🧬 Requirements for Reference-based Transcriptome Sequencing
1. Which species are suitable for reference-based eukaryotic transcriptome sequencing?
To perform reference-based eukaryotic transcriptome sequencing, the species must meet the following criteria:
It must be a eukaryote.
A reference genome must be available, assembled at least to the scaffold level.
Comprehensive genome annotation is required.
Note: For species without a reference genome, de novo transcriptome sequencing is the recommended alternative.
⛏️ Transcriptome Data Mining Strategies
2. How to perform transcriptome data mining?
Data mining can be conducted from two perspectives: all expressed genes and differentially expressed genes (DEGs).
For all expressed genes, mining can be based on functional annotation, gene IDs, gene names, and sequence information. Additionally, analyses such as Venn diagrams of expressed gene sets and Weighted Gene Co-expression Network Analysis (WGCNA) can be performed.
For DEGs, Venn diagrams are used to identify common differentially expressed genes across different treatment batches or comparisons. Since genes with similar expression trends often share similar functions, co-expression trend analysis is a powerful method for in-depth mining of DEGs.
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