10x Genomics Chromium X Series User manual

10xgenomics.com
User Guide | CG000396 | Rev G
Chromium X Series (X/iX)
with Readiness Test
For use with:
Chromium X & Accessory Kit, 12-Month Warranty, PN-1000331
Chromium iX Accessory Kit, PN-1000323 | Chromium X Upgrade Kit, PN-1000327
Chromium X & Accessory Kit, 24-Month Warranty, PN-1000332
Chromium iX Accessory Kit, PN-1000323 | Chromium X Upgrade Kit, PN-1000327
Chromium iX & Accessory Kit, 12-Month Warranty, PN-1000328
Chromium iX Accessory Kit, PN-1000323
Chromium iX & Accessory Kit, 24-Month Warranty, PN-1000329
Chromium iX Accessory Kit, PN-1000323
Chromium iX/X Refurbished, PN-1000326R

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CG000396 | Rev G
User Guide | Chromium X Series (X/iX) | Notices
Link to TOC | 10xgenomics.com
Notices Document Number
CG000396 | Rev G
Legal Notices
© 2023 10x Genomics, Inc. (10x Genomics). All rights reserved. Duplication and/or reproduction of
all or any portion of this document without the express written consent of 10x Genomics, is strictly
forbidden. Nothing contained herein shall constitute any warranty, express or implied, as to the
performance of any products described herein. Any and all warranties applicable to any products
are set forth in the applicable terms and conditions of sale accompanying the purchase of such
product. 10x Genomics provides no warranty and hereby disclaims any and all warranties as to the
use of any third-party products or protocols described herein. The use of products described
herein is subject to certain restrictions as set forth in the applicable terms and conditions of sale
accompanying the purchase of such product. A non-exhaustive list of 10x Genomics’ marks,
many of which are registered in the United States and other countries can be viewed at:
www.10xgenomics.com/trademarks. 10x Genomics may refer to the products or services offered
by other companies by their brand name or company name solely for clarity, and does not claim
any rights in those third-party marks or names. 10x Genomics products may be covered by one
or more of the patents as indicated at: www.10xgenomics.com/patents.The use of products
described herein is subject to 10x Genomics Terms and Conditions of Sale, available at
www.10xgenomics.com/legal-notices, or such other terms that have been agreed to in writing
between 10x Genomics and user. All products and services described herein are intended FOR
RESEARCH USE ONLY and NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Instrument & Licensed Software Updates Warranties
Updates to existing Instruments and Licensed Software may be required to enable customers to
use new or existing products. In the event of an Instrument failure resulting from an update, such
failed Instrument will be replaced or repaired in accordance with the 10x Limited Warranty,
Assurance Plan or service agreement, only if such Instrument is covered by any of the foregoing
at the time of such failure. Instruments not covered under a current 10x Limited Warranty,
Assurance Plan or service agreement will not be replaced or repaired.
Support
Email: [e-mail]
10x Genomics
6230 Stoneridge Mall Road
Pleasanton, CA 94588 USA

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CG000396 | Rev G
User Guide | Chromium X Series (X/iX) | Document Revision Summary
Link to TOC | 10xgenomics.com
Document
Revision
Summary
Document Number
CG000396 | Rev G
Title
Chromium X Series (X/iX) User Guide with Readiness Test
Revision
Rev F to Rev G
Revision Date
October 2023
General Changes
New instruments will begin to ship with a shipping lock in place within the tray door. Instructions
have been added for removal and replacement of the shipping lock.
The configuration of the Accessory Kit and Upgrade Kit have been updated.
Specific Changes
Items included in the Accessory Kit and Upgrade Kit and items included with the instrument
have been updated on page 13.
A new section has been added to Step 1: Installation under System Operation, that describes
how to remove a shipping lock, on page 17.
A new section has been added to Moving & Shipping the Instrument, which includes instruc-
tions for the new shipping lock on pages 36-37.

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CG000396 | Rev G
User Guide | Chromium X Series (X/iX) | Table of Contents
Link to TOC | 10xgenomics.com
Table of
Contents
Introduction 
Introduction 
Product Identification Label 
Product Specifications 
Safety & Compliance Information 
Safety 
Regulatory 
System Components 
System Components 
Accessory Kits 
System Operation 
Step : Installation 
Step : First-Time Use 
Step : Readiness Test 
Step : Main One-Touch Operation 
Tips & Best Practices 
Icons 
Chromium Next GEM Chip 
Chip Placement on Chromium X Tray 
x Genomics Cloud 
Menu Options 
Menu Options 
Firmware Update Procedure 
Maintenance 
System Maintenance 
Moving & Shipping the Instrument 
Troubleshooting 
Error Screens 

Introduction
Introduction
Product Identification
Product Specifications

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CG000396 | Rev G
Link to TOC | 10xgenomics.com
User Guide | Chromium X Series (X/iX) | Introduction
Introduction The Chromium X Series is the next generation of instrumentation,
purposefully designed to enable high-throughput experiments.
Compared to the Chromium Controller, the Chromium X Series has:
• Advanced sensors, improved pressure control systems, and precise
temperature control on the tray.
• A highly interactive user interface with familiar one-button operation.
• Seamless firmware upgrades, secure network connectivity, and easy
syncing to the 10x Genomics Cloud.
• Similar performance as assessed by multiplet rates, library complexity,
read mapping rates, and cell clustering.
• Ability to run an assay with the 10x Genomics low-throughput (LT),
standard and high-throughput (HT) kits.
• Low throughput: 100–1,000 cells per channel
• High throughput: 2,000–20,000 cells per channel
2,000–60,000 cells per channel with CellPlex
• Standard assay: 500-10,000 cells per channel
500-30,000 cells per channel with CellPlex
The Chromium X Series is available in the X and iX configurations.
Both the standard Next GEM chip and holder (silver color) and the HT Next
GEM chip and holder (black color) are compatible with the instrument.
Comparison of Controller, Chromium X and Chromium iX capabilities
Assay Controller* iX X
Single Cell Gene Expression Flex** Unsupported
PPPP
Single Cell ’ Gene Expression (Dual Index)
PPPPPP
Single Cell ’ Gene Expression HT Unsupported Upgrade required
PP
Single Cell Immune Profiling (Dual Index)
PPPPPP
Single Cell Immune Profiling HT Unsupported Upgrade required
PP
Single Cell ATAC
PPPPPP
Single Cell Multiome ATAC  Gene Expression
PPPPPP
Single Cell ’ Gene Expression (Single Index)*
PP
Unsupported Unsupported
Single Cell Immune Profiling (Single Index)*
PP
Unsupported Unsupported
Single Cell ’ Gene Expression LT*
PPPPPP
* Discontinued product
**Firmware version  or later required

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CG000396 | Rev G
Link to TOC | 10xgenomics.com
User Guide | Chromium X Series (X/iX) | Introduction
Product
Identification Label
Parameter Specifications
Weight  lb ( kg)
Instrument Dimensions with:
Tray close
Tray open
W D H
”[ cm]  ”[ cm]  ”[ cm]
”[ cm]  ”[ cm]  ”[ cm]
Electrical Requirements
Nominal
from a standard -prong wall
receptacle that includes a
safety ground pin
- VAC, / Hz,  W
- V operational range (/-  of nominal)
Overvoltage Category II (standard receptacle)
Pollution Degree  (Indoor Use Only)
Ventilation Requirement Minimum ” [ cm]
Around all sides
Operating Temperature -°F [-°C]
Use in a typical indoor laboratory environment. Extreme
temperature conditions will aect the sensitive reagents
used with the instrument.
Humidity - R.H. non-condensing
Altitude Altitude up to  ft [ m] above sea level
Power Cable Length
Power cables will be in
accordance with regional
specifications
- ft [ m] Standard
10.76”
12.2”
18.6”
Image of label for reference only
Product
Specifications

Safety & Compliance
Information
Safety
Regulatory

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CG000396 | Rev G
User Guide | Chromium X Series (X/iX) | Safety & Compliance Information
Link to TOC | 10xgenomics.com
Safety Before operation, ensure that all potential users have received:
• Instruction in general safety practices for laboratories.
• Instruction in specific safety practices for the instrument.
• All related Safety Data Sheet (SDS) documents.
Precautions are illustrated in the following way:
Symbols Description
The general Warning symbol indicates the possibility of
damaging the instrument or compromising the results of
a method.
The Electrical Hazard symbol indicates the presence of
electrical components that can be harmful to the operator
if handled incorrectly.
The Mechanical Hazard symbol indicates the presence
of moving mechanical parts that can be harmful to the
operator if handled incorrectly.
The Hazardous Materials symbol indicates the presence
of materials that are toxic or otherwise harmful to the
operator if handled incorrectly.
The Biohazard symbol indicates the presence of biological
samples that can be harmful to the operator if handled
incorrectly.
Ensure ground is reliably connected before plugging the instrument’s
power cord into the power source (receptacle). Grounding is required to prevent
electric shock. If the power source is not grounded, qualified personnel must first install a
reliable safety ground.
Warning: The tray door is capable of moving an object that is in its
opening path. If near the edge of the workspace, the object could fall and
create a hazard.
Pinch risk: Ensure no obstructions or fingers present near closing tray.
Warning: Avoid using the Chromium X/iX in a manner not specified
by 10x Genomics. The Chromium X/iX has been designed to protect the user. If used
improperly, the intended user protections can be impaired.
Heavy Load: Total Chromium iX box weight is 49.9 lb (22.6 kg). Two-
person lift required. Use the tote bag included in the packaging to lift the
instrument itself (41.4 lb [18.8 kg]).

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CG000396 | Rev G
User Guide | Chromium X Series (X/iX) | Safety & Compliance Information
Link to TOC | 10xgenomics.com
Regulatory The Chromium X Series has been designed, tested, and certified to be in
compliance with the following standards:
Certification Standards
TUV Certification only for Chromium X/iX
UL - and CAN/CSA C No. -- with a cTUVus mark to indicate
that the product has been tested and certified to Canadian and US standards by TUV
Rheinland and can be legally installed in those countries.
IEC/EN - (rd Edition): Safety Requirements for Electrical Equipment for
Measurement, Control, and Laboratory use.
EN -: Electrical Equipment for Measurement, Control and Laboratory Use.
EMC Requirements.
The RCM mark indicates an electrical product complies with all the requirements of the
electrical and EMC regulations of Australia and New Zealand in accordance with
AS/NZS Standards
CE Mark indicates that assembly is covered by a Declaration of Conformity, and has been
declared in conformity with the provisions of all applicable directives in the European
Union.
EN --: Specifies minimum requirements for immunity and emissions regarding
electromagnetic compatibility for in vitro diagnostic medical equipment, taking into
account the particularities and specific aspects of this electrical equipment and their
electromagnetic environment.
EN --: Electromagnetic compatibility (EMC) - Part -: Limits - Limits for
harmonic current emissions (equipment input current  A per phase).
EN --: Electromagnetic compatibility (EMC) - Part -: Limits - Limitation of
voltage changes, voltage fluctuations and flicker in public low-voltage supply systems,
for equipment with rated current  A per phase and not subject to conditional
connection.
RoHS Directive (//EU): Restriction of the use of certain hazardous substances in
electrical and electronic equipment.
WEEE Directive (//EU): Waste Electrical and Electronic Equipment.
FCC ID: NC-SDPAC, IC: A-SDPAC
FCC Part  Class A. NOTE: This equipment has been tested and found to comply with
the limits for a Class A digital device, pursuant to part  of the FCC Rules. These limits
are designed to provide reasonable protection against harmful interference when the
equipment is operated in a commercial environment. This equipment generates, uses,
and can radiate radio frequency energy and, if not installed and used in accordance
with the instruction manual, may cause harmful interference to radio communications.
Operation of this equipment in a residential area is likely to cause harmful interference in
which case the user will be required to correct the interference at his own expense.
This device complies with part  of the FCC Rules. Operation is subject to the following
two conditions: () This device may not cause harmful interference, and () this device
must accept any interference received, including interference that may cause undesired
operation.
ICES- (Canada): This Class A digital apparatus complies with Canadian ICES-.
Cet appareil numérique de la classe A est conforme à la norme NMB- du Canada.
CAN ICES- (A) / NMB- (A)
In accordance with the provisions on the Radio Regulations of the People’s Republic of
China, this radio transmission equipment, after examination, conforms to the provision
with its CMIIT ID.

System Components
System Components
Chromium X/iX Accessory Kits

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CG000396 | Rev G
User Guide | Chromium X Series (X/iX) | System Components
Link to TOC | 10xgenomics.com
Back
Power Supply USB Ports
Ethernet Port
Pressure Release Valve
See Troubleshooting
Fan
Tray
Locater Pins
Rim for chip holder placement
Indentations for
chip holder feet
Finger Access Area
System Components
Front
Touchscreen
Tray

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CG000396 | Rev G
Link to TOC | 10xgenomics.com
User Guide | Chromium X Series (X/iX) | Introduction
Product # Part Number
x Vortex Adapter  
x Strip Vortexer  
x Magnetic Separator  
Chromium Next GEM Secondary Holder  
Shipping/Readiness Test Block  
Blank Gasket,  Pack*  
Universal Power Cord,  Amp- V
(IEC  C-, with C- Detachable Adapters)

USB,  GB†
Product # Part Number
Chromium X Chip Holder  
x Magnetic Separator HT  
Product # Part Number
Shipping/Readiness Test Block‡  
Blank Gasket*‡  
Shipping Lock
Located inside the tray door during transportation; removed
during installation and stored apart from the instrument
1000657
Lifting Tote Bag 
* Blank gaskets are meant for use only with shipping/readiness test block and are not
compatible with the secondary chip holder.
† The Chromium X Series instrument is compatible with VFAT, FAT, and exFAT formatted USBs.
‡ A shipping/readiness test block and blank gasket assembly is located on the tray within
the instrument during shipping.
Chromium iX
Accessory Kit
PN-1000323
Chromium X
Upgrade Kit
PN-1000327
Additional Items
Accessory Kits

System Operation
Step : Installation
Step : First-Time Use
Step : Readiness Test
Main One-Touch Operation

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CG000396 | Rev G
User Guide | Chromium X Series (X/iX) | System Operation
Link to TOC | 10xgenomics.com
Step 1:
Installation
Verify Bench Space
Follow these instructions for installation to operate the Chromium X/
iX properly and obtain maximum performance of the system. Before
unboxing the instrument choose a location that:
• Is not situated in direct sunlight.
Direct sunlight leads to inadequate cooling conditions or rapid evaporation of reagents.
• Includes a level, sturdy laboratory bench that is not subject to movement
or vibration.
• Provides maximum bench space (front to back).
Avoid areas that have obstruction in the rear such as power strips or house lines (spigots
for vacuum or air).
• Allows access to the plug at the wall receptacle (to safely disconnect power).
• Allows access to the detachable power cord at the rear of the instrument
• Provides a minimum of 4” (10 cm) clearance around unit to allow free
air circulation.
• Provides a minimum of 6” (15 cm) directly in front of the instrument
for unobstructed movement of the tray door.
Warning: The tray door is capable of moving an object that is in its
opening path. If the object is near the edge of the workspace, it could fall
and create a hazard.
Warning: Avoid using the Chromium X/iX in a manner not specified
by 10x Genomics. The Chromium X/iX has been designed to protect the user. If used
improperly, the intended user protections can be impaired.
General Power Safety
Grounding is required to prevent electric shock. If the power source is not
grounded, qualified personnel must first install a reliable safety ground.
• DO NOT plug the instrument power cable into an electrical outlet if the
power cable is damaged.
• To prevent electric shock, plug the instrument power cable into
properly grounded outlets.
• When using an extension cable or power strip, ensure that the total
ampere rating of the instrument does not exceed the ampere rating
of the extension cable. The extension cable must be designed for
grounded plugs and plugged into a grounded wall outlet.
• Be sure to grasp the plug, not the cable, when disconnecting the
instrument from an electric socket.

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CG000396 | Rev G
User Guide | Chromium X Series (X/iX) | System Operation
Link to TOC | 10xgenomics.com
Unbox
Heavy Load: Total Chromium iX box weight is 49.9 lb (22.6 kg). Two-
person lift required. Use the tote bag included in the packaging to lift the
instrument itself (41.4 lb [18.8 kg]).
a. Open box according to box label “this side up.”
Carefully cut or remove the tape on the top of the box and open the top flaps. Ensure
that cut is not too deep as it may damage the Upgrade Kit box (present only if
Chromium X upgrade was purchased).
b. Remove the Upgrade Kit box (present only if Chromium X upgrade
was purchased) and packaging material. Carefully lift inner box out
and open inner box according to box label “this side up.”
c. Remove the Chromium iX Accessory Kit box and packaging material.
d. Carefully lift the tote bag holding the Chromium X/iX instrument out of
the box and place on bench top. Remove the instrument from the tote
bag. Remove all outer transportation packaging materials and tape.
Step 1:
Installation
contd. DO NOT POWER ON UNTIL READY FOR FIRST-TIME USE SETUP
Chromium X
Upgrade Kit
(only present
when X upgrade
purchased)
Chromium iX
Accessory Kit
Chromium X Series
Instrument
Inner Box
Inner Box
Outer Box
Part numbers used for
instrument sales dier from
part numbers on the Outer
Box label for Chromium X/iX
purchases (PN-1000378) or
replacements (PN-1000326).

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CG000396 | Rev G
User Guide | Chromium X Series (X/iX) | System Operation
Link to TOC | 10xgenomics.com
Remove Shipping Material from Tray
The instrument may now include a shipping lock that further secures and stabilizes internal
components to prevent damage during shipping. See Accessory Kits table for more information
and email support@xgenomics.com to request a shipping lock for pre-existing instruments.
The instrument ships with a shipping lock and shipping/readiness
test block in position on the tray. This hardware secures and stabilizes
internal components to prevent damage during shipping.
Follow these steps to remove the shipping lock.
a. Remove the shipping lock: grab the red sticker covering the tray door
by the “pull” tab and pull down carefully. This will manually open the
tray door. Unscrew (by hand) the red metal shipping lock. Retain
shipping lock in a marked bag or container in a convenient location in
case the instrument requires future transportation.
b. Close the tray door.
c. Within the Accessory Kit box, locate the universal power cord and plug
adaptors. Attach the correct country adaptor to the universal adaptor.
d. Plug the Chromium X/iX into a properly grounded outlet of proper
voltage.
DO NOT power on yet.
Ensure power source is reliably grounded before plugging the
instrument’s power cord into the power source (receptacle).
e. If using an Ethernet cable (not provided) to connect to the network,
connect cable directly to the instrument.
Use sticker tab to safely open the tray door, then remove the shipping lock
Step 1:
Installation
contd.

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CG000396 | Rev G
User Guide | Chromium X Series (X/iX) | System Operation
Link to TOC | 10xgenomics.com
The instrument will walk through a first-time setup protocol. Setup
requires the following:
• 10x Genomics Account
Onscreen instruction will guide account setup. Alternatively, visit cloud.10xgenomics.com
to create an account beforehand.
• Instrument serial number and instrument ID
Located onscreen during setup, and also on the label at the back of the instrument
• A computer with Internet access
Internet connection to the instrument is highly recommended.
Turn on the System
a. Power on the instrument using the power switch at the back of the unit.
If using Ethernet, connect the cable to the instrument Ethernet port.
b. Follow onscreen instruction for Network Setup (via ethernet).
c. Set the Date and Time.
Step 2:
First-Time Use

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User Guide | Chromium X Series (X/iX) | System Operation
Link to TOC | 10xgenomics.com
d. Register the instrument.
• Navigate to register.10xgenomics.com using the onscreen QR code on a
computer or phone with internet access. Create or log in to a 10x
Genomics account. Enter the serial number + instrument ID found on
the instrument screen. Read and accept the legal agreement.
e. Update the firmware.
• Internet connection (recommended): After registration, the instrument
will automatically search for the latest firmware update. Confirm
settings for instrument diagnostics and automatic firmware download.
Click Next (see screenshot above on left).
OR
• No Internet connection: Download the latest firmware update from your 10x
Genomics account to the USB provided in the Instrument Accessory Kit.
Insert USB into the back of the instrument (see screenshot above on right).
via internet connection via USB (no internet connection)
Step 2:
First-Time Use
contd.

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CG000396 | Rev G
User Guide | Chromium X Series (X/iX) | System Operation
Link to TOC | 10xgenomics.com
After the instrument updates, a recommended configuration screen
will appear. On this screen, the ability of the instrument to
automatically upload diagnostic data as well as automatically
download updates can be adjusted. 10x Genomics recommends
keeping these settings on. These settings can be changed later.
If either setting is turned off, the following warnings will appear:
Reference the Firmware Update Procedure section for more details.
See Troubleshooting section if an error occurs during the first-time setup protocol.
Step 2:
First-Time Use
contd.