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Gene Expression Analysis

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CD Genomics offers services to measure mRNA levels indirectly or directly using next-generation sequencing (NGS) and long-read sequencing technologies, a part of our complete solutions for microbial characterization. We provide professional services on microbial genomics with our years of experience in microbial identification, diversity analysis and characterization.

Our Advantages:
  • Standardized laboratory methods and quality assurance processes.
  • Advanced genomics solutions and genome-based analysis.
  • Stand at the frontiers of microbial strain characterization.
  • Short-read and long-read sequencing platforms.
Tell Us About Your Project

We are dedicated to providing outstanding customer service and being reachable at all times.

Request a Quote

Introduction to gene expression analysis

Microorganisms can be applied as production strain or food ingredient when they are stable and functional under certain conditions. For example, probiotic bacteria need to be resistant to gastric acid in the stomach and intestines. To ensure the consistent performance of microbial strains, it is necessary to investigate which genes are expressed in a desired physiological environment. Our gene expression analysis service enables the identification of phenotypic differences at molecular level, provides insight into the role of differential gene expression in microbial bio-processes, and help to discover novel genes and mRNA isoforms.

Metatranscriptomic analyses measure the expression of multiple genes and functions at once by detecting and quantitating mRNA transcripts. Metatranscriptomics explores the functional diversity of microbial community in different habitats, as well as to examine microbial response in an altered environment. Metatranscriptomics simultaneously investigates the structural and functional diversity of a certain microbial community. We also apply RNA-seq approach to detect, quantitate and compare mRNA transcript levels of a certain microbial strain under various conditions. We offer both microbial RNA-seq based on NGS and full-length, direct RNA sequencing based on PacBio or Oxford nanopore platform for gene expression analysis.

Gene expression analysis workflow

Bioinformatics Analysis

Our bioinformatics analysis pipeline includes data quality control, gene expression analysis and advanced analysis, which is flexible to your needs. Please feel free to contact us to discuss your project.

Bioinformatics Analysis Details
Data QC Read quality assessment, trimming and filtering.
Gene Expression Analysis Discover novel genes and mRNA isoforms, estimate gene expression levels, and quantify alternative splicing events.
Advanced Analysis Reveal the relationship between gene expression and environmental changes, provide insight into production strain optimization.

Sample requirement

    1. RNA amount ≥ 3 μg, concentration ≥ 50 ng/μL, RIN ≥ 7.0, 28s/18s ≥ 1.5, OD260/280 = 1.8~2.2; OD260/230 ≥ 1.8

Sampling kits: we provide a range of microbial sampling kits for clients, including MicroCollect™ oral sample microbial collection products and MicroCollect™ stool sample collection products.

Deliverables: raw sequencing data (FASTQ), trimmed and stitched sequences, quality-control dashboard, statistic data, and your designated bioinformatics report.


  1. Newman M M, Lorenz N, Hoilett N, et al. Changes in rhizosphere bacterial gene expression following glyphosate treatment. Science of the Total Environment, 2016, 553: 32-41.
* For Research Use Only. Not for use in diagnostic procedures or other clinical purposes.

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