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Related Concept Videos

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Related Experiment Video

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Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq
10:22

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Strand-specific deep sequencing of the transcriptome.

Ana P Vivancos1, Marc Güell, Juliane C Dohm

  • 1Centre for Genomic Regulation (CRG), UPF, 08003 Barcelona, Spain.

Genome Research
|June 4, 2010
PubMed
Summary
This summary is machine-generated.

Direct Strand Specific Sequencing (DSSS) enables strand-specific transcriptome sequencing. This method accurately maps gene expression and regulatory elements, offering higher resolution for prokaryotic and eukaryotic organisms.

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Last Updated: Jun 12, 2026

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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Antisense-mediated regulation impacts a significant number of genes.
  • Strand-specific transcriptome sequencing is crucial for accurate gene expression analysis.

Purpose of the Study:

  • To develop and validate a novel strand-specific protocol for transcriptome sequencing called Direct Strand Specific Sequencing (DSSS).
  • To assess the efficiency and applicability of DSSS in both prokaryotic and eukaryotic systems.

Main Methods:

  • Development of Direct Strand Specific Sequencing (DSSS) protocol using Illumina next-generation sequencing.
  • Testing DSSS on prokaryotic (Mycoplasma pneumoniae) and eukaryotic (Mus musculus) RNA samples.
  • Validation of DSSS results using strand-specific tiling arrays and quantitative PCR (qPCR).

Main Results:

  • DSSS successfully generated strand-specific transcriptome data for both prokaryotic and eukaryotic samples.
  • DSSS results were highly consistent with validation methods (tiling arrays and qPCR).
  • DSSS demonstrated a higher dynamic range and single-base resolution compared to existing methods, facilitating antisense detection and precise mapping of regulatory regions.

Conclusions:

  • DSSS is a simple, efficient, and reliable strategy for strand-specific transcriptome sequencing.
  • DSSS is a valuable tool for genome annotation, especially for identifying transcription start sites and untranslated regions.
  • The protocol is broadly applicable to both prokaryotic and eukaryotic transcription studies, leveraging advances in next-generation sequencing technology.