CrustyBase


32928113	CrustyBase: an interactive online database for crustacean transcriptomes. [PMID: 32928113] Cameron J Hyde, Quinn P Fitzgibbon, Abigail Elizur, Gregory G Smith, Tomer Ventura Abstract 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 https://crustybase.org 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. BMC Genomics. 2020:21(1) \| 10 Citations (from Europe PMC, 2025-03-29)

CrustyBase: an interactive online database for crustacean transcriptomes. [PMID: 32928113]

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

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 https://crustybase.org 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.

BMC Genomics. 2020:21(1) | 10 Citations (from Europe PMC, 2025-03-29)

URL:	https://crustybase.org
Full name:	Crustacean Transcriptome Database
Description:	CrustyBase is a repository and analysis suite for crustacean transcriptome data. Each dataset describes the activity of every expressed gene in a particular species, across a set of samples. CrustyBase currently contains 11 transcriptome datasets, but anyone can add to this in the future by uploading their own.
Year founded:	2020
Last update:
Version:
Accessibility:	Accessible
Country/Region:	Australia

Data type:	DNA Protein RNA
Data object:	Animal
Database category:	Expression Metadata Raw bio-data
Major species:	Macrobrachium nipponense Sagmariasus verreauxi Temora longicornis Caligus rogercresseyi Gecarcinus lateralis Litopenaeus vannamei Daphnia magna Panulirus ornatus
Keywords:	c'rustacean transcriptome

University/Institution:	University of the Sunshine Coast
Address:	Sippy Downs, Queensland, 4556, Australia
City:
Province/State:	Queensland
Country/Region:	Australia
Contact name (PI/Team):	Cameron J Hyde
Contact email (PI/Helpdesk):	chyde@crustybase.org

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Database Commons a catalog of worldwide biological databases