An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes

Abstract
Data availability
Article and author information
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Abstract

The zebrafish is ideal for studying embryogenesis and is increasingly applied to model human disease. In these contexts, RNA-sequencing (RNA-seq) provides mechanistic insights by identifying transcriptome changes between experimental conditions. Application of RNA-seq relies on accurate transcript annotation for a genome of interest. Here, we find discrepancies in analysis from RNA-seq datasets quantified using Ensembl and RefSeq zebrafish annotations. These issues were due, in part, to variably annotated 3' untranslated regions and thousands of gene models missing from each annotation. Since these discrepancies could compromise downstream analyses and biological reproducibility, we built a more comprehensive zebrafish transcriptome annotation that addresses these deficiencies. Our annotation improves detection of cell type-specific genes in both bulk and single cell RNA-seq datasets, where it also improves resolution of cell clustering. Thus, we demonstrate that our new transcriptome annotation can outperform existing annotations, providing an important resource for zebrafish researchers.

Data availability

All data generated in this study are available in accompanying source data files. Transcriptome annotation files described in this study are available for download at zf-transcriptome.umassmed.edu. Raw and processed RNA-seq data generated in this study are available at GEO (GSE152759).

The following data sets were generated

1. Lawson ND
(2020) Bulk RNA-seq data to assess an improved zebrafish transcriptome annotation
NCBI Gene Expression Omnibus, GSE152759.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152759

The following previously published data sets were used

1. Whitesell TR
2. Chrystal PW
3. Ryu JR
4. Munsie N
5. Grosse A
6. French CR
7. Workentine ML
8. Li R
9. Zhu LJ
10. Waskiewicz A
11. Lehmann OJ
12. Lawson ND
13. Childs SJ
(2019) Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish
NCBI Gene Expression Omnibus, GSE119718.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119718
1. Pauli A
2. Valen E
3. Lin MF
4. Garber M
5. Vastenhouw NL
6. Levin JZ
7. Sandelin A
8. Rinn JL
9. Regev A
10. Schier AF
(2011) Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis
NCBI Gene Expression Omnibus, GSE32900.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32900
1. Ulitsky I
2. Shkumatava A
3. Jan CH
4. Subtelny AO
5. Koppstein D
6. Bell G
7. Sive H
8. Bartel DP
(2012) Extensive alternative polyadenylation during zebrafish development
NCBI Gene Expression Omnibus, GSE37453.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37453

Article and author information

Author details

Nathan D Lawson

Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States

For correspondence
nathan.lawson@umassmed.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-7788-9619
Rui Li

Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States

Competing interests
The authors declare that no competing interests exist.
Masahiro Shin

Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States

Competing interests
The authors declare that no competing interests exist.
Ann Grosse

Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States

Competing interests
The authors declare that no competing interests exist.
Onur Yukselen

Department of Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States

Competing interests
The authors declare that no competing interests exist.
Oliver A Stone

Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom

Competing interests
The authors declare that no competing interests exist.
Alper Kucukural

Department of Bioinformatic and Integrative Biology, University of Massachusetts Medical School, Worcester, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-9983-394X
Lihua Zhu

Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States

Competing interests
The authors declare that no competing interests exist.

Funding

National Heart, Lung, and Blood Institute (R35HL140017)

Nathan D Lawson

National Human Genome Research Institute (U01HG007910)

Onur Yukselen
Alper Kucukural

National Center for Advancing Translational Sciences (UL1TR001453)

Onur Yukselen
Alper Kucukural

National Institute of Neurological Disorders and Stroke (R21NS105654)

Nathan D Lawson

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: Zebrafish studies were performed in accordance with protocols #A2613 and #A2632 approved by the University of Massachusetts institutional animal care and use committee (IACUC).

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.