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Protocol for mapping the three-dimensional organization of dinoflagellate genomes.
Marinov, Georgi K; Kundaje, Anshul; Greenleaf, William J; Grossman, Arthur R.
Afiliación
  • Marinov GK; Department of Genetics, Stanford University, Stanford, CA 94305, USA. Electronic address: marinovg@stanford.edu.
  • Kundaje A; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA.
  • Greenleaf WJ; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
  • Grossman AR; Carnegie Institution for Science, Division of Biosphere Sciences and Engineering, Stanford, CA 94305, USA.
STAR Protoc ; 5(2): 102941, 2024 Jun 21.
Article en En | MEDLINE | ID: mdl-38483898
ABSTRACT
Dinoflagellate genomes often are very large and difficult to assemble, which has until recently precluded their analysis with modern functional genomic tools. Here, we present a protocol for mapping three-dimensional (3D) genome organization in dinoflagellates and using it for scaffolding their genome assemblies. We describe steps for crosslinking, nuclear lysis, denaturation, restriction digest, ligation, and DNA shearing and purification. We then detail procedures sequencing library generation and computational analysis, including initial Hi-C read mapping and 3D-DNA scaffolding/assembly correction. For complete details on the use and execution of this protocol, please refer to Marinov et al.1.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Dinoflagelados / Genoma de Protozoos Idioma: En Revista: STAR Protoc Año: 2024 Tipo del documento: Article Pais de publicación: Estados Unidos
Texto completo
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Imprimir
XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Dinoflagelados / Genoma de Protozoos Idioma: En Revista: STAR Protoc Año: 2024 Tipo del documento: Article Pais de publicación: Estados Unidos