Single-Cell RNA-Seq

Single-cell RNA sequencing (single-cell RNA-Seq or scRNA-Seq) is a technique that provides transcriptional profiling of thousands of individual cells to uncover transcriptome diversity in heterogeneous cell populations. Due to advances in microfluidics and molecular barcoding, transcriptional profiling of individual cells is cost-effective and easy to interpret. This level of throughput analysis enables you to understand at the single-cell level which genes are expressed, in what quantities, and how they differ within your sample.

As an early adopter of the 10x Genomics® Chromium and Illumina® NovaSeq 6000, our optimized workflows for single-cell RNA-Seq, including pre-submission cryopreservation and post-submission dead cell removal, maximize project flexibility, speed, and data accuracy.

For bulk expression analysis of samples with picograms of RNA or just a few cells, use our ultra-low input RNA-Seq service. Unsure which service is the right fit for your research goals? Browse our frequently asked questions (FAQs).



What is the difference between RNA-Seq and scRNA-Seq?

RNA sequencing (RNA-Seq) is used to measure average gene expression levels in a bulk population of cells by extracting and sequencing RNA from cell populations. ScRNA-Seq) is used to analyze gene expression at the single-cell level by sequencing the whole transcriptome of an individual cell.


How does scRNA-Seq work?

ScRNA-Seq works by isolating cells into individual compartments for construction of barcoded libraries prior to sequencing. The sequencing data is parsed according to the cell-specific barcodes and analyzed.

Single-Cell RNA-Seq Workflow

1. Cell Partitioning

Cells and barcoded beads are isolated in oil droplets using the 10x Genomics Chromium

2. Library Preparation

Reverse transcription incorporates cell- and transcript-specific barcodes

3. Sequencing

Barcoded libraries are pooled and sequenced on the Illumina platform

4. Data Analysis

Receive custom analysis and visualize results through interactive software

scRNA-Seq Features & Benefits

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 6000, provide cost-effective single-cell solutions
Samples accepted at different stages of the 10x workflow - cells, Gel Beads in Emulsion (GEMs), and 10x barcoded cDNA libraries
Dead cell removal improves data quality, especially for projects with suboptimal samples (learn more)
Proprietary cell freezing protocol maintains cell viability during transit and provides a convenient method to ship samples
Interactive analysis report provides an intuitive way to explore the data and find biological insights

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.

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.

Webinar: Advancements to the 10x Genomics Chromium™, Single-Cell RNA-Seq System

In this webinar, we review how recent advancements of the 10x Genomics Chromium™ system, coupled with Azenta developmental efforts, can benefit the researcher. In addition, we spotlight our new Single-Cell V(D)J Solution, which can be used in conjunction with single-cell transcriptome profiling to identify pairing of full-length BCR and TCR sequences.

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.

Presentation: Optimized Workflows for Single-Cell RNA-Seq

Learn how Azenta’s single-cell workflows help customers more easily prepare samples and achieve the highest quality results from their sequencing projects. With our methods for cryopreservation and dead cell removal, we provide flexibility and convenience to scientists. This presentation was featured at the Deep Sequencing Forum 2018.

Poster: Highly Multiplexed Single-Cell Transcriptome and Epigenome Profiling of Cryopreserved Tissue Enables Multi-Omic Tissue Characterization in Clinical Settings

Single-cell analysis typically relies upon immediate processing of fresh tissue, presenting limitations for translational and clinical applications. Learn how Azenta’s robust cryopreservation workflow for downstream processing enabled high-quality, single-cell transcriptomic and epigenomic analysis of translational and clinical samples by coupling scATAC-seq and scRNA-seq. 

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.

Article: Which RNA-Seq Technique Should I Use?

With so many RNA sequencing assay types to choose from, how do you know which is best suited for your NGS project? In this article, we discuss the most common RNA-Seq approaches and what factors to consider when selecting the right one.

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.


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

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