Miseq/Miseq FGX System: Installationguide
Miseq/Miseq FGX System: Installationguide
Miseq/Miseq FGX System: Installationguide
InstallationGuide
03 March 2022 • Changed super flat beaded flow cell PN from 15031390S to
15031390.
• Removed Superman as an MTS password.
• Removed password for Windows to reduce security risk.
• Updated name of sample sheet under Set Up a Run Using Local
Run Manager.
• Updated section Record the Software and Firmware Versions:
changed section title to Record the Software Information; revised text
to be more generic; added instruction for FSE to refer to IQ/OQ
for required information; removed instruction to take screen
capture.
• Added new section, After Leaving the Customer Site.
• Updated section Equipment Required for Setup and Testing:
Changed section name to Items Required; added EDS wristband
and cable ties; changed Flow cell, beaded to Flow cell, super flat
beaded; deleted separate rows for beaded and wash flow cells.
Added note that beaded and wash flow cells are in the MiSeq
alignment toolkit.
• Revised UPS installation instructions under Install the Electrical and
Network Connections. Changed network cable to Ethernet cable.
• Added instructions for chilled wash tray to section Check the Chiller
TEC Temperature.
• Moved section Set Up the Computer Environment to end of Setup
chapter.
• Added section to reference optional MiSeq IQOQ.
• Updated Monitor and Analyze the Run on page 76:
• Analyzing the Run section: added step to verify that the
verification run was uploaded to BaseSpace under the correct
instrument serial number.
01 August 2016 • Corrected super flat beaded flow cell part number to 15031390
(was 15031390S).
• Added procedure for bug in MCS software (finding best focus Z -
0.035) prior to running Full Optics Test
• Changed install workflow to improve efficiency and reduce time
to install (see summary of workflow in section "Installation
Workflow").
• Corrected all instances of 0.002 - 0.005 to 0.002 - 0.0005
• Changed instructions to run the MCS Thermal Ramp Test instead
of using MTS to check the flow cell TEC.
• Made the instructions for using the OTT more flexible.
J January 2015 Revised the document so that it can be used for both MiSeq and
MiSeq FGx installations.
Document title: changed to MiSeq/MiSeq FGx Installation Guide
MiSeq FGx-specific information added to these sections:
• Chapter 1:
• About this Guide
• Logins and Passwords
• Equipment Required for Setup and Testing
• About the PhiX Qualification Run (new section added to
Chapter 1; also in Chapter 4)
• Chapter 2: MiSeq/MiSeq FGx Safety
• Chapter 3:
• Inspect the Lab
• Inventory and Inspect the System Components
• Install the Electrical and Network Connections
• Follow the First-Time Setup Screens
• Set Up the Computer Environment
• Final Set Up Activities (also reordered the steps).
• Chapter 4:
• Prepare the PhiX Library
• Start the Run
• Perform a Post-Run Wash
Updated the following information:
• Appendix D: Field Service Repair Kit section: updated the reagent
valve listed the v3 valve.
• Chapters 1 and 4: Table 3 and table 8: Updated the v3 MiSeq
Reagent Kit part number from 15043762 to 15046996 (kit for
internal use only by FSEs/FASs).
• Chapter 1:
• Installation and Qualification Workflow section: swapped the
position of the last two blue rectangles to Perform final installation
tasks followed by Train customer.
• Software Required section: updated the list to include only the
software used by the FSE/FAS to install and service the
instrument.
• Chapter 3:
• Inspect the Lab section: removed the list of laboratory
requirements.
• Combined the instructions under Remove the Protective Cover
with Prepare the Reagent Compartment.
• Removed the section titled: Perform the Remaining Tests.
Instead, the content that was cross referenced by this section
now appears in sequential order.
• Renamed chapters 5, 6 and 7, and reorganized the content. No
changes to the content. Content now organized as Chapter 5:
Adjustment Procedures; Chapter 6: Using MTS; and Chapter 7:
Reagent Delivery.
• Changed the reagent delivery test from manual to using the VCL
function in MTS.
• Updated the procedure Camera 2 Center Adjustment based on the
image now generated by the BoltCameraCenteringD50.exe script.
I May 2014 • Qualification Run: added back the step removed in error from rev
H (step 2, page 44: combine 5 ul of 0.2N NaOH with 5 ul of 4 nM
PhiX library).
• Removed references to the quick reference cards. No longer
shipped with the instrument.
• Revised the appendix, Returning a MiSeq to ILMN, to be more
generic. Also changed the title to Shipping a MiSeq to facilitate
reuse in other documents.
• Chapter 3 changes:
• Removed information under "Inspect the Lab" in Chapter 3.
Readers are now instructed to see the MiSeq Site Preparation
Guide for this information.
• Revised instrument set up instructions in chapter 3. Rev H
included both ship preparation methods (using red lab tape or
white dots). Deleted text and graphics that referred to the red
tape.
H August 2013 • Updated qualification run for v3 chemistry, and the flow cell
description for 19 tiles.
• Updated camera center procedure.
• Added completion of install certification to final tasks.
• Updated art and text to reflect the new appearance of instruments
when removed from the crate.
• Removed the shipping lockdown release video.
• Added extraction tool and level to the alignment toolkit; removed
15027882.
• Updated instrument leveling for the level in the toolkit.
G June 2013 • Added Tween 20 to post run wash list of items required.
• Added reference to WI, Uncrating an Illumin MiSeq or MiSeqDx
System (part # 15041141).
• Updated operating temperature to match site prep guide rev C
(15027615).
• Changed instructions for leveling the instrument.
• Updated the section "About the Instrument Control Computer"
• Updated instructions for moving to center of flow cell in "Adjust
the Rough Z-Motor Position"
• Removed reference to spec under "Determine the Best Focus Z-
Position"
• Added screen capture of focal plane Z position to annotated "Full
Optics Test Results".
• Updated environmental considerations.
• Renamed the System Setup and Qualification chapter to
Instrument Set Up and Testing. Reorganized the content to
improve usability.
• Updated tool kit names and added Fluke meter as separate tool.
F February 2013 • Added instructions for checking the LED power (mW) using MTS
to chapter 3.
• Removed Autofocus test information.
• Revised the instructions for the qualification run and post-run
wash. Added example of sample sheet.
• Updated start up screens to MCS 2.1.13.
• Updated DiagConfig file appendix (updated SW version and
removed autofocus test).
• Added chiller thermistor to repair kit.
• Updated MiSeq Alignment Toolkit (new manifold alignment tool
and fluidics wrench).
• Removed the section "What's New with MiSeq II".
• Removed note re bug in MCS for tip/tilt test results.
B 27 March 2012 • Updated flow cell TEC alignment in the lane rotation adjustment
procedure.
• Added reference in Common Procedures chapter regarding work
instruction that contains instructions for logging cases [Logging a
Standard Case in SFDC WI (15004045)] on SFDC Content.
• Changed type of qualification run to 2 x 101.
• Changed the C channel exposure time from 5000 to 200 ms now
that we don’t need to make thru focus image sets using an OTT.
Added the following:
• Info from installation reports such as a table listing Windows-
based tasks (set time zone; sbsuser password expiration,
windows defender and update disabled).
• Rear adjuster to imaging module component table (item 20),
and changed description of items 18 and 19.
• A note that it’s important to remove droplet from tip of PR2
sipper tube during volume check in MCS.
• Note to chromatism results section regarding saturated pixels.
• New style Z-stage to the Z-Motor Rough Position Adjustment
procedure. Also added instructions to check flow cell surface.
• Appendix describing the DiagConfig file.
• Index.
• Networking guidelines.
Revision History ii
Table of Contents xii
Chapter 2 Safety 8
Safety Information 9
Chapter 3 Setup 10
Items Required 11
Inspect the Lab 12
Inventory and Inspect the System Components 13
Set Up the Instrument on the Bench 14
Position the Instrument 14
Remove the Shipping Bracket and Release the Shipping Lockdowns 14
Prepare the Reagent Compartment 17
Install the Electrical and Network Connections 18
Level the Instrument 18
Install a Keyboard and Mouse 19
Install Workflow 20
First-time Setup Screens 21
First Time Set Up Screens 22
Run the Motion Tests 26
Check Lane Center and Rotation 27
Focus an OTT 27
Check Lane Center and Rotation 30
Test the Optics 32
Run The Full Optics Test 32
Run BoltPAC.exe 36
About Test Results 38
Determine the Best Focus Z–Position 42
Check the LED Power 44
Illumination Footprint Check 45
Check the Chiller TEC Temperature 49
Record the Software Information 50
Check the Reagent Line Delivery Volumes 51
Set Up the Computer Environment 52
Chapter 4 Verification 54
Verification Run Requirements 55
Prepare the Reagent Cartridge 56
Prepare the PhiX Library 58
Thaw and Mix the Reagents 58
Prepare a Fresh Dilution of NaOH 58
Denature and Dilute the PhiX Control 58
Load the v3 PhiX Library into the Reagent Cartridge 59
Perform a Verification Run Using Local Run Manager 60
Appendix A Troubleshooting 84
Imaging Module Components 85
Camera 2 Center Adjustment 87
Check Camera 2 Center 87
Adjust Camera 2 Center 88
Verify the Camera Center Adjustment 90
Camera XY Offset Adjustment 91
Adjust the Y Offset 91
Adjust the X-Offset 93
Verify the XY Offset Adjustment 95
Chromatism Adjustment 96
Run BoltChromatism.exe 96
Adjust L1 97
Compensator Adjustment 99
Flow Cell TEC Thermal Calibration 101
Prepare the Instrument for Flow Cell TEC Calibration 101
Calibrate the Flow Cell TEC 103
Qualify the Flow Cell TEC 105
Illuminated Area Adjustment 107
Prepare the Instrument for Illuminated Area Adjustment 107
Adjust L8 in X 108
Adjust L8 in Y 110
Qualify the Adjustment 112
Lane Center Adjustment 113
Lane Center Adjustment 113
Lane Rotation Adjustment 116
Adjust Lane Rotation 116
Qualify Lane Rotation 118
Check Tip/Tilt 119
Check Tip/Tilt Using MTS 119
Check Tip/Tilt Using the Instrument Control Software 120
Review Tip/Tilt Results 120
Tip/Tilt Adjustment—Camera 2 125
Make Sure that a Tip/Tilt Adjustment is Required 125
Adjust Tip/Tilt 126
Tip/Tilt Adjustment—Camera 1 129
Adjust Tip/Tilt on Camera 1 129
Z-Motor Rough Position Adjustment 131
About Z-Stage Travel and the Compensator 131
Adjust the Rough Z-Motor Position 131
Confirm Focus is on Top of Flow Cell 134
Generate Through Focus Image Sets (Stacks) 136
Move to the Center of a Super Flat Beaded Flow Cell 136
Index 206
Technical Assistance 208
Chapter 1
About this Guide 2
About Installation and Verification 4
About the Instrument Control Computer 7
Purpose
This guide describes how to install the MiSeq and MiSeq FGx instruments at customer
sites. It includes instructions for unpacking, setting up, calibrating, and verifying the
instrument.
Intended Audience
This guide is intended for qualified Field Service Engineers (FSEs) and Field Application
Scientists (FASs). Qualified FSEs and FASs have received the appropriate training, and are
authorized to carry out the procedures described in this guide.
Reference Documents
Use these documents to perform the installation. Refer to these documents for instrument
specifications, to record test results, and for other pertinent information.
Table 1 IQ/OQ Required
Instrument IQ/OQ Required
FSE completes and gives customer only the installation certification; customer does not receive
the IQ/OQ.
fas@forenseq.uas fasDefaultPwFGx
Items Required
Besides the accessories included with the instrument, the items listed here are required for
installation. See Verification Run Requirements on page 55 for verification run requirements.
Table 4 Equipment Required
Item Quantity Part Number
Pipettes and pipette tips (P10 or P20, P200, As required Customer supplied
and P1000)
Software Required
In addition to the software shipped on the instrument, the software listed here are required
for installation. Make sure that the latest versions are installed.
NOTE
Consult with the customer and determine their requirements before making any software
changes. Do not automatically install Local Run Manager on instruments with MiSeq
Reporter. The customer may require MiSeq Reporter. If the instrument has Local Run
Manager installed, but the customer requires MiSeq Reporter, downgrade the instrument to
MiSeq Reporter.
Software Required
Safety
Chapter 2
Safety Information 9
Setup
Chapter 3
Items Required 11
Inspect the Lab 12
Inventory and Inspect the System Components 13
Set Up the Instrument on the Bench 14
Install Workflow 20
First Time Set Up Screens 22
Run the Motion Tests 26
Check Lane Center and Rotation 27
Test the Optics 32
Determine the Best Focus Z–Position 42
Check the LED Power 44
Illumination Footprint Check 45
Check the Chiller TEC Temperature 49
Record the Software Information 50
Check the Reagent Line Delivery Volumes 51
Set Up the Computer Environment 52
A Rails run lengthwise under the front and back of the instrument
B Never grip the flow cell compartment to move or lift the instrument
A Label marked A
B Label marked B
2 Remove the red labels and replace them with the white cosmetic labels taped to the left
side of the instrument.
3 Facing the instrument, unlock the Z-stage by inserting the 5/64 in hex
T-handle Allen wrench through the hole in the red label marked C, and turning it
counterclockwise approximately 2-1/2 turns until it stops.
4 Remove the white dot from the flow cell compartment door and open the door.
5 Use a Phillips head screwdriver to remove the shipping bracket.
6 Close the flow cell compartment door.
Figure 5 Y-Stage Shipping Restraint Bracket
4 Select Save and Continue to accept the defaults, or optionally enter an IP address or
DNS server information.
Figure 10 Network Settings
5 Select Save and Continue to accept the defaults, or optionally change any of the
following fields:
NOTE
Changing any setting on this screen will force the instrument to reboot after the
next screen, where you are prompted to enter a user name and password.
NOTE
The shipping lockdowns must be disengaged, and the shipping bracket removed
before initializing the instrument. If they are not disengaged and removed, severe
damage to the instrument occurs. See Remove the Shipping Bracket and Release the
Shipping Lockdowns on page 14 for more information.
9 Select Stop Test on this screen, then select Yes and Done.
Figure 16 Stop Test
4 At the prompt, insert a super flat beaded flow cell, and select Next.
5 Select from the following:
If … Then …
All the tests pass 1. Select Export Results, and save the results
to the USB drive. Then select Done.
2. Enter the results on the IQ/OQ.
Focus an OTT
NOTE
If you see nothing in tiles 1 through 3, the OTT is loaded backwards.
1 Close the instrument control software, and launch MTS.
2 Initialize and home the instrument.
3 Load an OTT.
4 Go to the Motor tab.
5 Open the Tile drop-down list and select tile 6; then click Move to Tile.
6 Set the Mirror Position to Normal for Imaging.
Clicking the Flip button toggles between Normal for Imaging and Tilted for Focusing.
7 Enter –0.17 in the Z Motor Position field, and hit Enter.
This value represents the optimal Z-motor position.
Figure 18 Motor tab
b Click Zoom All, then click Contrast to view the image, and look for a small black
crosshair.
— If the image is not usable, try the following:
— Adjust the exposure time (for example, 400, 600).
— If the G channel is not usable, try other channels and exposure times until
the image quality is acceptable. You can also try using Camera 1.
— If no black crosshair is visible, try moving the upper and lower contrast bars.
NOTE
The Contrast button in the Image pane works as follows:
1. It measures the foreground and background based on the Z-motor position.
2. It adjusts the contrast to what it calculates as best focus.
If the Z-motor position changes by a large value, or changes several times, click the
Contrast and the Zoom All buttons again to “reset” the software for the new position.
Also click these buttons if you adjusted the position and no image is displayed.
11 Select the Motor tab, and focus the image as follows:
a Zoom in on the cross.
b Move the Z-motor up or down to bring the cross into good focus.
Increments of 0.002–0.0005 typically work well.
Out of spec for lane center 1. Adjust lane center by following the instructions
under Lane Center Adjustment on page 113.
2. Record the lane center values on the IQ/OQ.
3. Proceed to the next step.
Out of spec for lane 1. Adjust lane rotation by following the instructions under
rotation Lane Rotation Adjustment on page 116.
2. Record the lane rotation value on the IQ/OQ.
3. Change the exposure value back to 200 (Camera tab).
6 Using the wheel on the mouse and the sliders, zoom in on an area of beads.
See Image Tab in the Right Pane on page 143 for additional information.
Figure 29 Example of Well Focused Beads
7 On the Motor tab, bring the beads into sharp focus by moving the Z Motor up or down.
Increments of 0.002–0.0005 typically work well.
8 Record the value, and confirm that it is within spec.
9 Turn off the camera.
Run BoltPAC.exe
1 Generate through-focus image stacks for both surfaces of the flow cell using the center
of a super flat beaded flow cell (see Generate Through Focus Image Sets (Stacks) on page
136).
2 Minimize MTS.
3 Go to C:\Illumina | MiSeq Control Software | MatlabScripts.
Or go to the release scripts folder on the D drive.
4 Double-click the script to open a window with a command prompt.
5 Go to the D drive and open the folder you created for the top surface through-focus
image set.
7 Hit Enter.
A BoltPAC status bar is displayed while the script is running. The script runs for
approximately 40 min.
NOTE
If BoltPAC repeatedly fails, make sure that the proper file naming convention is being
applied to the 41x4 image generated. Sometimes the software can name one or more of
the files incorrectly, causing the script to fail.
8 Run BoltPAC again using the bottom surface through-focus image set.
e Move the right slider all the way down, and make sure that beads appear across
the bottom of the image (no blank strip across the bottom of the image).
9 Select from the following:
Within spec The illumination footprint is OK, record the result on the
IQ/OQ.
Out of spec Adjust the illuminated area until it is within spec (See
Illuminated Area Adjustment on page 107).
If the temperature
Then …
is …
Out of spec 1. Check the ambient temperature of the lab. If it is out of spec, ask
the customer to adjust the lab temperature. Then requalify the
chiller temperature.
2. If the ambient temperature of the lab is within spec, contact
Illumina Technical Support.
If using … Then …
MTS 1. Follow the instructions listed under Manually Check Reagent Delivery on
page 149.
2. Troubleshoot any lines with volumes that are out of spec.
3. When delivery for each line meets spec, note the result on the IQ/OQ.
MCS/MiSeq FGx 1. Fill the wash tray and the PR2 bottle with DI water, and load onto the
Control instrument.
Software 2. In the control software, run Prime Reagent Lines and Conduct
Volume Test.
3. Troubleshoot any lines with volumes that are out of spec.
4. When delivery for each line meets spec, note the result on the IQ/OQ.
CAUTION Speak with the on-site IT professionals. Advise them that the
Make sure that the network setting for Windows Updates must be turned off.
network setting for If turned on, Windows Updates override the instrument and
Windows Updates is forces it to reboot. If a run is in progress, the run fails.
turned off.
Task How To
If Local Run Manager is 1. Launch Chromium from the desktop, and log in to Local
installed on the Dx SSD, Run Manager (User Name=admin; Password=password).
create an 2. In the Local Run Manager dashboard navigation bar,
administrative select System | User Management.
customer account.
3. Select Create User in the User Management page.
4. In the Create New User field, enter first and last names,
user name, and password information. The password is
temporary, and is reset at initial login.
5. Toggle to Admin in the Role field by clicking User, then
select Create User and Continue.
6. Log out of Local Run Manager, and close the Chromium
browser.
7. Provide the customer the newly created user name and
temporary password and have them test the account log
in. Direct them to the Local Run Manager Software Reference
Guide for MiSeqDx (1000000011880).
Make sure that the Open folder and make sure that the CloudAPIKey.xml file is
CloudAPIKey.xml file present:
is present and ensure Dx: C:\ProgramData\Illumina\MiSeq
the serial number in RUO: C:\ProgramData\Illumina\MiSeqControlSoftware
this file matches the
serial number of the Note: Program Data may not show--select Hidden Items
instrument. from View tab of file explorer
Synchronize the See Synchronize the Instrument with an Internet Time Server
instrument with an on page 1.
internet time server
Verification
Chapter 4
Verification Run Requirements 55
Prepare the Reagent Cartridge 56
Prepare the PhiX Library 58
Perform a Verification Run Using Local Run Manager 60
Perform a Run Using MiSeq Reporter 70
Perform a Post-Run Wash 78
Pipettes and pipette tips (P10 or P20, P200, As required Customer supplied
and P1000)
4 Allow the reagent cartridge to thaw in the room temperature water bath for at
approximately 60 minutes or until thawed.
5 Remove the cartridge from the water bath and gently tap it on the bench to dislodge
water from the base of the cartridge.
6 If not using the reagent cartridge immediately, place on ice or in 4° C refrigerator.
7 Invert the reagent cartridge ten times to mix the thawed reagents.
8 Visually inspect the USM-2 and IMT-1 reagents to make sure that they are fully mixed
and free of precipitates.
9 Gently tap the cartridge on the bench to remove air bubbles in the reagents.
WARNING
A component in this set of reagents contains formamide, an aliphatic amide that is a
probable reproductive toxin. Personal injury can occur through inhalation, ingestion,
skin contact, and eye contact.
Dispose of containers and any unused contents in accordance with the governmental
safety standards for your region.
The SDSs for this kit are available at www.illumina.com/sds.
Table 11 Reagent Cartridge Map
Position Reagent Position Reagent
3 Lightly rinse the flow cell with labaoratory-grade water until both the glass and plastic
cartridge are thoroughly rinsed of excess salts.
Excess salts can affect flow cell seating on the instrument. If salt drys in the imaging
area, imaging can also be affected.
Figure 60 Rinse the Flow Cell
4 Using care around the black flow cell port gasket, thoroughly dry the flow cell and
cartridge with lint-free lens cleaning tissue; gently pat dry in the area of the gasket and
adjacent glass.
5 Clean the flow cell glass with an alcohol wipe, making sure that the glass is free of
streaks, fingerprints, and lint or tissue fibers.
NOTE
Do not use the alcohol wipe on the flow cell port gasket. Make sure that the
cartridge is securely closed before use.
5 Gently press down on the flow cell clamp to close it over the flow cell.
As the flow cell clamp closes, alignment pins position the flow cell. An audible click
indicates that tthe flow cell clamp is secure.
A Reagent cartridge
B PR2 bottle
C Waste bottle
4 Select Next to exit the Sequencing screen and proceed to the post-run wash.
3 Lightly rinse the flow cell with labaoratory-grade water until both the glass and plastic
cartridge are thoroughly rinsed of excess salts.
Excess salts can affect flow cell seating on the instrument. If salt drys in the imaging
area, imaging can also be affected.
Figure 69 Rinse the Flow Cell
4 Using care around the black flow cell port gasket, thoroughly dry the flow cell and
cartridge with lint-free lens cleaning tissue; gently pat dry in the area of the gasket and
adjacent glass.
5 Clean the flow cell glass with an alcohol wipe, making sure that the glass is free of
streaks, fingerprints, and lint or tissue fibers.
NOTE
Do not use the alcohol wipe on the flow cell port gasket. Make sure that the
cartridge is securely closed before use.
5 Gently press down on the flow cell clamp to close it over the flow cell.
As the flow cell clamp closes, alignment pins position the flow cell. An audible click
indicates that tthe flow cell clamp is secure.
A Reagent cartridge
B PR2 bottle
C Waste bottle
Leave the used flow cell in the instrument when the run has finished. Use it for the post-
run wash.
4 Select Next to exit the Sequencing screen and proceed to the post-run wash.
Items Required
Table 12 Items Required for Post-Run Wash
Items Quantity Part Number
Chapter 5
Final Installation Tasks at the Customer Site 81
After Leaving the Customer Site 82
Troubleshooting
Appendix A
Imaging Module Components 85
Camera 2 Center Adjustment 87
Camera XY Offset Adjustment 91
Chromatism Adjustment 96
Compensator Adjustment 99
Flow Cell TEC Thermal Calibration 101
Illuminated Area Adjustment 107
Lane Center Adjustment 113
Lane Rotation Adjustment 116
Check Tip/Tilt 119
Tip/Tilt Adjustment—Camera 2 125
Tip/Tilt Adjustment—Camera 1 129
Z-Motor Rough Position Adjustment 131
Generate Through Focus Image Sets (Stacks) 136
About MTS 141
Manually Check Reagent Delivery 149
3 M3 Focus 13 F4
(Sensor 1 X/Y tilt)
4 Red LED 14 M4
5 Green LED 15 M1
21 Compensator
If the … Then …
Top-bottom value and/or the left-right Adjust camera 2 (see Adjust Camera 2
value is > 0.20 μm Center on page 88).
Equipment Required
} Indelible marker or other type of marker
} Vertical adjustment tool
Procedure
TIP
Using an indelible marker or other type of marker, draw a line to use as a reference before
making an adjustment.
1 Remove the instrument skins.
2 Adjust camera 2 in the X direction as follows:
a Loosen the X-axis lockdown screw (Figure 82 on page 89).
b Move the camera left or right towards the highest left-right value.
Example Figure 83 on page 89:
Because 1.91 is the highest left-right value; you would move the camera left.
c Tighten the X-axis lockdown screw.
d Run BoltCameraCenteringD50.exe and review the image.
e Continue adjusting the camera position and rerunning
BoltCameraCenteringD50.exe until camera center is within spec.
3 Adjust camera 2 vertically as follows:
a Install the vertical adjustment tool shown in Figure 82.
b Loosen the Y-axis lockdown screw.
c Turn the micrometer on the adjustment tool so that the camera moves in the
direction of the highest top-bottom value.
NOTE
If turning the micrometer counterclockwise, move up the camera flush against the
tool before tightening the Y-axis lockdown screw.
Example Figure 83:
Because 1.97 is the highest top-bottom value; you would move the camera down.
d Tighten the Y-axis lockdown screw.
e Run BoltCameraCenteringD50.exe and review the image.
f Continue adjusting the camera position and rerunning
BoltCameraCenteringD50.exe until camera center is within spec.
NOTE
In this particular image, the camera is already centered. The image is being used to
illustrate the direction in which you would move the camera when center is out of spec.
Equipment Required
} Cam adjustment tool (for camera X-offset)
} Camera vertical adjustment tool
To the left 1. Place the cam adjustment tool in 1 of the holes to the right
of the camera (Figure 89 on page 95).
2. Turn the tool clockwise to push the camera to the left.
3. Cover the imaging module with a blackout cloth.
4. View the image, and make further adjustments until the
target is on the cursor.
Be sure that the appropriate camera is turned off.
5. Tighten the lockdown screw.
To the right 1. Place the cam adjustment tool in 1 of the holes to the right
of the camera.
2. Turn the tool counterclockwise 1/4 to 1/2 turn to create a
space, leaving the tool in place.
3. Move the camera to the right up against the tool.
4. Cover the imaging module with a blackout cloth.
5. View your image and make further adjustments until the
target is on the cursor.
Be sure that the appropriate camera is turned off.
6. Tighten the lockdown screw.
Equipment Required
} L1 adjustment tool
} Phillips screwdriver
Run BoltChromatism.exe
1 Load a super flat beaded flow cell.
2 Using MTS, move to any tile.
3 Generate 2 through-focus image sets (top and bottom of flow cell).
You can use any tile to extend the life of the flow cell. See Generate Through Focus Image
Sets (Stacks) on page 136.
4 Run BoltChromatism.exe for each image set.
See Running Scripts in MTS on page 144 for instructions.
5 View the results files.
A in Figure 90 indicates that the instrument has 15 microns of chromatism.
6 If chromatism is out of spec, adjust L1 as recommended in the last line of the results
file (B in Figure 90).
IMPORTANT
BoltPAC.exe chromatism results include only the information in the row labeled A in
Figure 90. The direction (negative or positive sign) of the recommended correction is the
opposite of the correct direction. BoltChromastism.exe results include the information in
rows A and B. The direction of the adjustment in the row labeled B is correct.
A BoltChromatism.exe result
B Adjustment recommended to improve chromatism
Adjust L1
1 Remove the instrument skins.
2 Install the L1 adjustment tool as follows:
a Make sure that the micrometer is installed as shown in Figure 91 so that you can
use the horizontal line on the barrel as a reference when turning the knob. Loosen
the nut to reposition the barrel.
b Position the tool in groove on base plate.
c Loosely tighten the adjustment tool lockdown screw.
d Tighten the micrometer to the point where it touches the lens and the ball spring is
slightly compressed.
e Lock down the tool.
Figure 91 L1 Adjustment Tool Installed
5 Tighten the lens lockdown screw, and back out the micrometer.
6 Reinstall the optical covers (no need to tighten them down).
7 Cover the imaging module with the blackout cloth.
8 Generate new through-focus image sets.
9 Run BoltChromatism.exe and assess the results.
10 Select from the following:
A Compensator adjuster
B M3 screw
C M4 screws
6 Holding the compensator firmly against the Z-stage, tighten down the M4 screws.
7 Make sure that the compensator is firmly in place by trying to move it.
8 Using MTS or the sequencing instrument, check tip/tilt on the bottom surface of a super
flat beaded flow cell.
Equipment Required
} Flow cell, open end
} Fluke meter
} Kapton tape
c When the graph has stabilized, record the Fluke meter reading.
d Deselect Enable.
4 Determine the high measured temperature as follows:
a Enter 96 in the Target field, and click Set.
b Select Enable.
c When the graph has stabilized, record the Fluke meter reading.
d Deselect Enable.
5 Calibrate the flow cell TEC as follows:
a In the Calibration pane, make sure that 16 and 96 are the values displayed in the
Low and High Target fields.
b Enter the Fluke meter readings in the Low and High Measured fields.
6 Do the following:
a Repeat step 3. Make sure that the value is 16° C ± 2° C.
b Repeat step 4. Make sure that the value is 96° C ± 2° C.
c If the either of the values is not within spec, the TEC was not calibrated. Repeat
this procedure.
7 Enter these values in the MiSeqOverride.cfg file:
a The high measured temperature from the Fluke meter that you entered into MTS to
calibrate the flow cell TEC (step 4).
b The low measured temperature from the Fluke meter that you entered into MTS to
calibrate the flow cell TEC (step 3).
c Save and close the file.
Figure 98 Measured High and Low Temperatures in the MiSeqOverride.cfg File
Out of spec Calibrate the flow cell TEC as described under Flow
Cell TEC Thermal Calibration on page 101.
Notice the X value on the right side of the image is 3212, which is < 3620.
Figure 101 Illuminated Area Out of Spec in X
3 If you are unable to bring the illumination area into spec by adjusting L8:
a Measure the LED power as described under Check the LED Power on page 44.
b If the power is too low, replace the LED assembly.
4 Attach CSV files for both surfaces to the work order.
5 Complete the post-service call tasks (Completing Post-Service Call Tasks on page 1).
Equipment Required
} Blackout cloth
} OTT
3 Cover the imaging module with the blackout cloth, making sure that the cloth does not
cover the rear fan.
Equipment Required
} OTT
} Beaded flow cell
} Y-stage alignment tool
} 2.5 mm and 3 mm Allen wrenches
} Phillips head screwdriver
6 Using a flat head screwdriver, carefully move the TEC so that the 3 TEC alignment
pins are seated up against the alignment tool.
A Carefully insert the flat head screwdriver in these slots to move the TEC
If using … Then …
MTS Navigate to the results folder that you created earlier for each
through-focus image set, double-click the image for Camera 1,
and assess the results.
If using … Then …
The circle is essentially a level. The point on the end of the line represents the bubble. If the
bubble falls outside of the circle, the instrument is out of spec for tile tilt. Here are examples
of what you might see and the type of adjustment required.
Figure 119 Tip/Tilt Images and Results File
If tip/tilt is … Then …
out of spec and a manual 1. Review the Brenner Metrics images to make sure that
adjustment are required the through-focus image set was generated
successfully (Review the Brenner Metrics Images on
page 122).
2. If tip/tilt must be adjusted, follow the instructions
listed under:
• Tip/Tilt Adjustment—Camera 2 on page 125 or
• Tip/Tilt Adjustment—Camera 1 on page 129
Figure 122 illustrates failed through-focus image set generation. A graph with this
appearance can be caused by not optimizing the Z-motor position before generating the
through-focus image set. Repeat the procedure listed under Generate Through Focus Image
Sets (Stacks) on page 136 to optimize the Z-motor position and generate a new set of
through-focus images. Then run BoltTileTilt.exe again.
Figure 122 Failed Through Focus Image Set Generation Due to Instrument Vibration
If … Then …
the results indicate that tip/tilt is out of continue to Adjust Tip/Tilt on page 126.
spec
A Back actuator
B Front actuator
6 Tighten all of the lock screws to barely snug (do not fully tighten).
a Gently tighten down each screw the same amount until barely snug.
b Gently tighten down each screw a little more by the same amount.
c Finish tightening down each screw.
IMPORTANT
Never fully tighten down one screw at a time. Tilt is reintroduced if the screws are fully
tightened down 1 at a time.
7 Refocus the beads (Motor tab in MTS). If the rough focus is out of spec, adjust the Z-
motor rough position (Adjust the Rough Z-Motor Position on page 131.
8 Enter the new Z-motor value in the Focus tab.
9 Run the tip/tilt test again for both surfaces of the flow cell (Check Tip/Tilt on page 119).
10 If tip/tilt is still out of spec, select from the following:
If tip/tilt … Then …
Is out of spec for the top surface of the flow Return to step 3 and repeat this procedure.
cell
Passes for the top surface of the flow cell, but 1. Adjust the compensator (Compensator
is out of spec for the bottom surface Adjustment on page 99).
2. Repeat this procedure for the bottom
surface only.
A Screw actuator
B Cam actuator
C Locking screw
3 Load a super flat beaded flow cell and move to the center of the flow cell.
Center = actualedgeofslide + 14 mm
4 Cover the imaging module with a blackout cloth.
5 Run the test again on both surfaces of the flow cell (Check Tip/Tilt on page 119).
6 Repeat steps 2 through 5 until tip/tilt is within spec.
7 If the cam actuator was rotated, lock it down now.
8 Run the tip/tilt test again for both surfaces of the flow cell, and make sure that tip/tilt is
still within spec.
9 If any settings were modified (eg, camera exposure, LED current), restore the default
values now.
10 Reinstall the instrument skins.
b Open the MiSeqOverride.cfg file and find the value for actualedgeofslide.
A Adjustment screw
B Straight and angled lockdown screws
C Insert Allen wrench through this opening to loosen the angled lockdown screw
Beads that are in You are on the bottom surface of the flow cell. Confirm by
relatively good focus 1. Click the up arrow one time to move back to the top
surface (correct result: you still see focused bead clusters.).
2. Click the up arrow 1 more time. Correct result: No bead
clusters are visible.
The Z-motor position is OK.
If the beaded flow cell is focused on the wrong (bottom) surface of the flow cell, a Brenner
graph similar to Figure 136is generated.
Figure 136 Brenner Graph Indicating Z-Stage Focused on Wrong (Bottom) Surface
Find Best Focus on the Top or Bottom Surface of the Flow Cell
NOTE
When generating an image stack for the bottom surface of the flow cell, it is good practice to
focus the beads on the top surface first. Then move the compensator in, and focus the beads
on the bottom surface of the flow cell.
1 On the Motor tab, set the Mirror Position to Normal for Imaging.
2 Type –0.17 in the Z Motor Position field, and hit Enter.
3 Open the LED tab, change the Green LED Default Snap Curr to 2000, and click Set.
The default snap current of 1500 for the red LED is OK.
Figure 139 LED Tab
6 Using the wheel on the mouse and the sliders, zoom in on an area of beads.
See Image Tab in the Right Pane on page 143 for additional information.
Figure 141 Example of Well Focused Beads
7 On the Motor tab, bring the beads into sharp focus by moving the Z Motor up or down.
Increments of 0.002–0.0005 typically work well.
8 Confirm that the value for best focus is within spec.
9 Turn off the camera.
• Z-Center field: paste the Z-Motor Position value copied from the Camera tab
• Select the Save Images checkbox.
• Deselect Compute Best Focus.
• Output Directory field: browse to the D drive and create a folder for the image
stack (eg, D:\Bottom\20July2012_OutputFolder)
Using MTS
MTS is used for some instrument installation activities, and for service procedures. This
section includes a brief description of MTS, and includes instructions on how to run the
MATLAB scripts. You can use MTS to run the Bolt scripts used to check instrument
alignment (automated in the first time setup screens). Most of these tests can also be run
from the sequencing instrument (Welcome screen | Manage Instrument).
To begin using MTS:
1 Double-click the MTS icon on the desktop.
Each view has a tab. However, all the tabs are not visible across the top of the left pane. If
a tab is not displayed, you can access it as follows:
1 Open the quick access view drop-down menu and selecting the tab.
2 Click the Views button and selecting the tab.
You can also hide tabs by deselecting them in the Views drop-down. If you hide a tab, it is
not displayed in the tab drop-down list.
Figure 145 Accessing Views (Tabs) in MTS
Select a channel Click the channel button so that the color of the button is
solid (A channel). A channel is off when the top of the
button fades to white (G channel).
4 Double-click the script to open a window with a command prompt (Figure 148).
5 Go to the D drive and open the folder with the top surface through-focus image stack.
About BoltPAC.exe
This script checks tip/tilt, uniformity, chromatism, camera offset and rotation, and D50.
NOTE
• Always use the center of a super flat beaded flow cell to generate the top
and bottom through-focus image sets, and to run the script.
• The BoltPAC script runs for approximately 40 min.
• Disregard saturation errors, and warnings in script results and the control
software.
• The Full Optics test in the sequencing instrument automatically generates the
2 through-focus image sets required, and runs BoltPAC.exe on both surfaces
of the flow cell.
Run BoltPAC.exe
1 Generate through-focus image stacks for both surfaces of the flow cell using the center
of a super flat beaded flow cell (see Generate Through Focus Image Sets (Stacks) on page
136).
2 Minimize MTS.
3 Go to C:\Illumina | MiSeq Control Software | MatlabScripts.
Or go to the release scripts folder on the D drive.
7 Hit Enter.
A BoltPAC status bar is displayed while the script is running. The script runs for
approximately 40 min.
NOTE
If BoltPAC repeatedly fails, make sure that the proper file naming convention is being
applied to the 41x4 image generated. Sometimes the software can name one or more of
the files incorrectly, causing the script to fail.
8 Run BoltPAC again using the bottom surface through-focus image set.
Chromatism Results
In the BoltPAC_Report file, the chromatism result is called Camera 1 – Camera 2 Offset. A
perfect chromatism value is 0 µm.
Figure 150 Example of Perfect Chromatism as Displayed in BoltPAC_Results File
Water As required
• MiSeq: Laboratory-grade water
• MiSeq FGx: DNase-free, RNase-free water
Gravimetric scale 1
DiagConfig File
Appendix B
About the DiagConfig.xml File 153
Here is a brief description of the contents of this file. Because the file is long, it is described
by section in linear order.
Table 19 DiagConfig.xml File for the MiSeq and the MiSeq FGx
Comments DiagConfig.xml Content
<MCSVersion>2.1.13/MCSVersion>
<CoarseThroughFocusSettings>
<ScanSettings>
<ExposureTimeMS_
ChA>
100</ExposureTimeMS_
ChA>
<ExposureTimeMS_
ChC>
100</ExposureTimeMS_
ChC>
<ExposureTimeMS_
ChG>
50</ExposureTimeMS_
ChG>
<ExposureTimeMS_
ChT>
50</ExposureTimeMS_
ChT>
<GreenLEDCurrent>
2000</GreenLEDCurrent>
<RedLEDCurrent>
1500</RedLEDCurrent>
<OTTExposureTimeMS_
ChA>
5000
</OTTExposureTimeMS_
ChA>
<OTTExposureTimeMS_
ChC>
2000
</OTTExposureTimeMS_
ChC>
<OTTExposureTimeMS_
ChG>
200
</OTTExposureTimeMS_
ChG>
<OTTExposureTimeMS_
ChT>
200
</OTTExposureTimeMS_
ChT>
<OTTGreenLEDCurrent>
6500
</OTTGreenLEDCurrent>
<OTTRedLEDCurrent>
1500
</OTTRedLEDCurrent>
</ScanSettings>
</CoarseThroughFocusSettings>
<FineThroughFocusSettings>
</ScanSettings>
</FineThroughFocusSettings>
<FullOpticsTestOptions>
<Camera12ZOffset>0</Camera12ZOffset>
Chromatism <Camera12ZOffsetDelta>
specification 40</Camera12ZOffsetDelta>
Focal plane <Camera12ZOffsetDeltaBot>
specification 60</Camera12ZOffsetDeltaBot>
<FocalPlaneZPosition>-
0.15</FocalPlaneZPosition>
<FocalPlaneZPositionDelta
>0.05</FocalPlaneZPositionDelta>
<MaxSaturatedPixels>1000</MaxSaturatedPixels>
<CameraOffsetTileCenter>
0</CameraOffsetTileCenter>
<CameraOffsetTileCenterXDelta>75</
CameraOffsetTileCenterXDelta>
<CameraOffsetTileCenterYDelta>40</
CameraOffsetTileCenterYDelta>
<CameraRotation>0</CameraRotation>
<CameraRotationDelta>
1</CameraRotationDelta>
<IlluminatedArea>0.54</IlluminatedArea>
<MaxD50>2.9</MaxD50>
<FullOpticsTestOptions>
<GreenLEDCurrent>2000</GreenLEDCurrent>
<RedLEDCurrent>1500</RedLEDCurrent>
<GreenADC>550</GreenADC>
<RedADC>8500</RedADC>
<LEDPowerOptions>
<PumpCommands>
<PumpToFlowcell
AspirationRate="2000"
Solution="17"
DispenseRate="2500"
Volume="500" />
<PumpToFlowcell
AspirationRate="2000"
Solution="18"
DispenseRate="2500"
Volume="500" />
<PumpToFlowcell
AspirationRate="2000"
Solution="19"
DispenseRate="2500"
Volume="500" />
<PumpToFlowcell
AspirationRate="2000"
Solution="20"
DispenseRate="2500"
Volume="500" />
<PumpToFlowcell
AspirationRate="2000"
Solution="21"
DispenseRate="2500"
Volume="500" />
<PumpToFlowcell
AspirationRate="2000"
Solution="22"
DispenseRate="2500"
Volume="500" />
<PumpCommands>
<PrimeReagentOptions>
<ThermalRampOptions>
<ThermalRampOptions>
<TipTiltTestOptions>
Tip/Tilt <useOTT>false</useOTT>
specifications <UpperLimit>400</UpperLimit>
for bead flow <LowerLimit>--400</LowerLimit>
cell
<BotUpperLimit>500</BotUpperLimit>
<BotLowerLimit>--500</BotLowerLimit>
<TipTiltTestOptions>
<VolumeCheckOptions>
<PrimeVolume>200</PrimeVolume>
<AirVolume>12</AirVolume>
<PreMeasurementVolume>
200</PreMeasurementVolume>
<TargetVolume>100</TargetVolume>
<PreAirDeliveryDelay>
10000</PreAirDeliveryDelay>
<PostPumpDelay>2000</PostPumpDelay>
<AirDeliveryRate>750</AirDeliveryRate>
<MeasurementDeliveryRate>
500</MeasurementDeliveryRate>
<PassFailSpecPerCent>5</PassFailSpecPerCent>
<PR2PrimeVolume>250</PR2PrimeVolume>
<PR2TargetVolume>100</PR2TargetVolume>
<PR2PreMeasurementVolume>
700</PR2PreMeasurementVolume>
<VolumeCheckOptions>
<VolumeCheckPositions>
<int>1</int>
<int>2</int>
<int>3</int>
<int>4</int>
<int>5</int>
<int>6</int>
<int>7</int>
<int>8</int>
<int>9</int>
<int>10</int>
<int>11</int>
<int>12</int>
<int>13</int>
<int>14</int>
<int>15</int>
<int>16</int>
<int>17</int>
<int>18</int>
<int>19</int>
<int>20</int>
<int>21</int>
<int>22</int>
<int>23</int>
<int>24</int>
<VolumeCheckPositions>
</DiagConfig>
Service Tools
Appendix C
Service Tools 163
Toolkits
The following toolkits are used to install, refresh, and service MiSeq instruments:
} MiSeq Alignment Toolkit (part # 15026398S)
} MiSeq Generic Tool Box (part # 15030145S)
} Field Service Repair Kit (part # 15028821S)
Interlock 15029220 1
override cable
Chromatism 15023706 1
adjustment tool
Manifold 15032247 1
alignment tool
Y-stage 15029808 1
alignment tool
Level 15042044 1
• MiSeq 15026129 1
Beaded Flow
Cell, open
• MiSeq 15026717 1
Beaded Flow
Cell, sealed
Syringe 1
(SPARE, SYRINGE, XC PUMP,
500 μl)
NOTE: Old style syringe here.
New style syringe in Syringe
Replacement on page 1.
Syringe Pump 1
(SPARE, SYRINGE PUMP, Tecan
XC, CERAMIC 3-WAY
DISTRIBUTION)
NOTE: Old style pump here. New
style pump in Syringe Pump
Replacement on page 1.
Chiller Thermistor 1
Appendix D
Specifications
Instrument Specifications 169
NOTE
The following specs are different for the top and bottom surface of a lane:
• Camera 1–Camera2 Z Offset
• Tip/Tilt
Max D50 < 2.90 pixels < 2.90 pixels < 2.90 pixels < 2.90 pixels
Appendix E
Returning an Instrument to Illumina 171
Prerequisites
For instructions on the following prerequisites, see Ordering the Crate Kit on page 171.
} Place a service order
} Order the crate kit
Items Required
} Allen wrenches, M6, and 5/64 inch T-handle
} Box for instrument accessories
} Crate kit
} Lab tape
} Shipping request form
Gather the instrument accessories and place them in a box. Ship the accessory box in the
crate with the instrument. Accessories include:
} Instrument safety and compliance guide
} Instrument user guide
} Wash tray (1 or 2 depending upon when the instrument was shipped)
} PR2 bottle
} Waste bottle with cap
} M6 T-handle hex wrench
6 Make sure that the Y-stage shipping restraint bracket can be properly installed
(Figure 163).
The Y-stage can be moved back too far, causing problems later when trying to install
the bracket.
7 Using an M6 T-handle Allen wrench, reengage the shipping lockdowns on the left side
of the instrument.
• Turn the lockdown marked B clockwise approximately 1/2 turn until it stops.
• Turn the lockdown screw marked A counterclockwise approximately 13 full turns
until it stops.
Figure 161 Left Side Shipping Restraints Re-Engaged
9 Open the flow cell compartment, and install the Y-stage shipping restraint bracket.
Figure 163 Y-Stage Shipping Restraint Bracket
4 Place the sides of the crate in position and lock them in place.
Figure 169 Position and Lock Sides of Crate
Appendix F
Cable Interconnect Diagram for the MiSeq 181
Subsystem Block Diagram for the MiSeq 182
Optical System for the MiSeq 183
Fluidics System for the MiSeq 184
Common Procedures
Appendix G
Adjust the Clock, Date, and Time (Windows 7) 187
Cleaning the Imaging Module Bench 189
Flow Cell Cleaning, Loading, and Imaging 190
Removing and Reinstalling the Instrument Skins 195
Rebooting the Computer 203
Shutting Down the Computer 204
Turning the Instrument On and Off 205
1 Select the time/date displayed in the lower right corner of the screen.
2 Select Change date and time settings.
Figure 171 Open the Clock
3 Select Change time zone to open the time zone settings window.
4 Open the drop-down menu and select the appropriate time zone.
5 Deselect this checkbox: Automatically adjust clock for Daylight Saving Time.
6 Select OK.
Figure 172 Automatic Adjustment for Daylight Saving Time Off
NOTE
If the date and time are not correct, the connection to BaseSpace Broker fails.
3 Lightly rinse the flow cell with labaoratory-grade water until both the glass and plastic
cartridge are thoroughly rinsed of excess salts.
Excess salts can affect flow cell seating on the instrument. If salt drys in the imaging
area, imaging can also be affected.
Figure 175 Rinse the Flow Cell
5 Clean the flow cell glass with an alcohol wipe, making sure that the glass is free of
streaks, fingerprints, and lint or tissue fibers.
NOTE
Do not use the alcohol wipe on the flow cell port gasket. Make sure that the
cartridge is securely closed before use.
5 Gently press down on the flow cell clamp to close it over the flow cell.
As the flow cell clamp closes, alignment pins position the flow cell. An audible click
indicates that tthe flow cell clamp is secure.
Figure 180 Close the Flow Cell Clamp
Equipment Required
} Allen wrench, 4 mm
} Screwdrivers, Phillips-head, and flat-head
Skin Removal
Remove the skins (also referred to as panels) from the instrument in the order indicated
here.
Figure 182 MiSeq Skin Removal
1 Using a 4 mm Allen wrench, remove the captive screw, centered in bottom of skin
(panel).
2 Pull the panel out and up.
Two clips are on the bottom, inner side of the panel. These clips are the same on the
left and right panels.
1 Using a 4 mm Allen wrench, remove the captive screw, centered in bottom of panel.
2 Pull the panel out and up.
Two clips are on the bottom, inner side of the panel.
Top Skin
Figure 185 Screw Locations for Top Skin
Figure 187 Proper Position to Rest the Top Cover on the Floor
Figure 189 Flow Cell Compartment Skin—Shoulder Screws and Slide Lock Holes
Skin Reinstallation
Reinstall the skins in the reverse order in which they were removed.
NOTE
The skins are designed to reseat easily. Do not try to force any skins back on. Forcing the
skins can create torque on internal components, and can affect optical alignment. If the skins
do not seat easily, especially the top skin, check the cabling in the affected area. Cables can
shift or be moved during repair or alignment.
TIP
Moving the flow cell stage to tile 12 makes it easier to reinstall the top skin and the flow cell
compartment skin.
} Flow cell compartment skin—Remember to:
• Remove the interlock defeat cable and reattach the cable on the flow cell
compartment skin to the connector on the chassis.
• Open the reagent chiller door when reinstalling this skin.
TIP
Curl one hand under the instrument, and guide both shoulder lock screws into the slide
lock holes (Figure 189 on page 200).
} Top skin—Fit it onto the back of the instrument first:
• Slide the slot on the back of the cover over the captive screw on the back of the
instrument.
• Position the bottom of the cover in the track, and slide it to the left so that the
cutout fits around the cables.
CAUTION
Be careful not to pinch any cables when installing the top skin.
Index
B
BoltPAC.exe, how to run 36, 145
Brenner graph examples
failed through focus image set
generation 124
focus on wrong surface of flow L
cell 123 lanes on a flow cell 194
good through focus image set 122 leveling the instrument 18
logins and passwords 4
C
calibration, flow cell TEC thermal 101 M
camera 2 moving the instrument 14
adjust centering 87 MTS
check centering 87 channel buttons 143
camera offset test results 147 Image tab 143
camera XY offset, how to adjust 91 running scripts 144
chromatism test results 146 views available 142
CloudAPIKey 53 working with images 143
crating instrument for return to
Illumina 171 N
customer support 208 network connections 18
D O
DiagConfig.xml file, about 153 optics, cleaning 189
documentation 208
documents, reference 2 P
E panels. See skins. 195
passwords and logins 4
equipment required 4 PhiX Control DNA preparation 58
F Q
flow cell qualification run 5, 55
lanes and tiles 194 cleaning flow cell 63, 71, 190
flow cell cleaning 63, 71, 190 items required 5, 55
flow cell TEC thermal calibration 101 loading sample libraries 59
flow cells PhiX Control DNA preparation 58
handling, loading, and imaging 190 reagent cartridge map 56
reagent cartridge preparation 56
H
help, technical 208 R
reagent cartridge map 56
I reagent cartridge preparation 56
illuminated area test results 148 reagent compartment setup 17
illuminated area, how to adjust 107 reagent delivery test, manual 149
imaging module bench reagents required 4
cleaning 189 recipes required 6
installation
system component inventory 13 S
instrument sample libraries, loading onto reagent
crating for return 171
turn off 205 cartridge 59
instrument leveling 18 sbsuser password expiration 52
instrument qualification 22 shipping bracket removal 14
inventory of system components 13 shipping lockdown release 14
skins, removal and reinstallation 195
K software required 6
startup screens 22
keyboard and mouse installation 19 about 21
T
TEC, chiller
how to qualify 49
TEC, flow cell
how to qualify 105
technical assistance 208
thermal ramp test results, example
of 41
through focus image set, generate using
a beaded flow cell 136
tile tilt
adjusting on camera 1 129
adjusting on camera 2 125
tile tilt. See tip tilt test. 119
tiles on a flow cell 194
tip tilt test
how to run 119
U
uncrating the instrument 12
UPS recommendations 18
W
wash, post run 78-79
Z
z-motor, adjusting rough position 131
z-position, determining best focus 42
Index
Region Toll Free International