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10xgenomics.com/products/single-cell-gene-expression Product Sheet 10x Genomics | Chromium | Single Cell Gene Expression HT Unlock the power of scale with high- throughput multiomic single cell profiling Single Cell Gene Expression HT As research questions become more complex and samples more diverse, increasing cell and sample throughput becomes paramount. Expand your high- throughput (HT) capabilities and bring million-cell experiments within reach with Single Cell Gene Expression HT. Analyze hundreds of thousands of cells per run, with up to 16 samples in a single chip, or go even further and maximize throughput with sample multiplexing. Scale up CRISPR screens, discover and validate protein or gene biomarkers, and dive deep into cell heterogeneity with a high-throughput single cell gene expression assay based on proven technology. Don’t let limited cell throughput hold you back. Explore your experimental possibilities today. Figure 1. Resolve cellular heterogeneity with high-throughput multiomic single cell profiling. A. Chromium Single Cell Gene Expression HT provides whole transcriptome 3’ profiling at the single cell level for thousands to tens of thousands of cells per sample. Narrow your focus with targeted gene expres- sion, using pre-designed or custom panels to concentrate on the genes most relevant to your research. B. The addition of Feature Barcode technology enables combined gene expression profiling and cell surface protein detection with tens to hundreds of antibodies. C. Scale functional genomics screens with tens to thousands of perturbations in a single experiment using Feature Barcode technology, which lets you concurrently detect single guide RNA (sgRNA) and perturbed gene expression profiles in each cell. Highlights • Achieve economy of scale for ambitious stud- ies with the ability to process thousands to hundreds of thousands of cells per run, mak- ing million-cell experiments routine • Accelerate drug discovery pipelines by scaling up your high-throughput drug screens with single cell resolution • Investigate complex genetic networks by scaling up simultaneous detection of CRISPR perturbations and single cell gene expression profiling • Detect ultra-rare cell populations with increased throughput and multiomic readouts of gene and cell surface protein expression Single cell analysis capabilities Whole transcriptome or targeted gene expression Profile whole transcriptome or targeted genes Profile whole transcriptome or targeted genes A. Gene expression and cell surface protein expression B. Profile whole transcriptome or targeted genes Detect sgRNA from CRISPR screen Analyze cell surface protein expression Gene expression and CRISPR pertubation screening C.
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10xgenomics.com/products/single-cell-gene-expression
Product Sheet10x Genomics | Chromium | Single Cell Gene Expression HT
Unlock the power of scale with high-throughput multiomic single cell profiling
Single Cell Gene Expression HT As research questions become more complex and samples more diverse, increasing cell and sample throughput becomes paramount. Expand your high-throughput (HT) capabilities and bring million-cell experiments within reach with Single Cell Gene Expression HT. Analyze hundreds of thousands of cells per run, with up to 16 samples in a single chip, or go even further and maximize throughput with sample multiplexing. Scale up CRISPR screens, discover and validate protein or gene biomarkers, and dive deep into cell heterogeneity with a high-throughput single cell gene expression assay based on proven technology. Don’t let limited cell throughput hold you back. Explore your experimental possibilities today.
Figure 1. Resolve cellular heterogeneity with high-throughput multiomic single cell profiling. A. Chromium Single Cell Gene Expression HT provides whole transcriptome 3’ profiling at the single cell level for thousands to tens of thousands of cells per sample. Narrow your focus with targeted gene expres-sion, using pre-designed or custom panels to concentrate on the genes most relevant to your research. B. The addition of Feature Barcode technology enables combined gene expression profiling and cell surface protein detection with tens to hundreds of antibodies. C. Scale functional genomics screens with tens to thousands of perturbations in a single experiment using Feature Barcode technology, which lets you concurrently detect single guide RNA (sgRNA) and perturbed gene expression profiles in each cell.
Highlights • Achieve economy of scale for ambitious stud-
ies with the ability to process thousands to hundreds of thousands of cells per run, mak-ing million-cell experiments routine
• Accelerate drug discovery pipelines by scaling up your high-throughput drug screens with single cell resolution
• Investigate complex genetic networks by scaling up simultaneous detection of CRISPR perturbations and single cell gene expression profiling
• Detect ultra-rare cell populations with increased throughput and multiomic readouts of gene and cell surface protein expression
Single cell analysis capabilities
Whole transcriptome ortargeted gene expression
Profile whole transcriptomeor targeted genes
Profile whole transcriptomeor targeted genes
A.Gene expression and cell surfaceprotein expression
B.
Profile whole transcriptomeor targeted genes
Detect sgRNA fromCRISPR screen
Analyze cell surface protein expression
Gene expression and CRISPRpertubation screening
C.
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Unlock the power of scale with high-throughput multiomic single cell profiling
Product features• Profile gene expression for thousands to hundreds
of thousands of single cells by barcoding mRNA at the 3’ end, allowing unbiased characterization of cell types and states
• Combine gene expression analysis with detec-tion of hundreds of cell surface proteins at high resolution for ultra-high parameter multiomic cytometry
• Simultaneously assess CRISPR perturbation phe-notypes and gene expression from the same cell to accelerate your functional genomics studies
• Add 3’ CellPlex for sample multiplexing and Targeted Gene Expression panels to reduce your experimental and sequencing costs even further, enabling your most ambitious single cell studies
• Achieve low multiplet rates to maximize the return on your single cell experiment
• Follow a ready-to-use, robust workflow with demonstrated protocols for diverse sample types, including cell lines, primary cells, and dissoci-ated tissue
Figure 2. Efficient and streamlined workflow for high-throughput multiomic profiling of biological systems. Start with a single cell suspension of unlabeled cells, oligo-conjugated antibody-labeled cells, or cells expressing compatible CRISPR guides. After GEM generation with Chromium X, separate libraries can be constructed from a single sample, including gene expression and cell surface protein or CRISPR guide libraries, generating multiple readouts that can be linked back to the same single cell. Process data with Cell Ranger and visualize sample heterogeneity with Loupe Browser, our fully integrated and easy-to-use analysis and visualization software tools.
GEM generation Sequencing Data
processingData
visualizationSample
prepLibrary
construction
310x Genomics
Product Sheet
Figure 3. Explore even further with Chromium Single Cell Gene Expression HT. Single Cell Gene Expression HT produces data comparable to that of the standard assay, with twice the cell number at reduced cost per cell. Peripheral blood mononuclear cell (PBMC) samples were split and processed with standard Single Cell Gene Expression and Single Cell Gene Expression HT workflows. Sequencing data was analyzed in Cell Ranger and manually annotated in Loupe Browser. A. t-SNE projection of approximately 10,000 PBMCs recovered using standard Single Cell Gene Expression, based on whole transcriptome gene expression. B. t-SNE projection of approximately 20,000 PBMCs recovered using Single Cell Gene Expression HT, based on whole tran-scriptome gene expression. The increased cell recovery allows for deeper understanding of cellular biology and pathways.
Figure 4. Advance translational studies with greater cell throughput and multiomic insights. Non-small-cell lung carcinoma (NSCLC) samples from seven donors were labeled with 3’ CellPlex, mixed together and processed in one Single Cell Gene Expression HT channel. Sequencing data was analyzed in Cell Ranger and manually annotated in Loupe Browser. A. t-SNE projection for approximately 27,000 singlets run with Single Cell Gene Expression HT, with clusters labeled based on manual cell type annotation using common marker genes. B. t-SNE projection of the same dataset, based on cell surface protein data, and showing comparable cluster number and cell type annotation. C. t-SNE projection based on 3’ CellPlex tags, showing clear separation between the different donors.
T cells
B cells
Monocytes
Natural killer cells
Dendritic cells
Tumor cells
EGFR-high tumor cells
Tumor stem cells
B cells
Mast cells/basophils
Memory T cells
Naive T cells
Dendritic cells
Natural killer cells
Plasma
Monocytes
Donor 1
Donor 2
Donor 3
Donor 4
Donor 5
Donor 6
Donor 7
A. Single Cell Gene Expression (standard)
A. Single Cell Gene Expression HT gene expression t-SNE
C. Single Cell Gene Expression HT 3’ CellPlex t-SNE
B. Single Cell Gene Expression HT
B. Single Cell Gene Expression HT cell surface protein t-SNE
Product SheetUnlock the power of scale with high-throughput multiomic single cell profiling
HT Gene Expression Profiling Products Product code
Chromium Next GEM Single Cell 3’ HT Kit v3.1, 8 rxns (includes 1 chip)
1000370
Chromium Next GEM Single Cell 3’ HT Kit v3.1, 48 rxns (includes 5 chips)
1000348
Library Construction Kit, 48 rxns 1000352
Dual Index Kit TT Set A, 96 rxns 1000215
Feature Barcode Technology Products Product code
3’ Feature Barcode Kit, 16 rxns* 1000262
3' CellPlex Kit Set A, 48 rxns 1000261
Dual Index Kit NT Set A, 96 rxns 1000242
Dual Index Kit NN Set A, 96 rxns 1000243
Instrument Compatibility Product code
Chromium X & Accessory Kit, 12 Mo. Warranty 1000331
Chromium X & Accessory Kit, 24 Mo. Warranty 1000332
Software
Cell Ranger
go.10xgenomics.com/scRNA-3/cell-ranger10xgenomics.com/cloud
Download
Run with Cloud Analysis
Loupe Browser go.10xgenomics.com/scRNA-3/loupe-cell
Download
Compatible Partner Products
Compatible Partner Product: Biolegend TotalSeq™-B
www.biolegend.com/totalseq
Learn More
Compatible Partner Product: SigmaAldrich®**
10x Genomics Custom CRISPR Lentiviral Products
www.SigmaAldrich.com/10xCRISPRpools
Learn More
Product specifications• Recover 2,000–20,000 cells per channel, for up to
320,000 cells per chip without 3' CellPlex, or up to 730,000 singlets † per chip with 3' CellPlex sample multiplexing
• Cell size flexibility, no lower limits
• Cell capture rates of up to 65%
• Low doublet rates of 0.4% per 1,000 cells
• Compatible with whole cells and nuclei
• Based on Next GEM technology
†Singlets are single cells or nuclei captured after multiplet removal.
Contact us 10xgenomics.com | [email protected] © 2021 10x Genomics, Inc. FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.LIT000126 - Rev A - Product Sheet - Unlock the power of scale with high-throughput multiomic single cell profiling
One HT reaction requires two Feature Barcode reactions.
Sigma-Aldrich is a trademark of Merck KGaA, Darmstadt, Germany or its affiliates. All other trademarks are the property of their respective owners. Detailed information on trademarks is available via publicly accessible resources.
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