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Updated: May 20, 2026
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Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish
Published on: October 27, 2017
Incorporating RNA-seq data into the zebrafish Ensembl genebuild
John E Collins1, Simon White, Stephen M J Searle
1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom. jec@sanger.ac.uk
Genome Research
|July 17, 2012
Summary
RNA sequencing (RNA-seq) data significantly improved zebrafish gene annotation in Ensembl version 62. This enhanced gene catalog aids in understanding gene structure and function for future research.
Area of Science:
- Genomics
- Transcriptomics
- Bioinformatics
Background:
- Ensembl gene annotation relies on public transcript data for accuracy.
- RNA sequencing (RNA-seq) offers a cost-effective method to enhance species-specific gene models.
Purpose of the Study:
- To present two improved zebrafish gene annotations in Ensembl version 62.
- To detail the integration of RNA-seq data for refining gene models.
Main Methods:
- Assembly of RNA-seq data from multiple tissues and developmental stages.
- Development of a 3'-end capture and sequencing protocol for transcript refinement.
- Integration of RNA-seq data with the Ensembl/VEGA genebuild.
Main Results:
- Generated 25,748 gene models using RNA-seq data.
- Refined 46.1% of initial models using a 3'-end protocol.
- Produced a comprehensive annotation of 26,152 genes through Ensembl/VEGA genebuild.
Conclusions:
- RNA-seq data significantly enhanced zebrafish gene annotation accuracy and completeness.
- The developed pipeline improves 3' untranslated regions and intron/exon boundaries.
- This approach is valuable for annotating organisms with limited cDNA data.
