Single cell gene expression with cell surface protein€¦ · LIT000032 Rev C Chromium Single Cell...
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PRODUCT SHEET 10xgenomics.com/single-cell Chromium | Single Cell Gene Expression Single cell gene expression with cell surface protein Feature Barcode technology for cell surface protein The Chromium Single Cell Gene Expression Solution with Feature Barcode 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 Barcode technology leverages antibodies 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 Addition of Cell Surface Protein Detection tSNE projections of 6000 peripheral blood mononuclear cells (PBMCs) output by Cell Ranger. A. PBMCs are grouped together based on digital gene expression information. B. PBMCs were then grouped by cell surface protein expression profiles. The additional information from antibody UMI counts better resolved many canonical cell types compared to gene expression data alone—naive and experienced T cells, CD4+ and CD8+ T cells (populations denoted with asterisk*), for example. tSNE2 A. Gene Expression B. Antibody T Regulatory 0.75% CD4+CD127-CD25+ Cytotoxic T Memory 7.84% CD3+CD8a+CD45RA- Natural Killer 6.4% CD16+CD56+ Natural Killer 6.4% CD16+CD56+ Monocyte Non-classical 0.79% CD14+CD16+ Monocyte Non-classical 0.79% CD14+CD16+ Other 4.59% Other 4.59% Double Negative T 2.16% CD3+CD4-CD8- Double Negative T 2.16% CD3+CD4-CD8- tSNE1 tSNE2 tSNE1 B 13.68% CD19+ B 13.68% CD19+ Helper T Memory 20.26% CD3+CD4+CD45RA- Helper T Memory 20.26% CD3+CD4+CD45RA- Helper T Naive 11.68% CD3+CD4+CD45RA+ Helper T Naive 11.68% CD3+CD4+CD45RA+ Monocyte Classical 26.28% CD14+CD16- Monocyte Classical 26.28% CD14+CD16- Cytotoxic T Memory 7.84% CD3+CD8a+CD45RA- * * Cytotoxic T Naive 5.56% CD3+CD8a+CD45RA+ * *
Transcript of Single cell gene expression with cell surface protein€¦ · LIT000032 Rev C Chromium Single Cell...
PRODUCT SHEET
10xgenomics.com/single-cell
Chromium | Single Cell Gene Expression
Single cell gene expression with cell surface protein
Feature Barcode technology for cell surface proteinThe Chromium Single Cell Gene Expression Solution with Feature Barcode 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 Barcode technology leverages antibodies 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 Addition of Cell Surface Protein Detection tSNE projections of 6000 peripheral blood mononuclear cells (PBMCs) output by Cell Ranger. A. PBMCs are grouped together based on digital gene expression information. B. PBMCs were then grouped by cell surface protein expression profiles. The additional information from antibody UMI counts better resolved many canonical cell types compared to gene expression data alone—naive and experienced T cells, CD4+ and CD8+ T cells (populations denoted with asterisk*), for example.
tSN
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A. Gene Expression
B. Antibody
T Regulatory 0.75% CD4+CD127-CD25+
Cytotoxic T Memory 7.84%
CD3+CD8a+CD45RA-
Natural Killer 6.4% CD16+CD56+
Natural Killer 6.4% CD16+CD56+
Monocyte Non-classical 0.79% CD14+CD16+
Monocyte Non-classical 0.79% CD14+CD16+
Other 4.59%
Other 4.59%
Double Negative T 2.16% CD3+CD4-CD8-
Double Negative T 2.16% CD3+CD4-CD8-
tSNE1
tSN
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tSNE1
B 13.68% CD19+
B 13.68% CD19+
Helper T Memory 20.26% CD3+CD4+CD45RA-
Helper T Memory 20.26% CD3+CD4+CD45RA-
Helper T Naive 11.68% CD3+CD4+CD45RA+
Helper T Naive 11.68% CD3+CD4+CD45RA+
Monocyte Classical 26.28% CD14+CD16-
Monocyte Classical 26.28% CD14+CD16-
Cytotoxic T Memory 7.84% CD3+CD8a+CD45RA-
*
*Cytotoxic T Naive 5.56% CD3+CD8a+CD45RA+*
*
Single cell gene expression with cell surface protein
10xgenomics.com/single-cell
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 transcripts of key protein markers
• Detect protein isoforms
• Evaluate differences between mRNA and cell surface protein expression profiles
• 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
Solution Features• Ready-to-use, robust protocols
including applications using Feature Barcode technology
• Compatible partners for oligo conjugated antibodies
• Documentation for custom conjugations for use with Feature Barcode technology
• Easy to use and convenient soft-ware with Cell Ranger Analysis Pipelines and Loupe Browser visualization tool
System Features• Partition 500 – 80,000+ cells
in under 9 minutes
• Scalable; run up to 8 samples in parallel
• Superior sensitivity
• Simple workflow
• Cell size flexibility, no lower limits
• High cell capture rates of up to 65%
• Low doublet rates of under 0.8% per 1000 cells
Differentiation of PTPRC Expressing PBMCs via Detection of CD45RA and CD45RO Isoforms 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.
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PTPRC/CD45 mRNA CD45RA Protein CD45RO Protein
tSNE1 tSNE1 tSNE1
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Product Sheet
10xgenomics.com/single-cell
Products Product Code
Chromium Single Cell 3’ Library & Gel Bead Kit v3, 4 rxn1 1000092
Chromium Single Cell 3' Library & Gel Bead Kit v3, 16 rxn1 1000075
Chromium Chip B Single Cell Kit, 48 rxn1 1000073 (EMEA) 1000153 (US & APAC)
Chromium Chip B Single Cell Kit, 16 rxn1 1000074 (EMEA) 1000154 (US & APAC)
Chromium i7 Multiplex Kit, 96 rxn 120262
Chromium Single Cell 3' Feature Barcode Library Kit, 16 rxn 1000079
Chromium Controller & Accessory Kit, 12 Mo. Warranty 120223
Chromium Controller & Accessory Kit, 24 Mo. Warranty 120246
Cell Ranger go.10xgenomics.com/scRNA-3/cell-ranger
Loupe Browser go.10xgenomics.com/vdj/loupe-cell
Compatible Partner Product: Biolegend TotalSeq™-B
go.10xgenomics.com/totalseq-B
Research areas• Cell Biology
• Cancer Research
• Basic & Translational Immunology
• Developmental Biology
• Stem Cell Biology
• Immuno-oncology & Immunotherapy
Applications • Biomarker Discovery
• Immunophenotyping
• Cell Atlassing and Cataloguing
• Disease Pathway Investigation
• Discovery of Rare Cell Types
• Enhanced Phenotyping of Tissues and Organs
• Pathway & Cell Signaling Analysis
Additional resourcesDatasets go.10xgenomics.com/scRNA-3/datasets
Seminars go.10xgenomics.com/scRNA-3/seminars
Application Notes go.10xgenomics.com/scRNA-3/app-notes
Technical Support go.10xgenomics.com/scRNA-3/support
Publications go.10xgenomics.com/scRNA-3/pubs
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Single cell gene expression with cell surface protein Product SheetFl
ow C
ytom
etry
(C
ount
s)Fe
atur
e Ba
rcod
e
Tech
nolo
gy (C
ount
s)
CD4
10 0 10 1 10 2 10 3 10 4 10 5
0
50
100
150
200
CD8a
10 0 10 1 10 2 10 3 10 4 10 5
0
50
100
150
CD19
10 0 10 1 10 2 10 3 10 4 10 5
0
50
100
150
200
CD45RA
10 0 10 1 10 2 10 3 10 4 10 5
0
30
60
90
120
CD45RO
10 0 10 1 10 2 10 3 10 4 10 5
0
30
60
90
120
Similar Cell Populations are Revealed Comparing Flow Cytometry and Feature Barcode Technology Data In PBMCs, flow cytometry and Feature Barcode technology reveal similar cell populations when fluorescence intensity is compared with UMI counts per cell.
1 Available for use only with the indicated Chromium Controller (PN-120223;120246) or Chromium Single Cell Controller (PN-120263;120212).
Chromium Chip B Single Cell Kit product code is region specific and should be used based on customer’s geographical location.
US: America; APAC: Asia Pacific; EMEA: Europe, Middle East and Africa
© 2020 10x Genomics, Inc. FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.LIT000032 Rev C Chromium Single Cell Gene Expression Cell Surface Protein Product Sheet
Resources from 10x GenomicsWe are dedicated to helping you get the most out of your 10x Genomics system by offering multiple helpful resources:
10x University Immerse yourself in 10x University, a comprehensive step-by-step learning and training environment containing video tutorials and trainings. 10xgenomics.com/10x-university
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Single cell gene expression with cell surface protein Product Sheet
