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Related Experiment Videos

DeepSAGE--digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples.

Kåre L Nielsen1, Annabeth Laursen Høgh, Jeppe Emmersen

  • 1Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University DK-9000 Aalborg, Denmark.

Nucleic Acids Research
|October 10, 2006
PubMed
Summary

Digital transcriptomics using pyrophosphatase-based DNA sequencing offers sensitive, cost-effective gene expression profiling. This method simplifies sample handling and reveals abundant stress-related potato transcripts, including novel ones.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Plant Science

Background:

  • Serial Analysis of Gene Expression (SAGE) is a traditional method for gene expression profiling.
  • SAGE involves complex sample preparation and handling.
  • There is a need for more sensitive, cost-effective, and user-friendly transcriptomics methods.

Purpose of the Study:

  • To evaluate digital transcriptomics using pyrophosphatase-based ultra-high throughput DNA sequencing of di-tags for gene expression profiling.
  • To compare the performance of DeepSAGE and LongSAGE methods.
  • To analyze gene expression changes in potato under stress conditions.

Main Methods:

  • Digital transcriptomics utilizing pyrophosphatase-based ultra-high throughput DNA sequencing of di-tags.
  • Comparison of DeepSAGE and LongSAGE data analysis pipelines.

Related Experiment Videos

  • Transcriptome analysis of dormant versus harvested potato samples.

    • Main Results:

    • Digital transcriptomics provides high sensitivity and cost-effective gene expression profiling.
    • DeepSAGE and LongSAGE demonstrate enhanced detection power and sample multiplexing capabilities compared to traditional SAGE.
    • Dormant potatoes exhibit a significant abundance of up-regulated transcripts associated with stress compared to harvested potatoes.
    • Numerous uncharacterized transcripts, likely involved in abiotic stress response, were identified in potato.

    Conclusions:

    • Pyrophosphatase-based digital transcriptomics is a powerful and simplified alternative to SAGE for gene expression profiling.
    • The method effectively identifies stress-responsive transcripts in potato, including novel genes.
    • This approach has significant implications for understanding plant stress responses and improving crop resilience.