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Generation and analysis of a mouse multitissue genome annotation atlas
Matthew Adams1, Christopher Vollmers2
1Department of Molecular, Cellular, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA.
Genome Research
|October 23, 2024
Summary
Researchers created a detailed mouse genome annotation by analyzing full-length transcript sequences from multiple tissues. This Tissue-level Atlas of Mouse Isoforms provides comprehensive gene expression data for diverse research applications.
Area of Science:
- Genomics
- Transcriptomics
- Bioinformatics
Background:
- Accurate genome annotation requires understanding tissue-specific gene and transcript isoform expression.
- Previous methods lacked the throughput and accuracy for comprehensive, tissue-level isoform information.
Purpose of the Study:
- To generate a high-resolution, tissue-level genome annotation for the mouse (Mus musculus).
- To provide a resource for understanding gene expression across different tissues.
Main Methods:
- Utilized nanopore-based R2C2 long-read sequencing for full-length cDNA.
- Generated 64 million high-accuracy consensus reads across a dozen mouse tissues.
- Employed the Mandalorion tool for read processing and data generation.
Main Results:
- Developed the Tissue-level Atlas of Mouse Isoforms, a comprehensive genome annotation.
- The atlas contains at least one full-length isoform for most expressed genes in each analyzed tissue.
- The data is accessible as a trackhub for the UCSC Genome Browser.
Conclusions:
- Long-read sequencing and advanced library preparation enable accurate, tissue-level genome annotation.
- The Tissue-level Atlas of Mouse Isoforms is a valuable resource for mouse research.
- This annotation facilitates deeper understanding of gene regulation and function across tissues.
