Ancient DNA

Methods and Protocols

Beth Shapiro, Axel Barlow, Peter D. Heintzman, Michael Hofreiter, Johanna L. A. Paijmans (Herausgeber)

Buch | Hardcover

216 Seiten

2019 | 2nd ed. 2019
Humana Press Inc. (Verlag)
978-1-4939-9175-4 (ISBN)

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This fully updated second edition explores protocols that address the most challenging aspects of experimental work in ancient DNA, such as preparing ancient samples for DNA extraction, the DNA extraction itself, and transforming extracted ancient DNA molecules for sequencing library preparation. The volume also examines the analysis of high-throughput sequencing data recovered from ancient specimens, which, because of the degraded nature of ancient DNA and common co-extraction of contaminant DNA, has challenges that are unique compared to data recovered from modern specimens.Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and cutting-edge, Ancient DNA: Methods and Protocols, Second Edition aims to serve both experts and beginners by presenting protocols in a manner that makes them easily accessible for everyday use in the lab.

Setting Up an Ancient DNA Laboratory.- Pretreatment: Removing DNA Contamination from Ancient Bones and Teeth Using Sodium Hypochlorite and Phosphate.- Pretreatment: Improving Endogenous Ancient DNA Yields Using a Simple Enzymatic Pre-Digestion Step.- Extraction of Highly Degraded DNA from Ancient Bones and Teeth.- Sampling and Extraction of Ancient DNA from Sediments.- Extraction of Ancient DNA from Plant Remains.- DNA Extraction from Keratin and Chitin.- Double-Stranded Library Preparation for Ancient and Other Degraded Samples.- A Method for Single-Stranded Ancient DNA Library Preparation.- Sequencing Library Preparation from Degraded Samples for Non-Illumina Sequencing Platforms.- Whole-Genome Capture of Ancient DNA Using Homemade Baits.- Generating RNA Baits for Capture-Based Enrichment.- Hybridization Capture of Ancient DNA Using RNA Baits.- Application of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA.- Targeted PCR Amplification and Multiplex Sequencing of Ancient DNA for SNP Analysis.- Targeted Amplification and Sequencing of Ancient Environmental and Sedimentary DNA.- Authentication and Assessment of Contamination in Ancient DNA.- Assembly of Ancient Mitochondrial Genomes without a Closely Related Reference Sequence.

Erscheinungsdatum	29.03.2019
Reihe/Serie	Methods in Molecular Biology ; 1963
Zusatzinfo	5 Illustrations, color; 10 Illustrations, black and white; X, 216 p. 15 illus., 5 illus. in color.
Verlagsort	Totowa, NJ
Sprache	englisch
Maße	178 x 254 mm
Themenwelt	Naturwissenschaften ► Biologie ► Evolution
Themenwelt	Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
Schlagworte	DNA Extraction • evolutionary research • Fossil specimen • Genomic library preparation • High-throughput sequencing • Sequencing platforms
ISBN-10	1-4939-9175-2 / 1493991752
ISBN-13	978-1-4939-9175-4 / 9781493991754
Zustand	Neuware