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dc.contributor.authorAparicio-Puerta, Ernesto
dc.contributor.authorGómez-Martín, Cristina
dc.contributor.authorGiannoukakos, Stavros
dc.contributor.authorMedina, José María
dc.contributor.authorScheepbouwer, Chantal
dc.contributor.authorGarcía-Moreno, Adrián
dc.contributor.authorCarmona-Saez, Pedro
dc.contributor.authorFromm, Bastian
dc.contributor.authorPegtel, Michiel
dc.contributor.authorKeller, Andreas
dc.contributor.authorMarchal, Juan Antonio
dc.contributor.authorHackenberg, Michael
dc.date.accessioned2022-12-06T12:52:20Z
dc.date.available2022-12-06T12:52:20Z
dc.date.issued2022-05-12
dc.description.abstractThe NCBI Sequence Read Archive currently hosts microRNA sequencing data for over 800 different species, evidencing the existence of a broad taxonomic distribution in the field of small RNA research. Simultaneously, the number of samples per miRNA-seq study continues to increase resulting in a vast amount of data that requires accurate, fast and user-friendly analysis methods. Since the previous release of sRNAtoolbox in 2019, 55 000 sRNAbench jobs have been submitted which has motivated many improvements in its usability and the scope of the underlying annotation database. With this update, users can upload an unlimited number of samples or import them from Google Drive, Dropbox or URLs. Micro- and small RNA profiling can now be carried out using high-confidence Metazoan and plant specific databases, MirGeneDB and PmiREN respectively, together with genome assemblies and libraries from 441 Ensembl species. The new results page includes straightforward sample annotation to allow downstream differential expression analysis with sRNAde. Unassigned reads can also be explored by means of a new tool that performs mapping to microbial references, which can reveal contamination events or biologically meaningful findings as we describe in the example. sRNAtoolbox is available at: <a href=https://arn.ugr.es/srnatoolbox/> https://arn.ugr.es/srnatoolbox/</a>en_US
dc.identifier.citationAparicio-Puerta, Gómez-Martín, Giannoukakos, Medina, Scheepbouwer, García-Moreno, Carmona-Saez, Fromm, Pegtel, Keller, Marchal, Hackenberg. sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms. Nucleic Acids Research (NAR). 2022;50(1):W710-W717en_US
dc.identifier.cristinIDFRIDAID 2043704
dc.identifier.doi10.1093/nar/gkac363
dc.identifier.issn0305-1048
dc.identifier.issn1362-4962
dc.identifier.urihttps://hdl.handle.net/10037/27715
dc.language.isoengen_US
dc.publisherOxford University Pressen_US
dc.relation.journalNucleic Acids Research (NAR)
dc.relation.projectIDinfo:eu-repo/grantAgreement/EC/H2020/765492/EU/European Liquid Biopsies Academy - Towards widespread clinical application of blood- based diagnostic tools/ELBA/en_US
dc.rights.accessRightsopenAccessen_US
dc.rights.holderCopyright 2022 The Author(s)en_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0en_US
dc.rightsAttribution 4.0 International (CC BY 4.0)en_US
dc.titlesRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organismsen_US
dc.type.versionpublishedVersionen_US
dc.typeJournal articleen_US
dc.typeTidsskriftartikkelen_US
dc.typePeer revieweden_US


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Attribution 4.0 International (CC BY 4.0)
Med mindre det står noe annet, er denne innførselens lisens beskrevet som Attribution 4.0 International (CC BY 4.0)