High-Throughput Single-Cell Analysis Powered by 10x Genomics

10x Genomics Chromium has transformed single-cell research by enabling high-throughput analysis of thousands to tens of thousands of individual cells in a single experiment. Unlike conventional bulk sequencing, which measures the average molecular profile of mixed cell populations, the 10x Genomics platform captures and profiles each cell independently, providing unparalleled insights into cellular heterogeneity, rare cell populations, and complex biological systems.

At N2Jenomics Lab Pvt. Ltd., we offer comprehensive 10x Genomics Single-Cell Sequencing Services that combine advanced Chromium technology, high-throughput next-generation sequencing (NGS), and expert bioinformatics analysis. Our end-to-end workflow empowers researchers to investigate cellular diversity, gene expression, immune responses, chromatin accessibility, and multi-omics interactions with exceptional accuracy and scalability.

Introduction to 10x Genomics Single-Cell Sequencing

Modern biological systems are composed of diverse cell populations, each with distinct molecular characteristics and functional roles. Traditional bulk sequencing methods generate an average molecular profile across all cells in a sample, often masking biologically important differences between individual cells.

The 10x Genomics Chromium System overcomes this limitation through a highly efficient droplet-based microfluidic technology that partitions thousands of individual cells or nuclei into microscopic reaction chambers. Within each partition, every cell is assigned a unique molecular barcode, enabling researchers to trace sequencing reads back to their original cell after sequencing.

This high-throughput approach provides unprecedented resolution for studying complex tissues, rare cell populations, developmental processes, and disease mechanisms.

How 10x Genomics Technology Works

The Chromium platform utilizes Gel Beads-in-Emulsion (GEM) technology to process thousands of individual cells simultaneously.

Step 1: Sample Preparation

A high-quality suspension of single cells or nuclei is prepared from the biological sample while maintaining optimal viability and integrity.

Step 2: Microfluidic Partitioning

Using advanced microfluidic technology, individual cells are encapsulated into nanoliter-sized oil droplets together with specially engineered gel beads.

Step 3: Unique Molecular Barcoding

Each gel bead contains millions of uniquely barcoded oligonucleotides. As cells are lysed inside each Gel Bead-in-Emulsion (GEM), their nucleic acids are labeled with a unique barcode and molecular identifier, allowing every sequencing read to be traced back to its original cell.

Step 4: Library Preparation and Sequencing

Barcoded nucleic acids from all GEMs are pooled to construct sequencing libraries that are compatible with Illumina next-generation sequencing platforms.

Step 5: Bioinformatics Analysis

Following sequencing, advanced computational pipelines use the barcode information to reconstruct cell-specific datasets, enabling comprehensive analysis of gene expression, chromatin accessibility, immune repertoires, or other molecular features at single-cell resolution.

Feature Barcoding for Cell Surface Protein Profiling

Feature Barcoding extends single-cell RNA sequencing by enabling the simultaneous measurement of gene expression and cell surface proteins within the same individual cell. This multi-modal approach provides a more comprehensive understanding of cellular identity and function.

Key Benefits

• • Simultaneous RNA and protein profiling.
• • Improved identification and classification of cell populations.
• • Enhanced discrimination of closely related cell types.
• • Detection of low-abundance proteins that may not correlate with transcript levels.
• • Increased phenotypic resolution through integrated molecular analysis.
• • Sample multiplexing to improve experimental efficiency.
• • Identification and removal of doublets for improved data quality.

• Feature Barcoding is particularly valuable for immunology, cancer research, stem cell biology, and clinical biomarker discovery.

Feature Barcoding for CRISPR Screening

The 10x Genomics Feature Barcoding workflow also supports single-cell CRISPR screening, enabling researchers to combine pooled CRISPR perturbation experiments with high-resolution transcriptomic analysis.

This approach allows investigators to determine how specific genetic perturbations influence cellular behavior by linking guide RNA identity with the transcriptome of each individual cell.

Applications

• • High-throughput functional genomics.
• • Genome-wide CRISPR screening.
• • Gene function characterization.
• • Target validation.
• • Pathway analysis.
• • Drug target discovery.
• • Mechanistic studies of disease biology.

By analyzing hundreds to tens of thousands of cells in a single experiment, Feature Barcoding for CRISPR screening enables scalable and comprehensive investigation of gene function at single-cell resolution.

Chromium™ Single Cell Copy Number Profiling

Genome-Wide Copy Number Variation Analysis at Single-Cell Resolution

The Chromium™ Single Cell Copy Number (CNV) Solution enables genome-wide detection of copy number variations across hundreds to thousands of individual cells within a single sample. This powerful approach provides valuable insights into genomic heterogeneity, clonal architecture, and disease progression that cannot be resolved using conventional bulk sequencing.

Using 10x Genomics Gel Bead-in-Emulsion (GEM) technology, DNA from individual cells is uniquely barcoded before library preparation. Following sequencing, advanced bioinformatics reconstructs the genomic profile of each cell, allowing precise identification of CNVs and clonal populations.

Key Features

• • Genome-wide copy number profiling at single-cell resolution.
• • Simultaneous analysis of hundreds to thousands of cells.
• • Unique molecular barcoding for accurate cell identification.
• • High-resolution detection of genomic heterogeneity.
• • Comprehensive clonal evolution analysis.
• • Scalable workflow for complex biological samples.

Applications

• • Cancer genomics.
• • Tumor evolution studies.
• • Copy number variation (CNV) analysis.
• • Clonal architecture reconstruction.
• • Genetic disorder research.
• • Precision oncology.

Chromium™ Single-Cell ATAC Sequencing

Explore Chromatin Accessibility and Gene Regulation

The Chromium™ Single-Cell ATAC Sequencing (scATAC-seq) solution enables genome-wide profiling of chromatin accessibility at the level of individual nuclei, providing critical insights into epigenetic regulation and gene expression control.

The workflow utilizes the Assay for Transposase-Accessible Chromatin (ATAC), in which a transposase enzyme selectively inserts sequencing adapters into regions of open chromatin. Each nucleus is uniquely barcoded, allowing chromatin accessibility profiles to be assigned back to individual cells after sequencing.

Key Features

• • Genome-wide chromatin accessibility profiling.
• • Single-nucleus epigenomic analysis.
• • High-throughput processing of hundreds to thousands of nuclei.
• • Identification of regulatory elements and transcription factor binding sites.
• • Comprehensive analysis of epigenetic heterogeneity.

Applications

• • Epigenomics research.
• • Regulatory element discovery.
• • Developmental biology.
• • Cancer epigenetics.
• • Stem cell biology.
• • Gene regulation studies.
• • Multi-omics integration.

Advantages of 10x Genomics Single-Cell Sequencing

• High Throughput

Efficiently profile thousands to tens of thousands of individual cells or nuclei in a single experiment, enabling large-scale studies with exceptional scalability.

• Deep Sequencing Coverage

Generate high-quality sequencing data with sufficient read depth for reliable transcriptomic, genomic, and epigenomic analyses.

• Efficient Cell Capture

Advanced microfluidic partitioning technology provides high cell recovery while preserving sample integrity, making it suitable for both abundant and rare cell populations.

• True Single-Cell Resolution

The Chromium platform minimizes multiplet formation by encapsulating individual cells within unique Gel Bead-in-Emulsion (GEM) partitions, ensuring accurate cell-specific molecular profiling.

• Broad Sample Compatibility

Supports a wide variety of sample types, including:

• - Tissue-derived cells.
• - Immune cells.
• - Peripheral blood cells.
• - Tumor specimens.
• - Neural cells.
• - Stem cells.
• - Single nuclei from frozen or difficult-to-dissociate tissues.

• Comprehensive Multi-Omics Capability

The Chromium platform supports multiple single-cell applications, including:

• - Single-Cell RNA Sequencing (scRNA-seq).
• - Single-Nucleus RNA Sequencing (snRNA-seq).
• - Single-Cell DNA Sequencing.
• - Single-Cell ATAC Sequencing.
• - Immune repertoire profiling (TCR/BCR).
• - Cell surface protein profiling (Feature Barcoding/CITE-seq).
• - Integrated multi-omics analysis.

Applications of 10x Genomics Single-Cell Sequencing

• Immunology

• - Identification of immune cell subpopulations.
• - Immune repertoire analysis.
• - Characterization of immune responses.
• - Discovery of novel immune biomarkers.
• - Investigation of autoimmune and infectious diseases.

• Cancer Research

• - Tumor heterogeneity analysis.
• - Clonal evolution studies.
• - Tumor microenvironment profiling.
• - Identification of therapy-resistant cell populations.
• - Biomarker discovery and precision oncology research.

• Neuroscience

• - Characterization of neuronal diversity.
• - Neural development studies.
• - Brain cell atlas construction.
• - Investigation of neurodegenerative diseases.
• - Analysis of neural differentiation pathways.

• Developmental Biology

• - Cell lineage tracing.
• - Embryonic development research.
• - Tissue differentiation studies.
• - Cellular fate mapping.

• Stem Cell Research

• - Stem cell heterogeneity analysis.
• - Identification of differentiation markers.
• - Characterization of developmental pathways.
• - Regenerative medicine research.

• Disease Research

• - Identification of disease-associated cell populations.
• - Molecular disease classification.
• - Biomarker discovery.
• - Precision medicine applications.

• Cell Atlas Projects

• - Comprehensive cell type identification.
• - Discovery of novel cellular populations.
• - Construction of tissue-specific cell atlases.
• - Identification of cell-type-specific marker genes.

10x Genomics Single-Cell Sequencing Workflow

Our standardized workflow integrates advanced laboratory procedures with rigorous quality control to generate reliable and reproducible single-cell data.

Step 1: Sample Preparation

• • Tissue dissociation or nucleus isolation.
• • Preparation of a high-quality single-cell suspension.
• • Cell viability assessment.
• • Sample quality control.

Step 2: GEM Generation

• • Microfluidic encapsulation of individual cells or nuclei.
• • Unique molecular barcoding using Gel Bead-in-Emulsion (GEM) technology.
• • Cell lysis and molecular indexing.

Step 3: Library Construction

• • Reverse transcription or DNA processing.
• • Amplification of barcoded molecules.
• • Sequencing library preparation.
• • Library quality assessment.

Step 4: Next-Generation Sequencing

• • High-throughput sequencing using Illumina platforms.
• • Generation of high-quality sequencing data.

Step 5: Bioinformatics Analysis

Our advanced bioinformatics pipeline includes:

• • Sequencing quality assessment.
• • Barcode processing and cell identification.
• • Cell clustering and annotation.
• • Differential gene expression analysis.
• • Copy number variation (CNV) analysis.
• • Chromatin accessibility analysis (scATAC-seq).
• • Cell trajectory and pseudotime analysis.
• • Cell–cell communication analysis.
• • Functional enrichment analysis (GO and KEGG).
• • Publication-ready visualizations and comprehensive reports.

Service Specifications• 

	Sample Requirements Cells Recommended Quantity & Quality：1-103, Single cells are stored in 1xPBS buffer (without Ca2+, Mg2+), the volume is within 2 μL Cell concentration: 700-1200 cells/μL Note: Sample amounts are listed for reference only. For detailed information, please contact us with your customized requests.
	Sequencing Strategy 10x Genomics 50000reads/cells Capture rate reaches 65%
	Bioinformatics Analysis We provide multiple customized bioinformatics analyses: Data quality control Genome alignment Cell counting Gene expression analysis Differential analysis of marker genes Cell type analysis Pseudotime analysis Note: Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Analysis Pipeline

Deliverables

• • The original sequencing data
• • Experimental results
• • Data analysis report
• • Details in 10x Single-Cell Sequencing for your writing (customization)

1. Why conduct Single-Cell Sequencing research?

Traditional sequencing methods analyze genetic material from large populations of cells, generating an average molecular profile that often masks the biological diversity present within complex tissues. However, even neighboring cells within the same tissue can exhibit distinct genetic and transcriptional characteristics. This cellular heterogeneity is especially evident in tumors, immune tissues, and developing organs.

Single-Cell Sequencing overcomes this limitation by profiling individual cells, enabling researchers to uncover cell-specific molecular signatures that are not detectable with bulk sequencing.

Single-cell sequencing is widely used to:

• • Reveal cellular heterogeneity within complex tissues.
• • Identify rare or previously unknown cell populations.
• • Investigate tumor evolution and clonal diversity.
• • Study embryonic development and cell differentiation.
• • Characterize immune cell diversity and function.
• • Understand disease mechanisms at single-cell resolution.
• • Discover novel biomarkers and therapeutic targets.

Over the past decade, advances in single-cell technologies have transformed biomedical research, making single-cell genomics an essential tool in cancer biology, immunology, neuroscience, developmental biology, and precision medicine.

2. What single-cell solutions are available with the 10x Genomics Chromium platform?

The 10x Genomics Chromium™ platform offers a comprehensive suite of single-cell and multi-omics solutions designed to analyze different molecular features of individual cells.

Available applications include:

• Single-Cell Gene Expression (scRNA-seq)

Profiles whole-transcriptome gene expression in thousands of individual cells, enabling cell type identification, differential expression analysis, and characterization of cellular heterogeneity.

• Single-Cell Copy Number Variation (CNV) Analysis

Detects genome-wide copy number variations in individual cells to study genomic instability, tumor evolution, and clonal architecture.

• Feature Barcoding

Measures cell surface proteins alongside gene expression using antibody-derived tags, improving cell phenotyping, sample multiplexing, and doublet detection.

• Single-Cell Immune Profiling (V(D)J Sequencing)

Characterizes T-cell receptor (TCR) and B-cell receptor (BCR) repertoires together with gene expression, providing valuable insights into adaptive immune responses.

• Single-Cell ATAC Sequencing (scATAC-seq)

Profiles chromatin accessibility at single-cell resolution to identify regulatory elements, transcription factor activity, and epigenetic landscapes.

• Multiome Analysis

Simultaneously measures gene expression and chromatin accessibility from the same individual cell, providing an integrated view of gene regulation and cellular function.

3. Is Single-Cell Sequencing feasible for plant research?

Yes, single-cell sequencing is increasingly being applied to plant research, although it presents additional technical challenges compared with animal samples.

One of the primary obstacles is the presence of a rigid plant cell wall, which must be removed to generate viable single-cell suspensions. This typically requires enzymatic digestion to produce protoplasts, and the success of this process depends on careful optimization of digestion conditions, enzyme composition, and osmotic balance.

Additional challenges include:

• • Efficient isolation of viable protoplasts.
• • Optimization of enzymatic digestion protocols.
• • Maintaining cell viability during sample preparation.
• • Lower cellular heterogeneity in certain plant tissues.
• • Large cell sizes in some plant species that may require protocol modifications or nucleus-based approaches.

Despite these challenges, advances in single-cell technologies—including single-nucleus RNA sequencing (snRNA-seq)—have significantly expanded the applicability of single-cell genomics to plant biology.

Today, plant single-cell sequencing is being used to investigate:

• • Plant development and organ formation.
• • Cell lineage and differentiation.
• • Stress response mechanisms.
• • Plant–microbe interactions.
• • Crop improvement and functional genomics.
• • Cellular responses to environmental changes.