounts of grease on the O-rings. Special care
must be taken to avoid grease on the nozzle head (i.e. the metal part). If
the nozzle head is accidentally greased, clean with the lens cleaning paper
supplied in the installation kit.
15.4 Ensure the the electrodes are in alignment.
16. Dry Run
16.1 Registry Setting Update
16.1.1 From the Start menu select Run and type regedit. Select OK
16.1.2 Navigate to HKEY_LOCAL_MACHINE\SOFTWARE\NanoString
\nCounter Prep Station\Configuration\Internal Flags\
IncludeBentElectrodeCheck
16.1.3 Change the value from 1 to 0.
16.1.4 Close the registry editor.
16.1.5 Launch the Dual Use Manager.
16.2 Dry Run
16.2.1 Ensure the deck is configured with a set of dry and empty consumables.
16.2.2 Initiate a 12 sample run in the GUI.
16.2.3 Ensure the dry run completes without error.
16.3 Registry Setting Update
16.3.1 From the Start menu select Run and type regedit. Select OK
16.3.2 Navigate to HKEY_LOCAL_MACHINE\SOFTWARE\NanoString
\nCounter Prep Station\Configuration\Internal Flags\
IncludeBentElectrodeCheck
16.3.3 Change the value from 0 to 1.
NanoString Technologies Company Confidential
All information contained herein is confidential and proprietary. All design, manufacturing, use, reproduction, &
sales rights are expressly reserved. Communication of this information to others is prohibited.
Page 13 of 14

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 SOP-M0281 Rev: 04, Title: Prep Station 5s Installation Procedure, InfoCard Type: Service, Effective Date: 01 Jul 2014 12:05 AM

SOP-M0281-04 Standard Operating Procedure

Prep Station 5s Installation
Title:
Procedure - RUO
Process Owner: Director of Instrument Service

16.3.4 Record in the form pass or fail.

17. Final File Backup
17.1 Save a copy of the LogData folder and store in the nanostring DHR.
17.2 Ensure that Solidcore is enabled.
17.3 Save a copy of the configuration and record the configuration name in the form.
17.4 Transfer the configuration to the nanostring DHR.
18. Delete Files
18.1 Delete the dated folders in the LogData folder with earlier dates than the installation
date.
19. Customer Acceptance
19.1 Enter the site name, customer name, and instrument serial numbers in to
FRM-M0395
19.2 Have the customer sign FRM-M0395 Installation Completion and Customer
Acceptance Form.

Revision History:

Rev DCR # Revision Date Summary of Change Author

01 856 11-Nov-2011 Initial release Afshin Mashadi-
Hossein
02 1304 22-Feb-2013 Add section 11 Steve Marriott
03 1523 03-Oct-2013 1. Edit formatting for reading Cory Cole
ease.
2. Move sections around to flow
better with the form.
3. Add the Operational
instructions to reduce the
number of SOPs and forms
during installation.

04 N/A N/A Update the purespike dilution Cory Cole

series to include 2 more
dilutions.

NanoString Technologies Company Confidential

All information contained herein is confidential and proprietary. All design, manufacturing, use, reproduction, &
sales rights are expressly reserved. Communication of this information to others is prohibited.
Page 14 of 14

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 SOP-M0281 Rev: 04, Title: Prep Station 5s Installation Procedure, InfoCard Type: Service, Effective Date: 01 Jul 2014 12:05 AM

530 Fairview Avenue North

Suite 2000
Seattle, WA 98109

Document Number: SOP-M0281

Document Title: Prep Station 5s Installation Procedure

Document Notes:
Update to purespike dilution

Document Information

Revision: 04 Vault: Service_Support-release

Doc Type: Service Status: Release

Date Information

Effective Date: 01 Jul 2014 12:05 AM Release Date: 01 Jul 2014 12:05 AM

Next Review Date: 11 Apr 2018 12:05 AM Expiration Date:

Control Information

Author: CCOLE Owner: pos-Dir Instrument Srvcs

Previous Number: Change Number: CO-00078

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SOP-M0281 Rev: 04, Title: Prep Station 5s Installation Procedure, InfoCard Type: Service, Effective Date: 01 Jul 2014 12:05 AM

Signature Manifest
Document Number: SOP-M0281 Revision: 04
Title: Prep Station 5s Installation Procedure
All dates and times are in Pacific Time.

Gen2 RUO Install Updates

Change Approval

Name/Signature Title Date Meaning/Reason

SENIOR QC/FIELD SERVICE
Cory Cole (CCOLE) 25 Jun 2014, 02:37:26 PM Approved
ENGINE
DIRECTOR OF INSTRUMENT
Steve Marriott (SMARRIOTT) 26 Jun 2014, 03:19:33 PM Approved
SERVICE
VICE PRESIDENT QUALITY
Gary Riordan (GRIORDAN) 30 Jun 2014, 02:36:13 PM Approved
& REGUL
Debra Collins (DCOLLINS) Sr Doc Control Specialist 30 Jun 2014, 04:14:51 PM Approved

Review: SOP-M0281 04

Review

Name/Signature Title Date Meaning/Reason

DIRECTOR OF INSTRUMENT
Steve Marriott (SMARRIOTT) 07 Apr 2016, 03:08:25 PM Reviewed
SERVICE
Sr DocCtrl Spec-Change
Linda Alcorn (LALCORN) 11 Apr 2016, 06:41:10 AM Reviewed
Control

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