10xgenomics.com/vdj

PRODUCT SHEET Chromium | Single Cell Immune Profiling

Unravel the specificity of the adaptive immune response

Feature Barcode technology for cell surface protein & antigen specificitySimultaneously examine the cellular context of the adaptive immune response and immune repertoires of hundreds to tens of thousands of T and B cells in human or mouse with the Chromium Single Cell Immune Profiling Solution. Now, you can also detect cell surface markers and determine antigen specificity by leveraging Feature Barcode technology. Decipher the mechanisms involved in the antigen-specific immune response by distinguishing antigen specificity of single T cells with DNA-barcoded peptide-MHC (pMHC) multimers. Additionally, you can gain further insight into

cellular phenotype via the combination of gene expression read-outs and cell surface protein expression using antibodies conjugated to barcodes instead of the fluorescent tags used in flow cytometry. The resulting barcode diversity vastly expands the breadth of cell surface markers that can be detected at the same time. Use the Single Cell Immune Profiling Solution with Feature Barcode technology to unveil a new understanding of the adaptive immune response including T-cell receptor (TCR) specificity, all within the landscape of the responding cell population.

Improved Resolution of Cell Types with the Addition of Cell Surface Protein Detection tSNE projections of ~8000 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—double negative and memory T cells, CD4+ and CD8+ T cells, and memory and naive CD4+ or CD8+ T cells (populations denoted with asterisk*), for example.

tSNE1

A. Gene Expression

B. AntibodytSNE1

tSN

E2tS

NE2

T Regulatory CD4+CD127-CD25+1.6%

Cytotoxic T Naive CD3+CD8a+CD45RA

+5.2%

Helper T Memory CD3+CD4+CD45RA-19.2%

Monocyte Classical CD14+CD16-31.7%

B cells CD19+13.9%

Natural Killer CD16+CD56+6.1%

Double Negative T CD3+CD4-CD8a-3.0%

Cytotoxic T Memory CD3+CD8a+CD45RA-5.5%

Helper T Naive CD3+CD4+CD45RA+9.6% Monocyte Non-classical CD14+CD16+1.5%

T Regulatory CD4+CD127-CD25+1.6%

Helper T Memory CD3+CD4+CD45RA-19.2%

Monocyte Classical CD14+CD16-31.7%

B cells CD19+13.9%

Natural Killer CD16+CD56+6.1%

Helper T Naive CD3+CD4+CD45RA+9.6%

Monocyte Non-classical CD14+CD16+1.5%

Cytotoxic T Memory CD3+CD8a+

CD45RA-5.5%*

Double Negative T CD3+CD4-CD8a-3.0%*

Cytotoxic T Naive CD3+CD8a+

CD45RA+5.2%*

*

10xgenomics.com/vdj

Unravel the specificity of the adaptive immune response

2

Highlights• Reveal clonality, diversity, antigen

specificity, and cellular context

• Pair α and β chain TCR sequences from individual T cells

• Pair heavy and light chain immunoglobulin (Ig) sequences from individual B cells with full isotype resolution

• Simultaneously measure TCR, B cell Ig, cell surface protein expression, and 5’ gene expression in the same cells

• Link full-length, paired TCR α and β chain sequences with TCR-pMHC specificity

Solution Features• Ready-to-use, robust protocols

including Feature Barcode technology

• Compatible partners for oligo conjugated antibodies and MHC multimers

• Documentation for custom conjugations for use with Feature Barcode technology

• Easy to use software includes Cell Ranger Analysis Pipelines, Loupe Browser and Loupe V(D)J Browser visualization tools

System Features• Partition 100 – 80,000+ cells

in under 7 minutes

• Superior sensitivity

• Simple workflow

• Cell size flexibility, no lower limits

• High cell capture rates of up to 65%

• Low doublet rates of under 0.9% in 1000 cells

Product sheet

10 0 10 1 10 2 10 3 10 4 10 5

0

50

100

150

PE Positive75.5

10 0 10 1 10 2 10 3 10 4 10 5

0

20

40

60

80

100

PE Positive35.2

Flow

Cyt

omet

ry

(Cou

nts)

CMV EBV

Feat

ure

Barc

ode

Tech

nolo

gy

(Cou

nts)

Detection of pMHC Specificity in Antigen-Expanded Cells Commercially available CD8+ T cells expanded against CMV and EBV antigens (CMV: HLA-A*0201 NLVPMVATV, EBV: HLA-A*0201 GLCTLVAML, Astarte Biologics). Flow cytometry and Feature Barcode technology identify similar Dextramer-binding cell populations when profiled with dCODE Dextramer reagents displaying the same pMHC specificities.

10xgenomics.com/spatial-gene-expression3

Unravel the specificity of the adaptive immune response Product sheet

V D J C

α TRAV26-2 - TRAJ43 TRAC

α TRAV40 - TRAJ53 TRAC

β TRBV30 - TRBJ2-4 TRBC2

CD3

CD19

CMV Dextramer EBV Dextramer NC Dextramer

CD4

CD45RA

CD8a

CD45RO

TCRα: TRAV26-2 : TRAJ43 : TRACTTTTATGGGGA A A ATTGA A ACCTGCCTGATGTGGGATGTGCTGTGGCTGCTGCTTTGTTGCTTGGGACCTCCTCTGACCTA GGATCAGACACAGAGTCTGAGTTCTGGGGCCTGGA ACCTCA ATGTGCACTTGA ACA ATGA AGTTGGTGACA AGCATTACTG TACTCCTATCTTTGGGTATTATGGGTGATGCTAAGACCACACAGCCAAATTCAATGGAGAGTAACGAAGAAGAGCCTGTTCACTTG CCTTGTAACCACTCCACAATCAGTGGAACTGATTACATACATTGGTATCGACAGCTTCCCTCCCAGGGTCCAGAGTACGTGAT TCATGGTCTTACA AGCA ATGTGA ACA ACAGA ATGGCCTCTCTGGCA ATCGCTGA AGACAGA A AGTCCAGTACCTTGATCCT GCACCGTGCTACCT TGAGAGATGCTGCTGTGTACTACTGCATCCTGA ACA ATA ACA ATGACATGCGCT T TGGAGCAGGGA CCAGACTGACAGTAAAACCAAATATCCAGAACCCTGACCCTGCCGTGTACCAGCTGAGAGACTCTAAATCCAGTGACAAGTC TGTCTGCCTATTCACCGATTTTGATTCTCAAACAAATGTGTCACAAAGTAAGGATTCTGATGTGTATATCACAGACAAAACTGT GCTAGACATGAGGTCTATGGACTTCAAGAGCAACAGTGCTGTGGCCTGGAGCAACAAATCTGACTTTGCATGTGCAAACGCCTTCA

TCRα: TRAV40 : TRAJ53 : TRACG A AT G AG G AC AG TAG T G AG G AC AC AC T G C AG A AC AC T G AG AG G C AG AT G AC G T C T TATA AC C T G T T C AT TA AC T T G C C A C T T G G G G G T G C TAT T C A C C AG T G A A AT C ATA AT T TAT G C AT G A AT T C T G AG TAC A AC T G T G A AT C C T C A C T T C A ACAGTG ATG CCCTCTG CTAGG CCAG AG ACACTA ACA ATG A ACTCCTCTCTGG ACT T TCTA AT TCTG ATCT TA ATGT T TG GAGGAACCAGCAGCAATTCAGTCAAGCAGACGGGCCAAATAACCGTCTCGGAGGGAGCATCTGTGACTATGAACTGCACAT ACACATCCACGGGGTACCCTACCCTTTTCTGGTATGTGGA ATACCCCAGCA A ACCTCTGCAGCTTCTTCAGAGAGAGACA A TGG A A A ACAG CA A A A AC T TCGG AGG CGG A A ATAT TA A AG ACA A A A AC TCCCCCAT TGTG A A ATAT TCAGTCCAGGTA TCAGACTCAGCCGTGTACTACTGTCT TCCGCTGCA AGGAGGTAGCA ACTATA A ACTGACAT T TGGA A A AGGA ACTCTCT T A ACCGTGA ATCCA A ATATCCAGA AGCCTGACCCTGCCGTGTACCAGCTGAGAGACTCTA A ATCCAGTGACA AGTCTGTCT GCCTATTCACCGATTTTGATTCTCA A ACA A ATGTGTCACA A AGTA AGGATTCTGATGTGTATATCACAGACA A A ACTGTGCTA GACATGAGGTCTATGGACTTCAAGAGCAACAGTGCTGTGGCCTGGAGCAACAAATCTGACTTTGCATGTGCAAACGCCTTCA

TCRβ : TRBV30 : TRBJ2-4 : TRBC2TTATGGGGGCAGAGTATAGCTGGTTCCCAGGGAGGCTGGGGGTGATTCACCACACTCTTAAAAGAAGACTAGCCTCATTTCCT CCCCAGCTCATGGGGTAGGATTCCTCTGCTCTGGCAGCAGATCTCCCAGAGGGAGCAGCCTGACCACATCACTGGCCCAGA AGAGGAGGCGTCTGTCCCCCAGACTAGCTGAAGGAAAGGCTGGCTTGGATGATGCTCTGCTCTCTCCTTGCCCTTCTCCTGG GCACTTTCTTTGGGGTCAGATCTCAGACTATTCATCAATGGCCAGCGACCCTGGTGCAGCCTGTGGGCAGCCCGCTCTCTCTG GAGTGCACTGTGGAGGGAACATCAAACCCCAACCTATACTGGTACCGACAGGCTGCAGGCAGGGGCCTCCAGCTGCTCTTCTACT CCGTTGGTATTGGCCAGATCAGCTCTGAGGTGCCCCAGAATCTCTCAGCCTCCAGACCCCAGGACCGGCAGTTCATCCTGAGTTCT A AGA AGCTCCTTCTCAGTGACTCTGGCTTCTATCTCTGTGCCTGGAGTATCTCAGACCTAGCCA A A A ACATTCAGTACTTCG GCGCCGGGACCCGGCTCTCAGTGCTGGAGGACCTGAAAAACGTGTTCCCACCCGAGGTCGCTGTGTTTGAGCCATCAGAAGC AGAGATCTCCCACACCCAAAAGGCCACACTGGTGTGCCTGGCCACAGGCTTCTACCCCGACCACGTGGAGCTGAGCTGGTGGGTGAAT GGGAAGGAGGTGCACAGTGGGGTCAGCACAGACCCGCAGCCCCTCAAGGAGCAGCCCGCCCTCAATGACTCCAGATACTGCCTGA

A.

B.

Profile PBMCs with CMV+ T cells Labeled with TotalSeq-C Antibodies and dCODE Dextramers CMV-PBMCs mixed with 2% CMV expanded T cells. A. Stained with a panel of TotalSeq-C antibodies and a panel of 3 dCODE Dextramer reagents displaying CMV, EBV, and negative control (NC) peptides, respectively. Cell populations are clustered based on surface protein expression: T cells (CD3+, CD4+ and CD8+, panels 1-3), and B cells (CD19+, panel 4). CD8+ T cells bind specifically to Dextramers displaying a CMV antigen (panel 7). The sample does not contain EBV-specific T cells, so the EBV Dextramer staining is similar to the negative control Dextramer staining (panels 8-9). B. Paired T cell receptor clonotypes are assembled for the CMV-specific T cells; these CMV+CD8+ T cells are highly expanded and experienced (CD45RO+). The table outlines gene calls for the most prevalent TCR clonotype alpha (α) and beta (β) chains. The paired α and β chain V(D)J sequences are shown and corresponding V(D)J nucleotides are color-coded (5’UTR: gray, V: red, D: yellow, J: green, C: purple).

© 2020 10x Genomics, Inc. FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.LIT000033 Rev D Chromium Single Cell Immune Profiling Feature Barcode Technology Product Sheet

Products Product Code

Chromium Single Cell 5’ Library Construction Kit, 16 rxn 1000020

Chromium Single Cell 5’ Library & Gel Bead Kit, 16 rxn1 1000006

Chromium Single Cell 5’ Library & Gel Bead Kit, 4 rxn1 1000014

Chromium Single Cell V(D)J Enrichment Kit, Human T Cell, 96 rxn 1000005

Chromium Single Cell V(D)J Enrichment Kit, Human B Cell, 96 rxn 1000016

Chromium Single Cell V(D)J Enrichment Kit, Mouse T Cell, 96 rxn 1000071

Chromium Single Cell V(D)J Enrichment Kit, Mouse B Cell, 96 rxn 1000072

Chromium i7 Multiplex Kit, 96 rxn 120262

Chromium i7 Multiplex Kit N, Set A, 96 rxn 1000084

Chromium Single Cell A Chip Kit, 16 rxn1

1000009 (EMEA) 1000151(US & APAC)

Chromium Single Cell A Chip Kit, 48 rxn1

120236 (EMEA) 1000152 (US & APAC)

Chromium Single Cell 5’ Feature Barcode Library Kit, 16 rxn 1000080

Chromium Controller & Accessory Kit, 12 Mo. Warranty 120223

Chromium Controller & Accessory Kit, 24 Mo. Warranty 120246

Cell Ranger go.10xgenomics.com/vdj/cell-ranger

Loupe Browser go.10xgenomics.com/vdj/loupe-cell

Loupe V(D)J Browser go.10xgenomics.com/vdj/loupe-vdj

Compatible Partner Product: Biolegend TotalSeq™-C

go.10xgenomics.com/totalseq-C

Compatible Partner Product: Immudex dCODE™ Dextramers®

go.10xgenomics.com/dCODE-Dextramers

Research areas• Basic & Translational Immunology

• Immuno-oncology & Immunotherapy

• Autoimmune Disorders & Inflammatory Diseases

• Infectious Disease & Vaccine Research

• Transplant & Immune Reconstitution

Applications • Immune Profiling

• T Cell Antigen Specificity

• Tumor Infiltrating Lymphocyte Characterization

• Immune Derived Cellular Therapy Discovery

• Characterization of the Tumor Microenvironment

• Immune Cell Atlasing

Additional resourcesDatasets go.10xgenomics.com/vdj/datasets

Seminars go.10xgenomics.com/vdj/seminars

Application Notes go.10xgenomics.com/vdj/app-notes

Technical Support go.10xgenomics.com/vdj/support

Publications go.10xgenomics.com/vdj/pubs

Unravel the specificity of the adaptive immune response Product sheet

1 Available for use only with the indicated Chromium Controller (PN-120223;120246) or Chromium Single Cell Controller (PN-120263;120212).

Chromium Chip A 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