CHROMIUM SOLUTIONS | SINGLE CELL GENE EXPRESSION | PRODUCT SHEET

Single Cell Gene Expression

with Cell Surface Protein

FEATURE BARCODING TECHNOLOGY FOR CELL SURFACE PROTEIN

The Chromium Single Cell Gene Expression Solution with Feature Barcoding technology combines cell surface protein detection
with an unbiased readout of each single cell transcriptome. Cell surface proteins serve as biomarkers to help distinguish
individual cells. As an alternative to the fluorescent tags used in flow cytometry, Feature Barcoding technology leverages anti-
bodies conjugated to DNA barcodes for single cell sequencing. Barcode diversity vastly expands the number of markers you can
analyze per assay and improves cell type resolution.

This robust solution allows you to gather highly multiplexed surface marker information in hundreds to tens of thousands of cells.
Layer cell surface protein expression data over digital gene expression data, on a cell-by-cell basis, to measure cell surface
protein markers and protein isoforms that are difficult to differentiate at the transcript level. These capabilities expand your ability
to identify cell types and states, as well as detect rare cell types, all in a single assay at single cell resolution.

Improved Resolution of Cell Types with the A. Gene Expression

Addition of Cell Surface Protein Detection

Other 4.59%

T Regulatory 0.75% Helper T Naive 11.68%

CD4+CD127-CD25+ CD3+CD4+CD45RA+
Helper T Memory 20.26%
CD3+CD4+CD45RA-
tSNE2

B 13.68% CD19+

Cytotoxic T
Memory 7.84%
CD3+CD8a+CD45RA-
Double Negative
Monocyte Classical T 2.16% Natural Killer 6.4%
26.28% CD14+CD16- CD3+CD4-CD8- CD16+CD56+
Monocyte Non-classical
0.79% CD14+CD16+
tSNE projections of 6000 peripheral blood mononu-
tSNE1
clear cells (PBMCs) output by Cell Ranger. A. PBMCs
B. Antibody
are grouped together based on digital gene expres-

*
sion information. B. PBMCs were then grouped by cell

* Cytotoxic T Naive 5.56% Cytotoxic T Memory 7.84%

surface protein expression profiles. The additional CD3+CD8a+CD45RA+ CD3+CD8a+CD45RA-

information from antibody UMI counts better resolved

many canonical cell types compared to gene expres- Monocyte Classical 26.28%
Double Negative
CD14+CD16- Natural Killer 6.4%
sion data alone— naive and experienced T cells, CD4+ CD16+CD56+ B 13.68% CD19+ T 2.16%
CD3+CD4-CD8-
and CD8+ T cells (populations denoted with asterisk*),
Other 4.59%
tSNE2

for example.

Monocyte Non-classical
0.79% CD14+CD16+

* Helper T Naive 11.68%

CD3+CD4+CD45RA+
* Helper T Memory 20.26%
CD3+CD4+CD45RA-

tSNE1

Learn More at
10xgenomics.com/single-cell
 Single Cell Gene Expression
with Cell Surface Protein
HIGHLIGHTS
• Perform cellular phenotyping to
identify novel targets, biomarkers,
and cell types and states without
the need for pre-selected gene
expression targets
• Simultaneously examine
gene expression and protein
abundance in the same cell
• Detect under-represented tran-
scripts of key protein markers
• Detect protein isoforms
• Evaluate differences between
mRNA and cell surface protein
expression profiles
SOLUTION FEATURES SYSTEM FEATURES
• Ready-to-use, robust protocols • Partition 500 – 80000+ cells
including applications using in under 9 minutes
Feature Barcoding technology
• Scalable; run up to 8 samples
• Compatible partners for oligo in parallel
conjugated antibodies
• Superior sensitivity
• Documentation for custom
• Simple workflow
conjugations for use with Feature
Barcoding technology • Cell size flexibility, no lower limits
• Easy to use and convenient soft- • High cell capture rates of up
ware with Cell Ranger Analysis to 65%
Pipelines and Loupe Cell Browser
• Low doublet rates of under 0.8%
visualization tool
per 1000 cells

• Obtain similar protein expression

performance as gold-standard
flow cytometry

• Better implement published

methods like CITE-Seq/REAP-Seq
using our new and improved
workflow

Differentiation of PTPRC Expressing PBMCs via Detection of CD45RA and CD45RO Isoforms
PTPRC/CD45 mRNA CD45RA Protein CD45RO Protein
tSNE2

tSNE2

tSNE2

tSNE1 tSNE1 tSNE1

tSNE feature plots depicting PTPRC mRNA (coding for CD45 protein), and CD45RA and CD45RO protein expression. Oligo-conjugated antibodies against CD45RA
(HI100) and CD45RO (UCHL1) were used to identify CD45 isoforms which are difficult to differentiate at the transcript level. Color gradient represents UMI counts
where dark blue associates with higher UMI counts (higher gene or protein expression levels). While PTPRC is expressed across most cells in the sample and
is detected at the mRNA level, the additional information from the isoform-specific antibodies allows differentiation of naive and memory populations.

Learn More at
10xgenomics.com/single-cell
 Single Cell Gene Expression
with Cell Surface Protein
Similar Cell Populations are Revealed Comparing Flow Cytometry and Feature Barcoding Technology Data
CD4 CD8a CD19 CD45RA CD45RO
200

200
120
Flow Cytometry

120
150

150
(Counts)

150 90
90

100
100

100 60
60

50
50
50 30 30

0 0 0 0 0
0 1 2 3 4 5 0 1 2 3 4 5 0 1 2 3 4 5 0 1 2 3 4 5 0 1 2 3 4 5
10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10
Technology (Counts)
Feature Barcoding

In PBMCs, flow cytometry and Feature Barcoding technology reveal similar cell populations when fluorescence intensity is compared with UMI counts per cell.

APPLICATIONS
PRODUCTS PRODUCT CODE
• Biomarker Discovery
Chromium Single Cell 3’ Library &
1000092
• Immunophenotyping Gel Bead Kit v3, 4 rxns
• Cell Atlassing and Cataloguing Chromium Single Cell 3' Library &
1000075
Gel Bead Kit v3, 16 rxns
• Disease Pathway Investigation
Chromium Chip B Single Cell Kit,
• Discovery of Rare Cell Types 1000073
48 rxns
• Enhanced Phenotyping of Tissues and Organs Chromium Chip B Single Cell Kit,
1000074
16 rxns
• Pathway & Cell Signaling Analysis
Chromium i7 Multiplex Kit,
120262
96 rxns
RESEARCH AREAS
Chromium Single Cell 3' Feature
1000079
• Cell Biology Barcode Library Kit, 16 rxns

• Cancer Research Chromium Single Cell Controller

120263
& Accessory Kit, 12 Mo. Warranty
• Basic & Translational Immunology
Chromium Single Cell Controller
• Developmental Biology 120212
& Accessory Kit, 24 Mo. Warranty
• Stem Cell Biology Chromium Controller & Accessory
120223
Kit, 12 Mo. Warranty
• Immuno-Oncology & Immunotherapy
Chromium Controller & Accessory
120246
Kit, 24 Mo. Warranty
ADDITIONAL RESOURCES go.10xgenomics.
Cell Ranger com/scRNA-3/
DATASETS go.10xgenomics.com/scRNA-3/datasets
cell-ranger
SEMINARS go.10xgenomics.com/scRNA-3/seminars go.10xgenomics.
Loupe Cell Browser com/scRNA-3/
APPLICATION NOTES go.10xgenomics.com/scRNA-3/app-notes loupe-cell
TECHNICAL SUPPORT go.10xgenomics.com/scRNA-3/support Compatible Partner Product: go.10xgenomics.
Biolegend TotalSeq™-B com/totalseq-B
PUBLICATIONS go.10xgenomics.com/scRNA-3/pubs

© 2018 10X Genomics, Inc. FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
LIT000032 Rev A Chromium Single Cell Gene Expression Cell Surface Protein Product Sheet