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E-raamat: Ancient DNA: Methods and Protocols

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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.
Preface v
Contributors ix
1 Setting Up an Ancient DNA Laboratory
1(14)
Tara L. Fulton
Beth Shapiro
2 Pretreatment: Removing DNA Contamination from Ancient Bones and Teeth Using Sodium Hypochlorite and Phosphate
15(6)
Petra Korlevic
Matthias Meyer
3 Pretreatment: Improving Endogenous Ancient DNA Yields Using a Simple Enzymatic Predigestion Step
21(4)
Hannes Scbroeder
Peter de Barros Damgaard
Morten E. Allentoft
4 Extraction of Highly Degraded DNA from Ancient Bones and Teeth
25(6)
Jesse Dabney
Matthias Meyer
5 Sampling and Extraction of Ancient DNA from Sediments
31(14)
Laura S. Epp
Heike H. Zimmermann
Kathleen R. Stoof-Leichsenring
6 Extraction of Ancient DNA from Plant Remains
45(12)
Nathan Wales
Logan Kistler
7 DNA Extraction from Keratin and Chitin
57(8)
Paula F. Campos
M. Thomas P. Gilbert
8 Double-Stranded Library Preparation for Ancient and Other Degraded Samples
65(10)
Kirstin Henneberger
Axel Barlow
Johanna L. A. Paijmans
9 A Method for Single-Stranded Ancient DNA Library Preparation
75(10)
Marie-Theres Gansauge
Matthias Meyer
10 Sequencing Library Preparation from Degraded Samples for Non-illumina Sequencing Platforms
85(8)
Renata F. Martins
Marie-Louise Kampmann
Daniel W. Forster
11 Whole-Genome Capture of Ancient DNA Using Homemade Baits
93(14)
Gloria Gonzalez Fortes
Johanna L. A. Paijmans
12 Generating RNA Baits for Capture-Based Enrichment
107(14)
Noah Snyder-Mackler
Tawni Voyles
Jenny Tung
13 Hybridization Capture of Ancient DNA Using RNA Baits
121(8)
Andre E. R. Soares
14 Application of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA
129(12)
Johanna L. A. Paijmans
Gloria Gonzalez Fortes
Daniel W. Forster
15 Targeted PCR Amplification and Multiplex Sequencing of Ancient DNA for SNP Analysis
141(8)
Saskia Wutke
Arne Ludwig
16 Targeted Amplification and Sequencing of Ancient Environmental and Sedimentary DNA
149(14)
Ruth V. Nichols
Emily Curd
Peter D. Heintzman
Beth Shapiro
17 Authentication and Assessment of Contamination in Ancient DNA
163(32)
Gabriel Renaud
Mikkel Schubert
Susanna Sawyer
Ludovic Orlando
18 Assembly of Ancient Mitochondrial Genomes Without a Closely Related Reference Sequence
195(20)
Christoph Hahn
Index 215
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