5PSeq Explorer-datafrysning 5PSeq Explorer Data Freeze 2025-350-1 https://doi.org/10.48723/zchv-5x22 Swedish National Data Service Svensk nationell datatjänst Landing page 5PSeq Explorer-datafrysning 5PSeq Explorer Data Freeze 2025-350-1 https://doi.org/10.48723/zchv-5x22 10.1186/s13059-023-02871-7 10.1016/j.cell.2015.05.008 oai:swepub.ki.se:462699 10.1016/j.xpro.2021.100447 oai:swepub.ki.se:496546 10.1093/nar/gkx479 oai:swepub.ki.se:475566 10.1101/gr.243378.118 oai:swepub.ki.se:445890 10.1038/s41564-023-01393-z oai:swepub.ki.se:901940 10.1371/journal.pone.0308195 10.1016/j.celrep.2021.109877 oai:swepub.ki.se:465782 10.1093/nar/gkaa1200 oai:gup.ub.gu.se/350230 10.1016/j.molcel.2025.04.022 oai:DiVA.org:su-240803 urn:nbn:se:su:diva-240803 10.1038/s41598-024-80435-w oai:swepub.ki.se:871626 10.1101/2024.05.29.596377 oai:swepub.ki.se:459365 10.1016/j.celrep.2021.109633 10.1371/journal.pgen.1007563 oai:swepub.ki.se:852942 10.1038/s44320-024-00026-9 oai:swepub.ki.se:453805 10.1016/j.crmeth.2021.100001 Stevens, Irene Stevens, Irene Pelechano, Vicent Pelechano, Vicent VR 2021-06112, 2022-05272, 2023-02026 and 2024-03210 VR 2021-06112, 2022-05272, 2023-02026 and 2024-03210 2021.0167 2021.0167 SciLifeLab, SFO, KID and KI funds SciLifeLab, SFO, KID and KI funds Swedish National Data Service Svensk nationell datatjänst Landing page Investigative Techniques Utredningsmetoder Gene Expression Profiling Genuttrycksprofilering RNA RNA SEQUENCING SCIENCE AND TECHNOLOGY VETENSKAP OCH TEKNOLOGI Biotechnology Bioteknik This data freeze accompanies 5PSeq Explorer and it contains 775 5PSeq datasets compiled from 18 published studies interrogating various aspects of biology at the interface of mRNA decay and translation, including both genetic and environmental perturbations. To enable comparability across conditions and cross-species we processed all data uniformly (see Methods). The generated database consists of: (1) metadata, (2) raw processed counts files of amino acid, codon, frame preferences, metagene counts around start and termination sites, additional count files as documented on the Fivepseq package output documentation, and (3) RNA composition. For Eukaryotes, the collection consists of 378 yeast samples (Ascomycota phylum) with an overrepresentation for Saccharomyces cerevisiae (n= 340). For bacteria, we provide 397 samples across Actinomycetota, Bacillota, Bacteroides, Bacteroidota, Proteobacteria, Pseudomonadota and Verrucomicrobiota phyla with an overreprepresentation for Bacillus subtilis (n= 67) and Aggregatibacter actinomycetemcomitans (n=59). Denna datafrysning medföljer 5PSeq Explorer och innehåller 775 5PSeq-dataset sammanställda från 18 publicerade studier som undersöker olika aspekter av biologi vid gränssnittet mellan mRNA-sönderfall och translation, inklusive både genetiska och miljömässiga störningar. För att möjliggöra jämförelse mellan olika förhållanden och mellan arter bearbetade vi all data enhetligt (se Metoder). Den genererade databasen består av: (1) metadata, (2) råa bearbetade räkningsfiler för aminosyra, kodon, rampreferenser, metagenräkningar kring start- och termineringsställen, ytterligare räkningsfiler som dokumenterats i Fivepseq-paketets utdatadokumentation och (3) RNA-sammansättning. För eukaryoter består samlingen av 378 jästprover (Ascomycota phylum) med en överrepresentation för Saccharomyces cerevisiae (n = 340). För bakterier tillhandahåller vi 397 prover från Actinomycetota, Bacillota, Bacteroides, Bacteroidota, Proteobacteria, Pseudomonadota och Verrucomicrobiota phyla med en överrepresentation för Bacillus subtilis (n=67) och Aggregatibacter actinomycetemcomitans (n=59). 2015 2024 CellsCells CellerCeller Molecular data (775 5PSeq datasets) collected from 18 published studies interrogating various mRNA decay and translation across genetic and environmental perturbations. For Eukaryotes, the collection consists of 378 yeast samples (Ascomycota phylum) with an overrepresentation of Saccharomyces cerevisiae (n= 340). For bacteria we provide 397 samples across Actinomycetota, Bacillota, Bacteroides, Bacteroidota, Proteobacteria, Pseudomonadota and Verrucomicrobiota phyla with an overreprepresentation for Bacillus subtilis (n= 67) and Aggregatibacter actinomycetemcomitans (n=59). Molekylära data (775 5PSeq-dataset) insamlade från 18 publicerade studier som undersöker olika mRNA-sönderfall och translation över genetiska och miljömässiga störningar. För eukaryoter består samlingen av 378 jästprover (Ascomycota-stammen) med en överrepresentation av Saccharomyces cerevisiae (n=340). För bakterier tillhandahåller vi 397 prover från Actinomycetota, Bacillota, Bacteroides, Bacteroidota, Proteobacteria, Pseudomonadota och Verrucomicrobiota-stammen med en överrepresentation av Bacillus subtilis (n=67) och Aggregatibacter actinomycetemcomitans (n=59). Numeric Text OtherOther ÖvrigtÖvrigt A collection of published molecular data was uniformly processed and relies on sampling carried out by the original study.A collection of published molecular data was uniformly processed and relies on sampling carried out by the original study. En samling av publicerade molekylära data bearbetades enhetligt och bygger på urval utfört av den ursprungliga studien.En samling av publicerade molekylära data bearbetades enhetligt och bygger på urval utfört av den ursprungliga studien. OtherOther ÖvrigtÖvrigt Data collection information for each record is available in the metadata file attached. The library preparation protocol for 5Pseq, and the version of the protocol used, is noted in the metadata (attached file). All records are accompanied by a GEO_ID, SRA_ID and PubMed ID for a detailed record of the biosample, collection and experimental details.Data collection information for each record is available in the metadata file attached. The library preparation protocol for 5Pseq, and the version of the protocol used, is noted in the metadata (attached file). All records are accompanied by a GEO_ID, SRA_ID and PubMed ID for a detailed record of the biosample, collection and experimental details. Information om datainsamling för varje post finns i den bifogade metadatafilen. Biblioteksförberedelseprotokollet för 5Pseq, och vilken version av protokollet som används, anges i metadata (bifogad fil). Alla poster åtföljs av ett GEO_ID, SRA_ID och PubMed-ID för en detaljerad registrering av bioprovet, insamlingen och de experimentella detaljerna.Information om datainsamling för varje post finns i den bifogade metadatafilen. Biblioteksförberedelseprotokollet för 5Pseq, och vilken version av protokollet som används, anges i metadata (bifogad fil). Alla poster åtföljs av ett GEO_ID, SRA_ID och PubMed-ID för en detaljerad registrering av bioprovet, insamlingen och de experimentella detaljerna. ExperimentExperiment ExperimentExperiment Access to data through SND. Data are freely accessible. Åtkomst till data via SND. Data är fritt tillgängliga. openAccess Allen, G., Weiss, B., Panasenko, O. O., Huch, S., Villanyi, Z., Albert, B., Dilg, D., Zagatti, M., Schaughency, P., Liao, S. 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