Dataset Information

Squalomix: shark and ray genome analysis consortium and its data sharing platform.

ABSTRACT: The taxon Elasmobranchii (sharks and rays) contains one of the long-established evolutionary lineages of vertebrates with a tantalizing collection of species occupying critical aquatic habitats. To overcome the current limitation in molecular resources, we launched the Squalomix Consortium in 2020 to promote a genome-wide array of molecular approaches, specifically targeting shark and ray species. Among the various bottlenecks in working with elasmobranchs are their elusiveness and low fecundity as well as the large and highly repetitive genomes. Their peculiar body fluid composition has also hindered the establishment of methods to perform routine cell culturing required for their karyotyping. In the Squalomix consortium, these obstacles are expected to be solved through a combination of in-house cytological techniques including karyotyping of cultured cells, chromatin preparation for Hi-C data acquisition, and high fidelity long-read sequencing. The resources and products obtained in this consortium, including genome and transcriptome sequences, a genome browser powered by JBrowse2 to visualize sequence alignments, and comprehensive matrices of gene expression profiles for selected species are accessible through https://github.com/Squalomix/info.

SUBMITTER: Nishimura O

PROVIDER: S-EPMC9561540 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Squalomix: shark and ray genome analysis consortium and its data sharing platform.

Nishimura Osamu O Rozewicki John J Yamaguchi Kazuaki K Tatsumi Kaori K Ohishi Yuta Y Ohta Tazro T Yagura Masaru M Niwa Taiki T Tanegashima Chiharu C Teramura Akinori A Hirase Shotaro S Kawaguchi Akane A Tan Milton M D'Aniello Salvatore S Castro Filipe F Machado André A Koyanagi Mitsumasa M Terakita Akihisa A Misawa Ryo R Horie Masayuki M Kawasaki Junna J Asahida Takashi T Yamaguchi Atsuko A Murakumo Kiyomi K Matsumoto Rui R Irisarri Iker I Miyamoto Norio N Toyoda Atsushi A Tanaka Sho S Sakamoto Tatsuya T Semba Yasuko Y Yamauchi Shinya S Yamada Kazuyuki K Nishida Kiyonori K Kiyatake Itsuki I Sato Keiichi K Hyodo Susumu S Kadota Mitsutaka M Uno Yoshinobu Y Kuraku Shigehiro S

F1000Research 20220921

The taxon Elasmobranchii (sharks and rays) contains one of the long-established evolutionary lineages of vertebrates with a tantalizing collection of species occupying critical aquatic habitats. To overcome the current limitation in molecular resources, we launched the Squalomix Consortium in 2020 to promote a genome-wide array of molecular approaches, specifically targeting shark and ray species. Among the various bottlenecks in working with elasmobranchs are their elusiveness and low fecundity ...[more]

PMID: 36262334

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Project description:BackgroundDespite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-using the large amount of data generated locally or internationally. Additionally, it is recognised that inconsistent and low quality experimental annotation in public data repositories significantly compromises the re-use of microarray data for meta-analysis. MiMiR, the Microarray data Mining Resource was designed to tackle some of these limitations and challenges. Here we present new software components and enhancements to the original infrastructure that increase accessibility, utility and opportunities for large scale mining of experimental and clinical data.ResultsA user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package.ConclusionThe new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies.

Dataset Information

Squalomix: shark and ray genome analysis consortium and its data sharing platform.

Publications

Squalomix: shark and ray genome analysis consortium and its data sharing platform.

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