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Generation of RNA sequencing libraries for transcriptome analysis of globin-rich tissues of the domestic dog

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Názov: Generation of RNA sequencing libraries for transcriptome analysis of globin-rich tissues of the domestic dog
Autori: DoGA consortium, Ezer, Sini, Yoshihara, Masahito, Katayama, Shintaro, Daub, Carsten, Lohi, Hannes, Krjutskov, Kaarel, Kere, Juha
Prispievatelia: Research Programs Unit, STEMM - Stem Cells and Metabolism Research Program, Helsinki One Health (HOH), Haartman Institute (-2014), Hannes Tapani Lohi / Principal Investigator, Veterinary Genetics, Veterinary Biosciences, Biosciences, Department of Medical and Clinical Genetics, Juha Kere / Principal Investigator
Informácie o vydavateľovi: Cell Press, Elsevier, Inc.
Rok vydania: 2022
Zbierka: Helsingfors Universitet: HELDA – Helsingin yliopiston digitaalinen arkisto
Predmety: Biomedicine, Genetics, developmental biology, physiology, Veterinary science
Popis: We have developed a protocol for barcoded cDNA libraries of 48 samples to study gene expression across tissues in the domestic dog, Canis familiaris, by modifying the Single-Cell Tagged Reverse Transcription (STRT) protocol (Islam et al., 2012, 2014). The cDNA reads represent mRNA 5′ ends, enabling the study of transcription start sites (TSS). Our modifications include longer UMIs for molecular counting and Globin-Lock® to deplete globin mRNAs that are abundant in blood and blood-rich tissues dominating all reads. ; Peer reviewed
Druh dokumentu: article in journal/newspaper
Popis súboru: application/pdf
Jazyk: English
Relation: All funding sources; The Academy of Finland , HiLife , Jane and Aatos Erkko Foundation , Sigrid Jusélius Foundation , Scandinavia–Japan Sasakawa Foundation , Japan Eye Bank Association , Astellas Foundation for Research on Metabolic Disorders , Japan Society for the Promotion of Science (JSPS) Overseas Research Fellowships. All funding sources; The Academy of Finland, HiLife, Jane and Aatos Erkko Foundation, Sigrid Jus?lius Foundation, Scandinavia?Japan Sasakawa Foundation, Japan Eye Bank Association, Astellas Foundation for Research on Metabolic Disorders, Japan Society for the Promotion of Science (JSPS) Overseas Research Fellowships. We thank Auli Saarinen and Mari Tervaniemi for technical assistance and Biomedicum Functional Genomics Unit (FuGU), University of Helsinki, for library sequencing services. Part of the computations were performed on resources provided by SNIC through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) under Project SNIC 2017/7-317. S.E. prepared the libraries and wrote the manuscript. K.K. developed the protocol. M.Y. and S.K. developed and performed the data analysis. J.K. C.D. and H.L. conceived and designed the project and directed the work. DOGA consortium collected and prepared the animal tissues. The authors declare no competing interests.; http://hdl.handle.net/10138/341385; 001052294000001
Dostupnosť: http://hdl.handle.net/10138/341385
Rights: cc_by_nc_nd ; info:eu-repo/semantics/openAccess ; openAccess
Prístupové číslo: edsbas.1BB5DE78
Databáza: BASE
Popis
Abstrakt:We have developed a protocol for barcoded cDNA libraries of 48 samples to study gene expression across tissues in the domestic dog, Canis familiaris, by modifying the Single-Cell Tagged Reverse Transcription (STRT) protocol (Islam et al., 2012, 2014). The cDNA reads represent mRNA 5′ ends, enabling the study of transcription start sites (TSS). Our modifications include longer UMIs for molecular counting and Globin-Lock® to deplete globin mRNAs that are abundant in blood and blood-rich tissues dominating all reads. ; Peer reviewed