RNA Sequencing (RNA-Seq)


RNA sequencing (RNA-Seq) is a highly effective method for studying the transcriptome qualitatively and quantitatively. It can identify the full catalog of transcripts, precisely define gene structures, and accurately measure gene expression levels.

Our RNA-Seq services provide unparalleled flexibility in analyzing different RNA species, including coding, non-coding, and small transcripts, from a wide range of starting material using long- or short-read sequencing. Various RNA-Seq service options are available, including total, small, and single-cell RNA-Seq with RNA-Seq data analysis from a wide range of starting materials using short- or long-read sequencing.

In addition to standard and stranded poly(A) selection methods, we offer rRNA depletion for FFPE, poor-quality samples, and ultra-low input samples containing as few as 10pg of RNA or just a few cells.



Engineering the Future: Unlocking the Potential of
Functional RNAs in Biology, Medicine, and Innovation

Thursday, July 25, 2024 | 11:00AM EDT


RNA Sequencing Services

Single-Cell RNA-Seq

Single-cell RNA sequencing analyzes gene expression at single-cell resolution for heterogeneous samples. The 10x Genomics® Chromium™ platform provides advanced transcriptional profiling of thousands of individual cells.

Ultra-Low Input RNA-Seq

Ultra-low input RNA sequencing provides bulk expression analysis of samples containing as few as 10 pg of RNA or just a few cells. Recommended for sequencing cells after fluorescence-activated cell sorting (FACS) or immunoprecipitation (RIP-Seq).


Iso-Seq (isoform sequencing) reads full-length contiguous transcripts. Applications include genome annotation, gene fusion detection, novel transcript discovery, and alternative splicing analysis.

Standard RNA-Seq

Standard RNA sequencing is our most popular option for profiling gene expression, enabling the analysis of coding (mRNA) and long non-coding RNA (lncRNA).

Strand-Specific RNA-Seq

Strand-specific RNA sequencing provides gene expression information with relation to strand orientation. Used for genome annotation, analysis of anti-sense/overlapping transcripts, and novel transcript discovery.

Small RNA-Seq

Small RNA sequencing enables analysis of miRNA and other small RNA species. Provides small RNA discovery and profiling.


RNA-Seq services performed in a CAP/CLIA laboratory for clinical applications. Custom CLIA validations for specific assays.


Unsure of the best RNA-Seq solution for your project?

Use our step-by-step guide


Find the right NGS solution for your project using our interactive guide.


Exploring Bioinformatics for Genomic and Transcriptomic Sequencing Data

A gateway into the world of bioinformatics

  • Discover what tools you'll need for
    bioinformatics analysis
  • Explore helpful resources to perform more in-depth exploration
  • Follow step-by-step instructions on how to analyze data

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Digital PCR (dPCR)

Detect your target sequences with unmatched accuracy

Features & Benefits

Highly Scalable

Submit one to hundreds of samples

Flexible Data Amounts

Starting at 10M paired end reads

Latest Platforms

Illumina® NovaSeq™ delivers the highest throughput

European Provider

Sequencing available at our lab in Leipzig, Germany

Superior data quality with a guarantee of ≥80% bases with ≥Q30 for 2x150 bp sequencing (>90% on average)

Industry-leading turnaround time as fast as 1 week

Dedicated support from Ph.D.-level project managers at every step including post-delivery support

Complete sample-to-analysis solutions including flexible extraction and data analysis options available

Transcriptomics Technical Resources

Technical Specifications

Example Data

Sample Submission Guidelines

Frequently Asked Questions

GENEWIZ Citations

Tech Note | High-Fidelity Production of In Vitro Transcription Plasmids with Long Poly(A) Sequences

Poly(A) tail sequences can impact the integrity of your mRNA plasmids for in vitro transcription. While longer poly(A) tails have been shown to increase their stability, tails greater than 100 bases are susceptible to truncations. Learn how the proprietary mRNA plasmid preparation protocol from Azenta can help you generate higher yields and preserve poly(A) tails of greater lengths compared to standard protocols for high-fidelity templates in our tech note.

Tech Note | Full-Length RNA-Seq: A Novel Method to Assess Sequence Integrity for RNA Therapeutics

Strict quality control is required to maintain the integrity of manufactured products for RNA therapies, but current assays often present limitations. Learn how the novel full-length RNA-Seq approach from Azenta allows you to preserve the entire length of and effectively sequence the poly(A) tails of your mRNA products.

Quick Start Guide | Exploring Bioinformatics for Genome and Transcriptome Sequencing Data

For those new to bioinformatics, analyzing massive amounts of NGS data can be a daunting task. Download Azenta’s bioinformatics quick start guide to learn how to analyze whole genome sequencing (WGS) and RNA sequencing (RNA-Seq) data with bioinformatics tools to reveal biological insights for your research.

Webinar| Non-Classical Sources of Tumour-Specific Antigen in Checkpoint Inhibitor Response

Developing immunotherapies for cancer can be difficult due to the variation of immune response from patient to patient. In this webinar, Dr. Litchfield from UCL Cancer Institute presents his team’s exploratory research using a multiomics approach to better understand the diversity of immune response to cancer and highlights their findings of an alternative source of a tumour-specific antigen in checkpoint inhibitor (CPI) response.

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.

RNA-Seq Bioinformatics Workshop & Roundtable Discussion

RNA-Seq bioinformatics can be complex and difficult to decipher. To help make it more approachable, this workshop and roundtable discussion, led by Azenta Life Sciences' bioinformatics manager Brian Sereni, explores the bioinformatics pipeline, explains NGS results, and addresses common challenges and FAQs for RNA-Seq bioinformatics analysis.

Dead Cell Removal

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.

Case Study: Uncovering Cell Type-Specific Expression Profiles in the Tumor Microenvironment with Ultra-Low Input RNA-Seq

Biomedical specimens are often restricted to minute quantities, posing major limitations to RNA-Seq. This case study shows how approximately 50 sorted cells from a glioblastoma can produce transcriptomic data comparable to RNA-Seq experiments that use millions of cells.

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: Isoform Sequencing on the PacBio Sequel® – Maximizing Output and Accuracy

Contiguous mRNA full-length sequencing (Iso-Seq) greatly simplifies genome annotation efforts and revolutionizes the discovery of novel RNA isoforms. This Tech Note discusses the advantages of the latest technologies combined with Azenta’s optimized workflow, and how this increases output and accuracy.

Webinar: Towards High Dimensional Sequencing: From Single-Cell to Spatial Omics

In comparison to traditional profiling methods which assess bulk populations, single-cell technologies empower researchers to examine diversity of heterogeneous cell populations and uncover new, and potentially unexpected, biological discoveries. This webinar highlights the unparalleled capabilities of single-cell sequencing.

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.

Tech Note: Achieving Phenotypic Profiling for Rapid Drug Discovery with High-Throughput Gene Expression Screening

High-throughput technologies are critical in performing phenotypic profiling for drug discovery applications. In this tech note, Azenta Life Sciences discusses the challenges associated with traditional approaches, such as microarrays and RNA sequencing, and offers an optimized assay to achieve high-quality phenotypic profiling at a reduced cost for rapid drug discovery.

Blog | NGS, PCR, or Sanger Sequencing: An Assay Selection Guide

This selection guide offers practical information about PCR + Sanger, qPCR, and NGS approaches to help you determine which assay best suits your project requirements, along with an interactive assay selection tool to aid your decision making.

Blog | Fine-Tuning mRNA Structure for Better mRNA Therapies

The structure of mRNA has been known for decades, but only in recent years have researchers unlocked its potential for therapeutic development. With the right delivery vehicle, mRNA products can replace defective proteins in the cell, generate antigens for immunization (e.g., COVID vaccines), or edit the genome via CRISPR technology. Let’s review the structural features of a functional mRNA molecule and discuss how to optimize these for therapeutic applications.

What is RNA sequencing (RNA-Seq) used for?

RNA sequencing, or RNA-Seq, is used to identify the nucleotide sequence of the RNA strand and detect the quantity of RNA in a sample.

RNA-Seq provides a deeper insight into the transcriptome of a cell— enabling discovery of novel transcripts and differential gene expression analysis—by generating count data. In analyzing the count data, researchers can quantify RNA fragments and associate RNA sequences to respective genes in the sample.

What is the process of RNA sequencing (RNA-Seq)?

The process of RNA-Seq starts by isolating and fragmenting the RNA strand, then undergoing reverse transcription— synthesizing complementary DNA (cDNA)— and adding nucleotides to an RNA strand while copying the RNA strand simultaneously using next generation sequencing (NGS) technology.

How does RNA sequencing (RNA-Seq) analysis work?

RNA sequencing (RNA-Seq) analysis works by using a reference genome or transcriptome to map sequencing reads, quantifying the expression levels of the individual genes and transcripts, and identifying target genes and transcripts that are differentially expressed between samples. Researchers can perform de novo transcriptome assembly for new species with RNA-Seq using low concentrations of a starting sample, and/or with low-quality sample solutions.



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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