CrustyBase: an interactive online database for crustacean transcriptomes

Cameron J Hyde; Quinn P Fitzgibbon; Abigail Elizur; Gregory G Smith; Tomer Ventura

doi:10.1186/s12864-020-07063-2

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CrustyBase: an interactive online database for crustacean transcriptomes

Journal article

Open access

Peer reviewed

CrustyBase: an interactive online database for crustacean transcriptomes

Cameron J Hyde, Quinn P Fitzgibbon, Abigail Elizur, Gregory G Smith and Tomer Ventura

BMC Genomics, Vol.21, pp.1-10

2020

DOI: https://doi.org/10.1186/s12864-020-07063-2

PMCID: PMC7490944

PMID: 32928113

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Abstract

Crab

Visualize

Lobster

RNA-seq

Gene

Expression

Database

Crayfish

Shrimp

Transcriptome sequencing has opened the field of genomics to a wide variety of researchers, owing to its efficiency, applicability across species and ability to quantify gene expression. The resulting datasets are a rich source of information that can be mined for many years into the future, with each dataset providing a unique angle on a specific context in biology. Maintaining accessibility to this accumulation of data presents quite a challenge for researchers. The primary focus of conventional genomics databases is the storage, navigation and interpretation of sequence data, which is typically classified down to the level of a species or individual. The addition of expression data adds a new dimension to this paradigm – the sampling context. Does gene expression describe different tissues, a temporal distribution or an experimental treatment? These data not only describe an individual, but the biological context surrounding that individual. The structure and utility of a transcriptome database must therefore reflect these attributes. We present an online database which has been designed to maximise the accessibility of crustacean transcriptome data by providing intuitive navigation within and between datasets and instant visualization of gene expression and protein structure. The site is accessible at <a href="https://crustybase.org">https://crustybase.org</a> and currently holds 10 datasets from a range of crustacean species. It also allows for upload of novel transcriptome datasets through a simple web interface, allowing the research community to contribute their own data to a pool of shared knowledge.

Details

Title: CrustyBase: an interactive online database for crustacean transcriptomes
Authors: Cameron J Hyde (Corresponding Author) - University of the Sunshine Coast, Queensland, GeneCology Research Centre - Legacy
Quinn P Fitzgibbon (Author) - University of Tasmania
Abigail Elizur (Author) - University of the Sunshine Coast, Queensland, GeneCology Research Centre - Legacy
Gregory G Smith (Author) - University of Tasmania
Tomer Ventura (Author) - University of the Sunshine Coast, Queensland, GeneCology Research Centre - Legacy
Publication details: BMC Genomics, Vol.21, pp.1-10
Publisher: BioMed Central Ltd.
Date published: 2020
DOI: 10.1186/s12864-020-07063-2
ISSN: 1471-2164
PMID: 32928113; PMC7490944
Copyright note: Copyright © The Author(s). 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
Grants: The ARC Research Hub for Sustainable Lobster Aquaculture, IH190100014, Australian Research Council (Australia, Canberra) - ARC
Redefining the molecular mechanism underlying crustacean metamorphosis, DP160103320, Australian Research Council (Australia, Canberra) - ARC
Understanding masculinity, the crustacean way, DE130101089, Australian Research Council (Australia, Canberra) - ARC
Organisation Unit: School of Science and Engineering - Legacy; School of Education and Tertiary Access; School of Science, Technology and Engineering; Centre for Bioinnovation
Language: English
Record Identifier: 99479407502621
Output Type: Journal article

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