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mRNA Sequencing (mRNA-seq)

Introduction to mRNA Sequencing

Messenger RNA sequencing (mRNA-seq) has revolutionized the exploration of cellular functionality, offering researchers unparalleled insights into the transcriptional landscape of cells. By leveraging high-throughput and precise next-generation sequencing (NGS) techniques, RNA-seq unveils gene expression profiles and highlights the dynamic variations within the transcriptome. This innovative technique selectively captures or enriches single-stranded messenger RNAs (mRNAs), converting them into complementary DNA (cDNA) for streamlined library preparation.

At Novogene, we employ cutting-edge Illumina NovaSeq platforms for sequencing cDNA libraries. These platforms utilize a paired-end 150 bp sequencing strategy, providing high-quality short-read data. Leveraging our extensive experience and robust sequencing capacity, Novogene offers a diverse range of services to meet various research objectives. Our offerings extend beyond eukaryotic mRNA sequencing (mRNA-seq). Novogene can also deliver data on prokaryotic transcripts, non-coding RNAs, full-length isoforms (long-reads), whole transcriptomes, and meta-transcriptomes.

Unlocking the Potential of mRNA Sequencing

Discover the power of mRNA-seq with Novogene’s services, designed to assist in a variety of research goals:

  • Explore Diversity: Understand transcript profiles across different tissues, conditions, and treatments.
  • Uncover Novel Insights: Identify new transcripts, alternative splicing, and variations for a comprehensive view.
  • Navigate Development: Study developmental mechanisms and drug resistance through time-course gene expression.
  • Find Biomarkers: Discover potential biomarkers using novel transcripts, SNP/InDel identification, and fusion gene analysis.
  • Comprehensive Analysis: Combine transcriptome data with omics analysis for a holistic perspective.
  • Clinical Insight: Investigate pathogenic mechanisms and clinical subtypes for precise clinical diagnosis.

Why Choose Novogene for Your mRNA-seq Needs?

  • Precision and Efficiency: Benefit from high throughput and accuracy with a remarkable Q30 score of ≥ 85%. Plus, our process requires minimal initial RNA input.
  • Proven Expertise: With a rich history of successfully completing thousands of projects, Novogene brings extensive experience to the table. Many researchers have relied on our services to publish in high-impact factor journals.
  • Comprehensive Solutions: Novogene provides all-encompassing solutions, covering quantification, differential gene expression, annotation of novel transcripts, alternative splicing, discovery of fusion genes, and exploring potential variations.
  • Expert Bioinformatics: Our highly qualified bioinformaticians ensure your data is publication-ready. We use personalized pipelines tailored to species, whether they have a reference genome or not.

Choose Novogene for mRNA-seq that not only meets but exceeds your expectations. Elevate your research with us.

mRNA-seq Specifications: Sample Requirements

Library Type Sample Type Amount RNA Integrity Number (Agilent 2100) Purity (NanoDrop)
Eukaryotic RNA-Seq (non-stranded library) Total RNA ≥ 100 ng ≥ 4.0, with smooth base line A260/280 = 1.8-2.2
A260/230 ≥ 1.8
Total RNA (Blood) ≥ 400 ng ≥ 5.8, with smooth base line
Eukaryotic RNA-Seq (strand specific library) Total RNA ≥ 400 ng ≥ 5.8, with smooth base line A260/280 = 1.8-2.2
A260/230 ≥ 1.8

Note: Sample amounts are listed for reference only. For detailed information, please contact us with your customized requests.

mRNA-seq Specifications: Sequencing and Analysis

Sequencing Platform Illumina NovaSeq 6000 and X-Plus Sequencing Platform
Read Length Paired-end 150 bp
Data Output
  • ≥ 20 million read pairs per sample for species with reference genome
  • ≥ 50 million read pairs per sample for species without reference genome (de novo transcriptome assembly projects)
  • Data Analysis Capability
  • Data Quality Control
  • Gene expression quantification
  • Differential expression profiling
  • Functional enrichment analysis
  • Novel transcripts identification
  • SNP & InDel analysis
  • Alternative splicing (AS) analysis
  • Fusion gene prediction
  • Protein-Protein Interaction (PPI) analysis
  • Transcription factors and oncogene functional annotation
  • Note: Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

    Project Workflow of Novogene mRNA-seq Services

    The project workflow at Novogene for mRNA-seq services begins with Sample Quality Control (Sample QC), ensuring that the provided samples meet the stringent criteria of the RNA-Seq technique. Following this, tailored libraries are meticulously crafted based on the target organism and application, with the library’s quality assessed through Library QC. Subsequently, a 150 bp paired-end sequencing strategy, employing Illumina PE150 technology, captures the essence of the samples. The resulting data undergoes thorough quality checks (Data QC), and our experienced bioinformaticians perform in-depth analyses to extract valuable insights. The culmination of this journey is the delivery of comprehensive, publication-ready results.

    Featured Publications using Novogene’s RNA-seq service

    RNA-seq (mRNA-seq) is the most frequently cited NGS method. Here we have summarized some outstanding academic publications that used Novogene RNA sequencing (mRNA Sequencing) services.

    Error Rate Distribution

    error rate for Novogene RNA-seq

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

    GC Content Distribution

    GC Content Distribution for Novogene RNA-seq

    The x-axis for reads position, the y-axis for single base percentage. Different color for different base type.

    Classification of Raw Reads

    Classification of Raw Reads for Novogene RNA-seq

    Reads Distribution on Reference Genome

    Reads Distribution on Reference Genome for Novogene RNA-seq

    Gene Expression Quantification

    Gene Expression Quantification for Novogene RNA-seq

    The x-axis represents the name of sample, the y-axis indicates the log10(FPKM+1), parameters of box plots are indicated, including maximum, upper quartile, mid-value, lower quartile and minimum.

    Volcano Plot of changes on Gene Expression

     Volcano Plot of changes in Gene Expression for Novogene RNA-seq

    The x-axis shows the fold change of genes in different samples. The y-axis shows the statistically significant degree of changes in gene expression levels. The smaller the corrected pvalue, the bigger -log10(corrected pvalue), the more significant the difference. The points represent genes, blue dots indicate no significant difference in gene expression, red dots indicate upregulated differentially expressed genes, green dots indicate downregulated differentially expressed genes.

    Hierarchical Clustering Heatmap of Differential Expression

    Hierarchical Clustering Heatmap of Differential Expression for Novogene RNA-seq

    The overall results of FPKM cluster analysis, clustered using the log10(FPKM+1) value. Red denotes genes with high expression levels, and blue denotes genes with low expression levels. The color ranging from red to blue indicates log10(FPKM+1) value from large to small.