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AgriSeqDB: an online RNA-Seq database for functional studies of agriculturally relevant plant species
journal contributionposted on 17.12.2020, 05:03 by Andrew Robinson, Muluneh Oli, Rachel Salby, Clayton Bolitho, Andrew Williams, Simon Huggard, Eva Fisch, K Unsworth, James Whelan, Mathew Lewsey
© 2018 The Author(s). Background: The genome-wide expression profile of genes in different tissues/cell types and developmental stages is a vital component of many functional genomic studies. Transcriptome data obtained by RNA-sequencing (RNA-Seq) is often deposited in public databases that are made available via data portals. Data visualization is one of the first steps in assessment and hypothesis generation. However, these databases do not typically include visualization tools and establishing one is not trivial for users who are not computational experts. This, as well as the various formats in which data is commonly deposited, makes the processes of data access, sharing and utility more difficult. Our goal was to provide a simple and user-friendly repository that meets these needs for data-sets from major agricultural crops. Description: AgriSeqDB ( https://expression.latrobe.edu.au/agriseqdb ) is a database for viewing, analysing and interpreting developmental and tissue/cell-specific transcriptome data from several species, including major agricultural crops such as wheat, rice, maize, barley and tomato. The disparate manner in which public transcriptome data is often warehoused and the challenge of visualizing raw data are both major hurdles to data reuse. The popular eFP browser does an excellent job of presenting transcriptome data in an easily interpretable view, but previous implementation has been mostly on a case-by-case basis. Here we present an integrated visualisation database of transcriptome data-sets from six species that did not previously have public-facing visualisations. We combine the eFP browser, for gene-by-gene investigation, with the Degust browser, which enables visualisation of all transcripts across multiple samples. The two visualisation interfaces launch from the same point, enabling users to easily switch between analysis modes. The tools allow users, even those without bioinformatics expertise, to mine into data-sets and understand the behaviour of transcripts of interest across samples and time. We have also incorporated an additional graphic download option to simplify incorporation into presentations or publications. Conclusion: Powered by eFP and Degust browsers, AgriSeqDB is a quick and easy-to-use platform for data analysis and visualization in five crops and Arabidopsis. Furthermore, it provides a tool that makes it easy for researchers to share their data-sets, promoting research collaborations and data-set reuse.
This work was supported by a grant from the Australian National Data Service (ANDS) grant as well as by in-kind contributions from La Trobe University Information and Communication Technology and the La Trobe Genomics Platform.
JournalBMC Plant Biology
Rights StatementThe Author reserves all moral rights over the deposited text and must be credited if any re-use occurs. Documents deposited in OPAL are the Open Access versions of outputs published elsewhere. Changes resulting from the publishing process may therefore not be reflected in this document. The final published version may be obtained via the publisher’s DOI. Please note that additional copyright and access restrictions may apply to the published version.
Science & TechnologyLife Sciences & BiomedicinePlant SciencesRNA-SeqTranscriptomicsGene-expressionVisualisationDatabaseAgricultureBarleyMaizeRiceWheatTomatoEXPRESSION ATLASGENE-EXPRESSIONTRANSCRIPTOMEARABIDOPSISGERMINATIONPATTERNSREVEALSSATIVACrops, AgriculturalRNA, PlantSequence Analysis, RNAInternetUser-Computer InterfaceDatabases, GeneticTranscriptomePlant Biology & Botany