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Metatranscriptome Sequencing


Metatranscriptome refers to the total content of gene transcripts (RNA copies of the genes) in a nature community (i.e. soil, water, sea, feces, and gut), considered as a unique entity, at a specific moment of sampling. Metatranscriptome changes with time and environmental variation. Metatranscriptome sequencing using the next-generation sequencing (NGS) can now be applied to obtain the whole expression profile in a community and to follow the dynamics of gene expression patterns over time or environmental parameters, improving our understanding of the structure, function, and adaptive mechanisms in complex communities.

Metatranscriptome sequencing identifies gene expression of microbes, both eukaryotes and prokaryotes, within natural environments. Specifically, this service allows you to obtain whole gene expression profiling of complex microbial communities, taxonomic analysis of species, functional enrichment analysis of differently expressed genes, and more.

Service Specifications


Microbial ecology research

  • Functional active bacteria characterization
  • Community metabolic interaction

Clinical research

  • Immune recognition
  • Immune education
  • Autoimmune processes trigger

Biotechnology research


  • Extensive experience with thousands of samples being successfully sequenced.
  • Unsurpassed data quality with a guaranteed Q30 score ≥ 80% that exceeds Illumina’s official benchmarks.
  • Comprehensive analysis using industry standard software and mature in-house pipeline to meet multiple bioinformatic requests.

Sample Requirements


Library Type Sample Type Amount RNA Integrity Number
(Agilent 2100)
Meta-transcriptome Library
Total RNA
≥ 2.5 μg
≥ 6.5, smooth base line
OD260/280 = 1.8-2.2;
OD260/230 ≥ 1.8;

Sequencing Parameter and Analysis

Platform Illumina Novaseq 6000
Read length Pair-end 150
Recommended Sequencing Depth ≥ 40 million read pair per sample
Standard Data Analysis
  • Data Quality Control
  • De novo Assembly
  • Gene Functional Annotation
  • rRNA& mRNA Taxonomic Analysis
  • Gene expression quantification & Differential expressed genes profiling & Enrichment analysis
  • Comparative Analysis between Various Samples
  • Note: For detailed information, please refer to the Service Specifications and contact us for customized requests.

    Project Workflow


    Water in long island sound

    Sequencing Strategy:

    Library preparation: Directional RNA library
    Sequencing: Illumina HiSeq 2000 platform

    Figure 1. Red-tide bloom and the causative organisms.

    (A) Photograph of the red tide.
    (B) Light microscopic image of the causative ciliate.
    (C) 18S rDNA phylogenetic tree verifying that the causative ciliate was M. rubrum.

    Figure 2. Metabolic circuit map constructed from the cryptophyte subset of the metatranscriptome. Highlighted in this circuit are pathways of nucleotide metabolism (red), carbohydrate metabolism (blue), energy metabolism (purple), lipid metabolism (cyan), and amino acid metabolism (yellow) in cryptophytes.

    The Mesodinium-farming-Teleaulax model not only distinguishes itself from the current model of Mesodinium enslaving cryptophyte chloroplasts or the organelle complex, but by promoting the proliferation of the endosymbiotic cells also differs from the conventional whole-cell endosymbiont models in which only binary division synchronous with host division is expected. The ecological significance in each case should be further studied in the future.

    Figure 1 Error Rate Distribution

    The x-axis shows the base position along each sequencing read and the y-axis shows the base error rate.

    Figure 2 GC Content Distribution

    Horizontal axis for reads position, vertical axis for single base percentage. Different color for different base type.

    Figure 3 Composition of raw data.

    Figure 4 Length distribution of transcripts and unigenes.

    Figure 5 Species abundance clustering.

    Figure 6 Quantification of transcripts.

    Figure 7 Volcano diagram of differential expression genes.

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