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Benchmarking ultra-...
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Dahn, Hollis A.Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, Canada.
(författare)
Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing
- Artikel/kapitelEngelska2022
Förlag, utgivningsår, omfång ...
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2022-08-10
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Oxford University Press,2022
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electronicrdacarrier
Nummerbeteckningar
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LIBRIS-ID:oai:DiVA.org:uu-484903
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https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-484903URI
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https://doi.org/10.1093/gigascience/giac068DOI
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Språk:engelska
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Sammanfattning på:engelska
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Ämneskategori:art swepub-publicationtype
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Background: Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types.Results: We find that storage temperature was the strongest predictor of uHMW fragment lengths. While immediate flash-freezing remains the sample preservation gold standard, samples preserved in 95% EtOH or 20-25% DMSO-EDTA showed little fragment length degradation when stored at 4 degrees C for 6 hours. Samples in 95% EtOH or 20-25% DMSO-EDTA kept at 4 degrees C for 1 week after dissection still yielded adequate amounts of uHMW DNA for most applications. Tissue type was a significant predictor of total DNA yield but not fragment length. Preservation solution had a smaller but significant influence on both fragment length and DNA yield.Conclusion: We provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for phase 1 of the Vertebrate Genomes Project, whose ultimate mission is to generate chromosome-level reference genome assemblies of all similar to 70,000 extant vertebrate species.
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Biuppslag (personer, institutioner, konferenser, titlar ...)
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Mountcastle, JacquelynRockefeller Univ, New York, NY 10065 USA.
(författare)
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Balacco, JenniferRockefeller Univ, New York, NY 10065 USA.
(författare)
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Winkler, SylkeMax Planck Inst Mol Cell Biol & Genet, D-01307 Saxony, Germany.
(författare)
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Bista, IlianaWellcome Sanger Inst, Tree Life Program, Hinxton CB10 1SA, Cambs, England.;Univ Cambridge, Dept Genet, Cambridge CB2 3EH, Cambs, England.
(författare)
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Schmitt, Anthony D.Arima Genom Inc, San Diego, CA 92121 USA.
(författare)
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Vinnere, OlgaUppsala universitet,Institutionen för immunologi, genetik och patologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)olvin020
(författare)
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Formenti, GiulioRockefeller Univ, New York, NY 10065 USA.
(författare)
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Oliver, KarenWellcome Sanger Inst, Tree Life Program, Hinxton CB10 1SA, Cambs, England.
(författare)
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Smith, MichelleWellcome Sanger Inst, Tree Life Program, Hinxton CB10 1SA, Cambs, England.
(författare)
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Tan, WenhuaMax Planck Inst Mol Cell Biol & Genet, D-01307 Saxony, Germany.
(författare)
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Kraus, AnneMax Planck Inst Mol Cell Biol & Genet, D-01307 Saxony, Germany.
(författare)
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Mac, StephenArima Genom Inc, San Diego, CA 92121 USA.
(författare)
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Komoroske, Lisa M.Univ Massachusetts, Dept Environm Conservat, Amherst, MA 01003 USA.
(författare)
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Lama, TanyaUniv Massachusetts, Dept Environm Conservat, Amherst, MA 01003 USA.
(författare)
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Crawford, Andrew J.Univ Los Andes, Dept Biol Sci, Bogota 111711, Colombia.
(författare)
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Murphy, Robert W.Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, Canada.
(författare)
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Brown, SamaraRockefeller Univ, New York, NY 10065 USA.
(författare)
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Scott, Alan F.Johns Hopkins Univ, Dept Med, Baltimore, MD 21287 USA.
(författare)
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Morin, Phillip A.NOAA, Southwest Fisheries Sci Ctr, Natl Marine Fisheries Serv, La Jolla, CA 92037 USA.
(författare)
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Jarvis, Erich D.Rockefeller Univ, New York, NY 10065 USA.;Howard Hughes Med Inst, Chevy Chase, MD 20815 USA.
(författare)
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Fedrigo, OlivierRockefeller Univ, New York, NY 10065 USA.
(författare)
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Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, Canada.Rockefeller Univ, New York, NY 10065 USA.
(creator_code:org_t)
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Ingår i:GigaScience: Oxford University Press112047-217X
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- Av författaren/redakt...
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Dahn, Hollis A.
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Mountcastle, Jac ...
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Balacco, Jennife ...
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Winkler, Sylke
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Bista, Iliana
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Schmitt, Anthony ...
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visa fler...
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Vinnere, Olga
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Formenti, Giulio
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Oliver, Karen
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Smith, Michelle
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Tan, Wenhua
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Kraus, Anne
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Mac, Stephen
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Komoroske, Lisa ...
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Lama, Tanya
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Crawford, Andrew ...
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Murphy, Robert W ...
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Brown, Samara
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Scott, Alan F.
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Morin, Phillip A ...
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Jarvis, Erich D.
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Fedrigo, Olivier
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