10x Genomics Chromium X Series User manual

10xgenomics.com
User Guide | CG000396 | Rev C
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

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CG000396 | Rev C
User Guide | Chromium X Series (X/iX) | Notices
Link to TOC | 10xgenomics.com
Notices Document Number
CG000396 | Rev C
Legal Notices
© 2021 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.Notice to Customer:
The listed products and their use are the subject of United States Patent Nos. 6,159,736, and
6,294,385, European Patent No. 1115856 and related patents and patent applications licensed from
the Wisconsin Alumni Research Foundation.
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 C
User Guide | Chromium X Series (X/iX) | Document Revision Summary
Link to TOC | 10xgenomics.com
Document
Revision
Summary
Document Number
CG000396 | Rev C
Title
Chromium X Series (X/iX) User Guide with Readiness Test
Revision
Rev B to Rev C
Revision Date
September 2021
Specific Changes
Network connectivity recommendations updated on pages 17, 26, and 27.
General Changes
N/A

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CG000396 | Rev C
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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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:
• Additional sensors, more accurate pressure, and tray temperature control.
• A highly interactive user interface with familiar one-button operation.
• Seamless firmware upgrades, network connectivity and syncing to the
10x Genomics Cloud, to log run information and experimental setups.
• Similar performance as assessed by multiplet rates, library complexity,
read mapping rates, and cell clustering.
• Ability to run an assay with low throughput (LT) or high throughput (HT).
• 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 one instrument, available in two firmware
options (Chromium X and Chromium iX).
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, X, and iX capabilities
Assay Controller iX X
Single Cell ’ Gene Expression LT
PPPPPP
Single Cell ’ Gene Expression (Dual Index)
PPPPPP
Single Cell ’ Gene Expression HT No Upgrade
required
PP
Single Cell Immune Profiling (Dual Index)
PPPPPP
Single Cell Immune Profiling HT No 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

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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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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: 41.4 lb (18.8 kg). Two-person lift required.

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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.

System Components
 System Components
 Chromium X/iX Accessory Kits

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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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Link to TOC | 10xgenomics.com
User Guide | Chromium X Series (X/iX) | Introduction
Product # Part Number (Item)
x Vortex Adapter  
x Strip Vortexer  
x Magnetic Separator  
Chromium Next GEM Secondary Holder  
Chromium Next GEM Chip Gaskets,  Pack  
Chip Gasket, HT,  pack  
Universal Power Cord,  Amp- V
(IEC  C-, with C- Detachable Adapters)

USB,  GB*  
Product # Part Number (Item)
Chromium X Chip Holder  
Chip Gasket, HT,  Pack  
x Magnetic Separator HT  
USB,  GB*  
*The Chromium X Series instrument is compatible with VFAT and exFAT formatted USBs.
Product # Part Number (Item)
Shipping/Readiness Test Block  
Chip Gasket, HT  
The shipping/readiness test block and 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
 Installation
 First-Time Use
 Readiness Test
 Main One-Touch Operation

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User Guide | Chromium X Series (X/iX) | System Operation
Link to TOC | 10xgenomics.com
Step 1:
Installation
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.
• Provides maximum bench space (front to back).
Avoid areas that have obstruction in the rear such as power strips or house lines (spigets
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
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.
• Includes a level sturdy laboratory bench that is not subject to movement
or vibration.
• 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.

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User Guide | Chromium X Series (X/iX) | System Operation
Link to TOC | 10xgenomics.com
Unbox
Heavy Load: 41.4 lb (18.8 kg). Two-person lift required.
a. Open box according to box label “this side up.”
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 Chromium X/iX instrument out of the box and place
on bench top. Remove all transportation packaging materials and
tape.
e. Within the Accessory Kit box, locate the universal power cord and plug
adaptors. Attach the correct country adaptor to the universal adaptor.
f. Plug the Chromium X/iX into a properly grounded outlet of proper
voltage.
DO NOT power on yet.
g. If using an Ethernet cable (not provided) to connect to the network,
connect cable directly to the instrument.
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

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User Guide | Chromium X Series (X/iX) | System Operation
Link to TOC | 10xgenomics.com
The instrument will walk through a first-time setup protocol to ensure a
proper setup and up-to-date firmware.
Setup requires the following:
• 10x Genomics Account
Onscreen instruction will guide account setup. Alternatively, visit cloud.10xgenomics.com
to create an account beforehand.
First-time setup (listed below) describes onscreen steps to register your instrument and
receive firmware updates.
See Tips & Best Practices for more information on 10x Genomics Cloud.
• Instrument serial number and instrument ID
• Network server settings
• Networked device (computer or phone)
• Internet connection (optional)
Ethernet connection is recommended for optimal performance.
Turning on the system
a. Power on the instrument using the power switch at the back of the unit.
b. The touchscreen will display an initialization progress bar, followed
by a welcome screen.
c. Walk through the Internet Connectivity Setup (optional) and the Date
and Time Setup.
d. On a networked device, login to your 10x Genomics account at
activate.10xgenomics.com and register the instrument. Enter the
serial number + instrument ID. Read and accept the legal agreement.
e. Update the firmware.
• Network connection:
After registration, the instrument will automatically search for
the latest firmware update. Confirm data transmission settings for
automatic upload/download.
• No network connection:
Download the latest firmware update from your 10x Genomics
account to the USB provided in the Accessory Kit. Insert USB
into the back of the instrument. See Firmware Update Procedure
section for more details.
f. A confirmation screen will display the instrument name and the current
firmware version number. Click Reboot to complete installation.
See Troubleshooting section if an error occurs during the first-time setup protocol.
Step 2:
First-Time Use

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User Guide | Chromium X Series (X/iX) | System Operation
Link to TOC | 10xgenomics.com
The readiness test verifies that all systems are working optimally. The
first-time setup protocol will prompt the initial readiness test:
a. Follow screen instruction to launch the readiness test.
b. Verify that the shipping/readiness test block is properly placed on the tray:
• Press the eject button.
• Ensure that the gasket is properly attached (see 10x Gasket Attachment).
• Replace the assembled block on the tray.
• Place the eject button again to close the tray.
c. After the test is complete, follow screen instruction to remove the block
with gasket from the tray.
d. Store the assembled block and gasket in a plastic bag, away from sun-
light and extreme temperature. Retain for future use.
e. A successful readiness test marks the end of setup. The instrument is
now ready for use.
Initiate subsequent readiness tests through the home screen by loading
the shipping/readiness test block with gasket into the instrument. For
optimal performance, tests are recommended at the following times:
• During first-time use (the shipping/readiness test block will already be
present in the instrument)
• After any update
• After moving the instrument
• At regular intervals (daily/weekly/monthly, at user’s discretion)
Step 3:
Readiness Test

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User Guide | Chromium X Series (X/iX) | System Operation
Link to TOC | 10xgenomics.com
The home screen indicates the instrument is ready for use. This is the
most common state of the instrument. There are several key functions
that provide valuable information.
Main Operation
f. Press eject button on the touchscreen to eject the tray. A chime will
sound.
g. Load an assembled chip and holder (see Tips & Best Practices as well
as the appropriate assay kit user guide).
h. Press the eject button again to close the tray.
• If the eject button is not touched within 1 min, it will automatically
close on its own.
• System requires a few seconds before the tray can be reopened again.
Pinch risk: Ensure no obstructions or fingers present near closing tray.
The home screen will now display a play symbol and the name of the
chip type. (Use Eject button in lower left corner of the screen to abort).
i. Press the play button to start the run.
• Midrun progress bar will show the time remaining in the run.
• Yellow indicates a user-recoverable error after loading chip (see
Troubleshooting).
Step 4:
Main One-Touch
Operation
Clock
Set up during first
time use
Access through
menu option >
System/Date & Time
Status Icons
Displays successfully-
connected devices
Press icon to navigate
to that menu option
Menu Options
Main Button
Eject shown when
ready for use

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User Guide | Chromium X Series (X/iX) | System Operation
Link to TOC | 10xgenomics.com
j. At the end of a run, the button will display an eject symbol and a
“Run Info” tab at the bottom of the screen.
• Green indicates a successful completed run.
• Red indicates a failed run/error (see Troubleshooting).