PUBLICATION
Identification of Novel Transcribed Regions in Zebrafish (Danio rerio) Using RNA-Sequencing
- Authors
- Wang, J., Vesterlund, L., Kere, J., Jiao, H.
- ID
- ZDB-PUB-160728-3
- Date
- 2016
- Source
- PLoS One 11: e0160197 (Journal)
- Registered Authors
- Keywords
- Zebrafish, RNA sequencing, RNA extraction, Genomic databases, Genome annotation, Transcriptome analysis, Gene expression, Reverse transcriptase-polymerase chain reaction
- MeSH Terms
-
- Animals
- Gene Expression Regulation, Developmental
- Molecular Sequence Annotation
- Transcriptome*
- Zebrafish/genetics*
- Zebrafish/growth & development
- PubMed
- 27462902 Full text @ PLoS One
Citation
Wang, J., Vesterlund, L., Kere, J., Jiao, H. (2016) Identification of Novel Transcribed Regions in Zebrafish (Danio rerio) Using RNA-Sequencing. PLoS One. 11:e0160197.
Abstract
Zebrafish (Danio rerio) has emerged as a model organism to investigate vertebrate development and human genetic diseases. However, the zebrafish genome annotation is still ongoing and incomplete, and there are still new gene transcripts to be found. With the introduction of massive parallel sequencing, whole transcriptome studies became possible. In the present study, we aimed to discover novel transcribed regions (NTRs) using developmental transcriptome data from RNA sequencing. In order to achieve this, we developed an in-house bioinformatics pipeline for NTR discovery. Using the pipeline, we detected 152 putative NTRs that at the time of discovery were not annotated in Ensembl and NCBI gene database. Four randomly selected NTRs were successfully validated using RT-PCR, and expression profiles of 10 randomly selected NTRs were evaluated using qRT-PCR. The identification of these 152 NTRs provide new information for zebrafish genome annotation as well as new candidates for studies of zebrafish gene function.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping