Single-Cell Sequencing


Single-cell sequencing provides analysis of thousands of individual cells within complex environments, as opposed to traditional bulk sequencing methods that only provide a representative average of all cells. With developments in microfluidics and molecular barcoding, NGS-based technologies have increasingly focused on single-cell analysis – this has allowed researchers to examine the diversity of heterogenous cell populations and uncover new biological discoveries.

As one of three exclusive 10x Genomics Global Clinical Research Organizations (CROs) and an early adopter of the 10x Genomics® Chromium X, Illumina® NovaSeq X series, and PacBio® Revio systems, we offer single-cell sequencing solutions for various research areas, including transcriptomics, epigenomics, immunogenomics, and more. Our optimized workflows, including pre-submission cryopreservation and post-submission dead cell removal, and specialized Ph.D.-level scientists maximize project flexibility, speed, and data accuracy for precise single-cell sequencing.



What is single-cell sequencing and why does it matter?

Single-cell sequencing is a technology used to isolate and examine nucleic acid sequences—whole genomes or transcriptomes— of individual cells. This method allows for multiomic studies in cellular interactions and analysis of evolving cell populations.

Single-cell sequencing provides a high-quality genomic picture of an individual cell, rather than a broad genomic snapshot from bulk DNA or RNA sequencing of tissue or sample. Single-cell sequencing is important in gene regulation studies and analyzing differences in gene expression between cells. Researchers can greatly benefit from single-cell sequencing in tumor studies and oncology research.


Single-Cell Sequencing Services

Single-Cell RNA-Seq

Analyze transcriptome heterogeneity at the single-cell level. Azenta offers optimized workflows for 5’ and 3’ gene expression libraries to uncover cellular differences that are masked by bulk RNA sequencing.


Single-Cell ATAC-Seq

Identify chromatin accessibility in the epigenome by profiling thousands of single cells in parallel, and discover how chromatin structure and DNA-binding proteins regulate gene expression in varying states and cellular processes.


Single-Cell Immuno-Profiling

Examine the immune repertoires of individual B and T cells by physically pairing VH/VL or α/β chains in B- or T-cell receptors, respectively, while simultaneously capturing data for gene expression, V(D)J clone types, and cell surface protein expression. 


Single-Cell Multiome ATAC + RNA

Simultaneously profile gene expression and open chromatin from the same cell with Multiome ATAC-Seq and RNA-Seq to gain deeper insights into underlying gene regulatory mechanisms with RNA and DNA readouts from every cell.


Single-Cell Gene Expression Flex

Ideal for sensitive cell populations with reduced viability after cryopreservation and FFPE samples, this targeted capture panel is an excellent alternative to traditional approaches. For human and mouse samples only.


Single-Cell CITE-Seq

Simultaneously quantify cell surface protein and transcriptomic data within a single cell readout. Can be combined with Single-Cell Immuno-Seq for comprehensive expression results.


Regulated Single-Cell Sequencing Services

Single-cell processing for all services listed in our GCP-compliant, CAP-accredited and CLIA-certified laboratory environment for clinical applications.


SINGLE-CELL sequencing workflow 

1. Sample Submission

Sample types include live, cryopreserved and fixed: isolated cells, cultured cells, primary tissue, organoids and more.

2. Sample QC and Cell Partitioning

Assessment of cell counting, viability testing and dead cell removal, when indicated, maximizes sample quality prior to loading. Cells and barcoded beads are then isolated in droplets using the 10x Genomics Chromium X.

3. Library Preparation

Unique barcodes for each individual cell are added to RNA or DNA prior to library preparation. Short-read and long-read library preparation options are available.

4. Sequencing

Barcoded libraries are pooled and sequenced on the Illumina NovaSeq X Plus or PacBio Revio system, as indicated by library preparation, for high-throughput characterization.

5. Data Analysis

Receive custom analysis and visualize results through interactive software. Complimentary Ph.D.-level support is available post-delivery to help drive biological insights.

Single-Cell Sequencing Features & Benefits

  • Building

    10x Genomics Certified Service Provider

    And one of three exclusive 10x Global Clinical Research Organizations (CROs)

  • Building

    Real-Time Project Updates

    Through our online system

  • Building

    Ph.D.-Level Support

    At every step

Early adopter of 10x Genomics Chromium with optimized workflows that maximize project flexibility, speed, and data accuracy
Highest throughput sequencing platforms, including the Illumina NovaSeq, provide cost-effective single-cell sequencing solutions
Samples accepted at different stages of the 10x workflow including cells, Gel Beads in Emulsion (GEMs), or 10x barcoded cDNA libraries for maximum workflow flexibility
Proprietary cell freezing protocol maintains cell viability during transit and provides a convenient method to ship samples
Dead cell removal to improve data quality, especially for projects with suboptimal samples
Send us flash-frozen tissues for nuclei extraction and high-quality single-cell sequencing gene expression data

Webinar | Expanding Opportunities for Single-Cell RNA Sequencing

Single-cell sequencing can be a powerful tool used to discover new targets for therapeutic development. In this webinar, co-sponsored by Azenta and 10x Genomics, learn about the latest developments in single-cell technologies and their use in uncovering novel therapeutic discoveries.

Webinar Series | Advancing Transcriptomics: Gene Expression Screening, Single-Cell RNA-Seq, and Beyond

With this two-part webinar series, go beyond traditional transcriptomics and learn about the various NGS approaches available for gene expression analysis. In part 1, we take an in-depth look at various gene expression approaches, including RNA-Seq, single-cell RNA-Seq, digital spatial profiling, and more. In part 2, we explore the data generated from these approaches and how they can complement each other and confirm findings.

Webinar: Improving Single-Cell RNA-Seq Workflow Efficiency to Scale Clinical Research

In this webinar co-hosted by Azenta Life Sciences and 10x Genomics, learn how Clinical Research Organizations (CROs) provide expertise across the single-cell RNA sequencing (scRNA-Seq) workflow, including sample prep and experimental execution. This enables pharmaceutical and biotech clients to perform single-cell analysis at greater scale, efficiency, and reproducibility for clinical research.

Top 3 Factors to Consider Before Starting a Single-Cell Sequencing Project

With several commercial platforms available, high-throughput single-cell sequencing is now more accessible than ever. In this article, we’ll touch upon the 3 most important factors to consider before embarking on your single-cell project to ensure you select the right NGS approach for your research.

Poster | Utilizing an alternate cell fixation method to expand opportunities for single-cell RNA sequencing

The complexity of sample preparation for single-cell sequencing remains a bottleneck for researchers interested in performing analysis at the cellular level. In this poster, we highlight an alternative sample preparation and processing workflow to standard methods that help to broaden the usage of single-cell sequencing approaches.

Case Study: Single-Cell RNA-Seq Analysis Identifies Rare Drug-Resistant Cancer Stem Cells

Cell populations are rarely homogeneous and synchronized in their characteristics. Standard RNA-Seq approaches are limited to reporting general expression levels thus omitting minor subpopulation profiles. This study highlights new single-cell RNA sequencing capabilities for identifying rare cells, characterizing their transcriptomes, and discovering potential biomarkers.

Tech Note: Add More Life to Your Data: Optimizing Single-Cell RNA-Seq with Dead Cell Removal

Obtaining samples with high cell viability can be difficult for many experiments but is necessary for success on the 10x Genomics® Chromium™ platform. This tech note describes how Azenta scientists used optimized single-cell workflows, including dead cell removal, to overcome low viability and generate high-quality sequencing data.

NGS Platforms

For information on our NGS platforms as well as recommended configurations of your projects, please visit the NGS Platforms page. Azenta does not guarantee data output or quality for sequencing-only projects.

10x Genomics

How To Order

Email | Phone 1-877-436-3949, Ext. 1