Transcriptomic Analysis Pipeline (TAP) for quality control and functional assessment of transcriptomes

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• RNA-sequencing (RNA-seq) is crucial for understanding biological mechanisms and non-coding RNAs like lncRNAs.
• Gaps exist in understanding how RNA-seq library protocols impact lncRNA analysis, especially in non-mammalian models.
• Next-generation sequencing (NGS) technologies offer cost-effective, comprehensive genetic analysis.

Approach:

• Comparative analysis of polyA+ RNA capture and rRNA-depletion RNA-seq library protocols in Drosophila melanogaster under thermal stress.
• Development and application of a Transcriptome Analysis Pipeline (TAP) for systematic RNA-seq data assessment.
• Evaluation of technical and functional dimensions of RNA-seq data for lncRNA expression.

Key Points:

• The polyA+ protocol effectively captures most expressed lncRNAs in the Drosophila melanogaster transcriptome.
• rRNA-depletion showed limited advantages for lncRNA analysis in this specific non-mammalian study.
• PolyA+ protocol yielded more usable reads and improved splice junction detection accuracy.

Conclusions:

• The study introduces TAP, a versatile pipeline for uniform RNA-seq data processing across organisms with reference genomes.
• Highlights the critical importance of selecting appropriate RNA-seq library protocols based on research objectives.
• Provides insights into optimizing lncRNA expression analysis in non-model organisms.