Single Cell

Buyer’s Guide
Gene Expression
Immune Profiling
Epigenomic Profiling
Protein Expression

10xgenomics.com
10xgenomics.com
Single Cell

Introduction
Why single cell sequencing?
Cell heterogeneity is a key contributor to biological complexity that is often masked by bulk techniques, like RNA
sequencing (RNA-seq) or microarray analysis. Rather than providing an average snapshot of how cells work, single
cell sequencing technology gives researchers the ability to more fully characterize tissue heterogeneity, identify
rare cell types, and dissect molecular mechanisms cell by cell. This high level of resolution leads to groundbreaking
insights, as evidenced by over 6,000 publications featuring 10x Genomics technology, the majority of which use
single cell approaches.

Single cell publications featuring 10x Genomics technology

5,700+
Total single cell
publications
115 300 332

How does it work?

Single cell sequencing starts with a suspension of single cells or nuclei. Droplets containing a single cell or nucleus are
generated using advanced microfluidics with a Chromium instrument. Library construction follows a streamlined
workflow. After sequencing, data can be processed and analyzed using our integrated data analysis pipelines and
visualization software—intuitive enough for novice users yet powerful enough for the experts. Support resources
provide guidance for the entire workflow, from sample preparation to data analysis.

Sample prep Droplet formation Library construction Sequencing Data processing Data visualization

Prepare
cell or
nuclei
suspension

Tackle your single cell experiments confidently with personalized support and detailed guidance across an end-to-end workflow.

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Single cell product offerings

10x Genomics provides robust solutions that let you analyze gene and protein expression, perform comprehensive
immune phenotyping, and map regions of open chromatin, all at single cell resolution.

Gene Expression
Perform molecular and cellular characterization
of cells at scale with single cell RNA-sequencing
for whole transcriptome gene expression.

Immune Profiling
Gain a comprehensive view of the immune
system with paired, full-length receptor
sequences from T and/or B cells, surface
protein expression, antigen specificity, and
gene expression, all from a single cell.

Epigenomic Profiling
Uncover hidden insights with single cell
epigenomic profiling using the assay for
transposase-accessible chromatin, ATAC-seq,
alone or in combination with single cell RNA-
seq to simultaneously measure chromatin
accessibility and gene expression.

Protein Expression
Reveal cell phenotypes and uncover functional
information at single cell resolution with
simultaneous measurement of hundreds of cell
surface proteins and gene expression.

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Single Cell

Single Cell Gene Expression

Characterize cellular heterogeneity, explore
mechanisms driving development and disease, and
trace cell lineages with 3'-, 5'-, or probe-based
transcriptome sequencing at single cell resolution
for hundreds to hundreds of thousands of cells.

At-a-glance comparison
Single Cell Gene Expression Flex Single Cell Gene Expression Single Cell Immune Profiling
Description A probe-based solution for whole tran- A versatile solution providing 3' gene Enhanced immune profiling combining
scriptome gene expression, starting from expression with multiomic capabilities 5’ gene expression with multiomic
fresh or fixed samples, including FFPE profiling
Additional Cell Surface Protein Cell Surface Protein Cell Surface Protein
multiomic CRISPR Screening Antigen Specificity
capabilities
BCR/TCR sequencing
CRISPR Screening

Extensions Built-in sample mulitplexing Sample multiplexing Automated workflow

Automated workflow
Throughput Singleplex: 10,000 cells per channel; Standard: 10,000 cells per channel; up to Standard: 10,000 cells per channel; up
up to 80,000 cells per chip 80,000 cells per chip; 140,000 cells per chip to 80,000 cells per chip
with 3’ CellPlex
Multiplex: 128,000 cells per channel; High: 20,000 cells per channel; up to
up to 1,024,000 cells per chip High: 20,000 cells per channel; up to 320,000 320,000 cells per chip
cells per chip; up to 730,000 cells per chip
with 3’ Cellplex
Sample Cells or nuclei Cells or nuclei Cells
compatibility
Tested on diverse sample types, Tested on diverse sample types, including cell Tested on diverse sample types,
including cell lines, primary cells, and lines, primary cells, and dissociated fresh including cell lines, primary cells, and
dissociated fresh or fixed tissue, tissue dissociated fresh tissue
including FFPE
Species Human and mouse Demonstrated on multiple species, including Demonstrated on multiple species,
compatibility human, mouse, and rat including human and mouse
Amplification of human or mouse TCR/
BCR sequences

Instrument Chromium X/iX Chromium X/iX Chromium X/iX

compatibility Chromium Connect Chromium Connect
Analysis software Cell Ranger Cell Ranger Cell Ranger
Cloud Analysis Cloud Analysis Cloud Analysis
Visualization Loupe Browser Loupe Browser Loupe Browser
software Loupe V(D)J Browser
Resources Product sheet Product sheet Product sheet
Kits and part numbers Kits and part numbers Kits and part numbers

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Choosing the right gene expression assay for your experiment

When should I use the Single Cell Gene Expression Flex assay?

We recommend this for everyone running single cell experiments with human or mouse samples who
is looking to measure gene expression alone or simultaneously with cell surface protein expression.

Single Cell Gene Expression Flex is our most sensitive, cost-effective, and flexible assay.
Key benefits include:

• Streamlined processing provides compatibility for fresh or PFA-fixed tissues, cells, or nuclei, plus
access to FFPE samples

• Built-in multiplexing capabilities provide the flexibility to run 1–128 samples or up to 1 million
cells in a single run

• Highly sensitive probe-based chemistry combined with sample multiplexing provides our
lowest cost per sample

When should I use other 10x gene expression assays?

SIngle Cell Gene Expression

• 3’ gene expression in non-human or non-mouse samples

• Automated workflows on the Chromium Connect instrument

Single Cell Immune Profiling

• High-resolution immune cell characterization: 5’ gene
expression & full length VDJ sequences

• CRISPR screening: 5’ gene expression & CRISPR perturbations

• 5’ gene expression in non-human or non-mouse samples

• Automated workflows on the Chromium Connect instrument

SIngle Cell Multiome Gene Expression + ATAC

• Epigenomics applications: 3’ gene expression and chromatin
accessibility in the same single cell

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Single Cell Immune Profiling

Reveal the full diversity of the immune system
to understand clonal expansion, accelerate
immunotherapy, and investigate disease states.

At-a-glance comparison
Immune Receptor Profiling Barcode Enabled Antigen Mapping Single Cell 5’ Gene Expression
(BEAM)

Description Perform BCR/TCR sequencing to Perform multiplexed antigen screening Study innate and adaptive immunity by
obtain paired, full-length receptor to obtain comprehensive cellular combining single cell 5’ gene
sequences from T cells and/or B cells profiles of antigen-specific B-cell expression with multiomic profiling
with complete isotype resolution (BEAM-Ab) and T-cell (BEAM-T)
clonoypes

Additional multiomic Antigen Specificity BCR/TCR sequencing Antigen Specificity

capabilities Gene Expression Gene Expression BCR/TCR sequencing
Cell Surface Protein Cell Surface Protein Cell Surface Protein
CRISPR Screening CRISPR Screening

Extensions Automated workflow - Automated workflow

Throughput Standard or high Standard or high Standard or high

Sample compatibility Cells Cells Cells or nuclei

Tested on diverse sample types, Tested on diverse sample types, Tested on diverse sample types,
including cell lines, primary cells, and including PBMCs, splenocytes, lymph including cell lines, primary cells, and
dissociated fresh tissue node aspirates, and enriched B or T dissociated fresh tissue
cells
Amplification of human or mouse TCR/ Demonstrated on multiple species,
BCR sequences Amplification of human or mouse TCR/ including human and mouse
BCR sequences
Demonstrated on multiple species,
including human and mouse Compatible with human and mouse

Analysis software Cell Ranger Cell Ranger Cell Ranger

Cloud Analysis Cloud Analysis

Visualization software Loupe Browser Loupe Browser Loupe Browser

Loupe V(D)J Browser Loupe V(D)J Browser Loupe V(D)J Browser

Resources Product sheet Product sheet Product sheet

Kits and part numbers Kits and part numbers Kits and part numbers

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Adapt the scale you need for immune cell profiling

From clonotyping studies to large-scale antibody and TCR discovery projects, Single Cell Immune Profiling lets you
scale up easily. Select the kit and instrument that enable your projects, from discovery to translational research.

Standard scale Large scale

• Process 500–10,000 cells per sample; up to 8 • Process 2,000–20,000 cells per sample; up to 16
samples per chip samples per chip
• Explore adaptive and innate immune • Perform large-scale antibody and TCR discovery
cell diversity for novel antigens
• Identify and characterize rare cell types • Detect ultra-rare cell populations with increased
and biomarkers throughput and multiomic readouts
• Analyze tissue microenvironments, disease • Perform large-scale time course experiments for
progression, and drug immune response clonal tracking
• Characterize immune response to infection • Achieve economy of scale for immune repertoire
by measuring clonal expansion and immune profiling with simultaneous capture of gene
cell phenotypes expression and cell surface protein

Kit: Chromium Single Cell Immune Profiling Kit: Chromium Single Cell Immune Profiling HT

Instrument: Chromium X, Chromium iX, Instrument: Chromium X

Chromium Connect

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Single Cell Epigenomic Profiling

Unmask epigenomic profiles, explore gene regulatory
interactions, and resolve cell lineage relationships to
transform your understanding of biology and uncover
hidden insights.

At-a-glance comparison
Single Cell Multiome ATAC + Gene Expression Single Cell ATAC

Description Simultaneously profile single cell 3’ gene expression Profile chromatin accessibility with single cell resolution
and open chromatin from the same nucleus

Chromatin accessibility profiling Yes Yes

Transcriptional profiling Yes No

Throughput Standard Standard

Sample & species compatibility Nuclei Nuclei

Demonstrated with cell lines, primary cells, Demonstrated with cell lines, primary cells, cryopreserved
cryopreserved samples, and fresh- and samples, and fresh- and flash-frozen tissue
flash-frozen tissue Demonstrated on multiple species, including human and
Demonstrated on multiple species, mouse
including human and mouse

Analysis software Cell Ranger ARC Cell Ranger ATAC

Cloud Analysis

Visualization software Loupe Browser Loupe Browser

Resources Product sheet Product sheet

Kits and part numbers Kits and part numbers

Closed chromatin
Why ATAC-seq?
Coils Nucleosome
The assay for transposase-accessible chromatin (ATAC)
is a sequencing method that surveys the physical
structure of the genome by identifying regions of open Supercoils
Open chromatin

chromatin, where regulatory sequences are accessible Transpososome

to DNA-binding proteins. Single cell ATAC-seq can provide

Chromosome
information about gene regulatory elements, including
their cell-type specificity and binding site motifs.

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Single Cell Protein Expression

Comprehensively resolve cell types and phenotypes,
validate your single cell RNA-seq, and unravel cell
signaling pathways to explore molecular mechanisms
or transform drug discovery.

At-a-glance comparison
Single Cell Gene Expression Flex Single Cell Gene Expression Single Cell Immune Profiling

Description A probe-based solution for whole A flexible multiomic solution providing Enhanced immune profiling combining
transcriptome gene expression and single cell 3' gene expression and cell single cell 5’ gene expression with cell
cell surface protein expression surface protein profiling surface protein profiling

Additional Antigen Specificity

multiomic capabilities - -
BCR/TCR sequencing

Extensions Built-in sample multiplexing Sample multiplexing -

Throughput Singleplex: 10,000 cells per channel; Standard: 10,000 cells per channel; up Standard: 10,000 cells per channel; up
up to 80,000 cells per chip to 80,000 cells per chip; 140,000 cells to 80,000 cells per chip
Multiplex: 128,000 cells per channel; per chip with 3’ CellPlex High: 20,000 cells per channel; up to
up to 1,024,000 cells per chip High: 20,000 cells per channel; up to 320,000 cells per chip
320,000 cells per chip; up to 730,000
cells per chip with 3’ Cellplex

Sample compatibility Cells Cells Cells

Tested on diverse sample types, Tested on diverse sample types, Tested on diverse sample types,
including cell lines, primary cells, and including cell lines, primary cells, and including cell lines, primary cells, and
dissociated fresh or PFA-fixed tissue dissociated fresh tissue dissociated fresh tissue

Species compatibility Human and mouse Demonstrated on multiple species, Demonstrated on multiple species,
including human and mouse including human and mouse
Amplification of human or mouse TCR/
BCR sequences

Instrument compatibility Chromium X/iX Chromium X/iX Chromium X/iX

Chromium Connect Chromium Connect

Analysis software Cell Ranger Cell Ranger Cell Ranger

Cloud Analysis Cloud Analysis Cloud Analysis

Visualization software Loupe Browser Loupe Browser Loupe Browser

Loupe V(D)J Browser

Resources Product sheet Product sheet Product sheet

Kits and part numbers Kits and part numbers Kits and part numbers

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Instrumentation that works for you

Key to our single cell sequencing technology is the ability to generate tens of thousands of single cell partitions,
each containing an identifying barcode for downstream analysis. Each of the Chromium instruments uses
advanced microfluidics to perform single cell partitioning and barcoding in a matter of minutes.

Next-generation technology for ultimate single

cell flexibility
The Chromium X Series is designed with modern
functionality plus enhanced hardware technology
to offer the most optimized approach to single cell
studies, with the option to match the scale of single
cell research at any level and enable routine high-
throughput experiments. All of our single cell assays
are supported on Chromium X Series instruments.

Learn more about the Chromium X Series

Automate your single cell workflows

Chromium Connect provides automation of the full
single cell gene expression and immune profiling
workflows, including cell partitioning and library
construction, letting you go from single cell
suspensions to up to eight sequencing-ready libraries
with walk-away convenience.

Learn more about Chromium Connect

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Resources from 10x Genomics

We are dedicated to helping you get the most out of your 10x Genomics system by offering multiple
helpful resources:

Technology brochure 10x Genomics publications

Discover the power of single cell partitioning and learn Get inspired by more than 4,500 peer-reviewed
how Next GEM technology enables integrated analysis publications and search papers by product,
of single cells at massive scale. research area, or sample type.

Learn more Learn more

Support 10x Genomics compatible products

Visit the support site for documentation, software, and Access our list of key partner products that have
datasets that will help you get the most out of your 10x been certified compatible to work with our
Genomics products. various solutions.

Learn more Learn more

10x Genomics library 10x Blog

Learn more about what you can do with our single cell Keep up to date with the 10x Genomics Blog,
solutions from our collection of product literature, where you’ll find everything from tips and tricks
application notes, and scientific posters. to the latest 10x news.

Learn more Learn more

Contact us
10xgenomics.com | [email protected]
© 2023 10x Genomics, Inc. FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
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