Chromium Single Cell Gene Expression Cell Surface Protein Product Sheet

PRODUCT SHEET 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 This robust solution allows you to gather highly multiplexed Feature Barcode technology combines cell surface protein surface marker information in hundreds to tens of thousands detection with an unbiased readout of each single cell of cells. Layer cell surface protein expression data over digital transcriptome. Cell surface proteins serve as biomarkers to gene expression data, on a cell-by-cell basis, to measure cell help distinguish individual cells. As an alternative to the surface protein markers and protein isoforms that are fluorescent tags used in flow cytometry, Feature Barcode difficult to differentiate at the transcript level. These technology leverages antibodies conjugated to DNA capabilities expand your ability to identify cell types and barcodes for single cell sequencing. Barcode diversity vastly states, as well as detect rare cell types, all in a single assay at expands the number of markers you can analyze per assay single cell resolution. and improves cell type resolution.

A. Gene Expression Improved Resolution of Cell Types with the Addition of Cell Surface Protein Detection tSNE projections of 6000 Other 4.59% peripheral blood mononuclear cells (PBMCs) output by

T Regulatory 0.75% Helper T Naive 11.68% Cell Ranger. A. PBMCs are grouped together based on CD4+CD127-CD25+ CD3+CD4+CD45RA+ digital gene expression information. B. PBMCs were then Helper T Memory 20.26% grouped by cell surface protein expression profiles. The CD3+CD4+CD45RA- additional information from antibody UMI counts better resolved many canonical cell types compared to gene B 13.68% CD19+ expression data alone—naive and experienced T cells,

tSNE2 CD4+ and CD8+ T cells (populations denoted with asterisk*), for example. Cytotoxic T Memory 7.84% CD3+CD8a+CD45RA- Double Monocyte Classical Negative T 2.16% Natural Killer 6.4% 26.28% CD14+CD16- CD3+CD4-CD8- CD16+CD56+ Monocyte Non-classical 0.79% CD14+CD16+

tSNE1 B. Antibody

Cytotoxic T Naive 5.56% Cytotoxic T Memory 7.84% * CD3+CD8a+CD45RA+ * CD3+CD8a+CD45RA-

Monocyte Classical 26.28% Double CD14+CD16- Natural Killer 6.4% CD16+CD56+ B 13.68% CD19+ Negative T 2.16% CD3+CD4-CD8-

Other 4.59% tSNE2

Monocyte Non-classical 0.79% CD14+CD16+ Helper T Naive 11.68% Helper T Memory 20.26% * CD3+CD4+CD45RA+ * CD3+CD4+CD45RA- tSNE1

10xgenomics.com/single-cell Single cell gene expression with cell surface protein Product Sheet

Highlights Solution Features System Features

• Perform cellular phenotyping to • Ready-to-use, robust protocols • Partition 500 – 80,000+ cells identify novel targets, biomarkers, including applications using in under 9 minutes and cell types and states without Feature Barcode technology • Scalable; run up to 8 samples the need for pre-selected gene • Compatible partners for oligo in parallel expression targets conjugated antibodies • Superior sensitivity • Simultaneously examine • Documentation for custom • Simple workflow gene expression and protein conjugations for use with Feature • Cell size flexibility, no lower limits abundance in the same cell Barcode technology • High cell capture rates of up • Detect under-represented • Easy to use and convenient soft- to 65% transcripts of key protein markers ware with Cell Ranger Analysis • Detect protein isoforms Pipelines and Loupe Browser • Low doublet rates of under 0.8% per 1000 cells • Evaluate differences between visualization tool 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

PTPRC/CD45 mRNA CD45RA Protein CD45RO Protein tSNE2 tSNE2 tSNE2

tSNE1 tSNE1 tSNE1

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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CD4 CD8a CD19 CD45RA CD45RO

200

200 120 120 150

150

150 90 90

100 100

100 60 60 (Counts)

50 50 50 30 30 Flow CytometryFlow

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

Feature Barcode Barcode Feature Technology (Counts) Technology

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.

Research areas Products Product Code

• Cell Biology Chromium Single Cell 3’ Library & Gel 1000092 Bead Kit v3, 4 rxn1 • Cancer Research Chromium Single Cell 3' Library & Gel • Basic & Translational Immunology 1000075 Bead Kit v3, 16 rxn1 • Developmental Biology 1000073 (EMEA) Chromium Chip B Single Cell Kit, 48 rxn1 • Stem Cell Biology 1000153 (US & APAC) • Immuno-oncology & Immunotherapy 1000074 (EMEA) Chromium Chip B Single Cell Kit, 16 rxn1 1000154 (US & APAC) Applications Chromium i7 Multiplex Kit, 96 rxn 120262 Chromium Single Cell 3' Feature 1000079 • Biomarker Discovery Barcode Library Kit, 16 rxn • Immunophenotyping Chromium Controller & Accessory Kit, 12 120223 Mo. Warranty • Cell Atlassing and Cataloguing Chromium Controller & Accessory Kit, 24 • Disease Pathway Investigation 120246 Mo. Warranty • Discovery of Rare Cell Types go.10xgenomics.com/ Cell Ranger • Enhanced Phenotyping of Tissues and Organs scRNA-3/cell-ranger • Pathway & Cell Signaling Analysis go.10xgenomics.com/ Loupe Browser vdj/loupe-cell

Compatible Partner Product: go.10xgenomics.com/ Additional resources Biolegend TotalSeq™-B totalseq-B Datasets go.10xgenomics.com/scRNA-3/datasets 1 Available for use only with the indicated Chromium Controller Seminars go.10xgenomics.com/scRNA-3/seminars (PN-120223;120246) or Chromium Single Cell Controller (PN-120263;120212). Application Notes go.10xgenomics.com/scRNA-3/app-notes Chromium Chip B Single Cell Kit product code is region specific and should be used based on customer’s geographical location. Technical Support go.10xgenomics.com/scRNA-3/support US: America; APAC: Asia Pacific; EMEA: Europe, Middle East and Africa Publications go.10xgenomics.com/scRNA-3/pubs

3 10xgenomics.com/single-cell Single cell gene expression with cell surface protein Product Sheet

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