Identification of Novel Transcribed Regions in Zebrafish (Danio rerio) Using RNA-Sequencing

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http://hdl.handle.net/10138/167015

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Wang , J , Vesterlund , L , Kere , J & Jiao , H 2016 , ' Identification of Novel Transcribed Regions in Zebrafish (Danio rerio) Using RNA-Sequencing ' , PLoS One , vol. 11 , no. 7 , 0160197 . https://doi.org/10.1371/journal.pone.0160197

Title: Identification of Novel Transcribed Regions in Zebrafish (Danio rerio) Using RNA-Sequencing
Author: Wang, Jingwen; Vesterlund, Liselotte; Kere, Juha; Jiao, Hong
Contributor organization: Juha Kere / Principal Investigator
Medicum
Department of Medical and Clinical Genetics
Date: 2016-07-27
Language: eng
Number of pages: 16
Belongs to series: PLoS One
ISSN: 1932-6203
DOI: https://doi.org/10.1371/journal.pone.0160197
URI: http://hdl.handle.net/10138/167015
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.
Subject: SEQ
GENE
EMBRYOGENESIS
TOPHAT
3111 Biomedicine
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion


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