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Reference Transcriptome Sequencing

Reference Transcriptome Sequencing
Use reference transcriptome sequencing to:
  • Conduct a differential gene expression analysis when there is no reference genome
  • Discover differential gene expression where no one has looked before


Considerations before starting a reference transcriptome sequencing project:

  • Is there a „nearby“ reference genome?
  • Deep sequencing or cDNA normalization?
  • Aim of the study versus limits of a reference transcriptome?
  • Short term goals and long term goals?
  • Initial setup (expression states)?
  • Functional setup (replicates and conditions)?

Let us guide you – from design to analysis

Example projects using reference transcriptome sequencing:

  • Functional expression study on an organism with vague taxonomy
  • Breeding studies and selection
  • Gene expression for interesting/selected phenotypes

Applications related to reference transcriptome sequencing:

  • RNA sequencing
  • small RNA sequencing


A typical workflow for a reference transcriptome project is shown in the graphic below. Please note that our highly-modular processes allow you various entry and opting out options. If you outsource your entire NGS project to Microsynth or only parts of it is up to you.
For further reading and a detailed technical description, please download our Application Note Reference Transcriptome Sequencing (see related downloads).



Our analysis module provides de novo information on previously unknown transcriptomes. The results provided include a broad overview of the transcriptome, the transcript sequences and their detailed annotation.

  1. Information on the GC content and size distribution of the assembled transcripts. (see Figure 1)
  2. Information on the exact transcript sequences. (see Table 1)
  3. Annotation of the transcript sequences and links to available information found in public databases. (see Table 2)


Figure 1: Histogram of transcipt sizes and their GC content.


Table 1: This detail of a result table lists two exemplary transcripts.


Table 2: Detail of a results table listing parts of the annotation for the two exemplary transcripts.

Turnaround Time

  • Delivery of data within 30 working days upon sample receipt (includes library preparation and sequencing)
  • Additional 10 working days for data analysis (bioinformatics)
  • Express service possible on request