Ancient DNA: Methods and Protocols

ISBN-13: 9781493991754 / Angielski / Twarda / 2019 / 216 str.

Beth Shapiro; Axel Barlow; Peter D. Heintzman

Spis treści

1. Setting Up an Ancient DNA Laboratory

            Tara L. Fulton and Beth Shapiro

 

2. Pretreatment: Removing DNA Contamination from Ancient Bones and Teeth Using Sodium Hypochlorite and Phosphate

            Petra Korlević and Matthias Meyer

 

3. Pretreatment: Improving Endogenous Ancient DNA Yields Using a Simple Enzymatic Pre-Digestion Step

            Hannes Schroeder, Peter de Barros Damgaard, and Morten E. Allentoft

 

4. Extraction of Highly Degraded DNA from Ancient Bones and Teeth

            Jesse Dabney and Matthias Meyer

 

5. Sampling and Extraction of Ancient DNA from Sediments

            Laura S. Epp, Heike H. Zimmermann, and Kathleen R. Stoof-Leichsenring

 

6. Extraction of Ancient DNA from Plant Remains

            Nathan Wales and Logan Kistler

 

7. DNA Extraction from Keratin and Chitin

            Paula F. Campos and M. Thomas P. Gilbert

 

8. Double-Stranded Library Preparation for Ancient and Other Degraded Samples

            Kirstin Henneberger, Axel Barlow, and Johanna L.A. Paijmans

 

9. A Method for Single-Stranded Ancient DNA Library Preparation

            Marie-Theres Gansauge and Matthias Meyer

 

10. Sequencing Library Preparation from Degraded Samples for Non-Illumina Sequencing Platforms

            Renata Martins, Marie-Louise Kampmann, and Daniel W. Förster

 

11. Whole-Genome Capture of Ancient DNA Using Homemade Baits

            Gloria Gonzalez-Fortes and Johanna L.A. Paijmans

 

12. Generating RNA Baits for Capture-Based Enrichment

            Noah Snyder-Mackler, Tawni Voyles, and Jenny Tung

 

13. Hybridization Capture of Ancient DNA Using RNA Baits

            André E.R. Soares

 

14. Application of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA

            Johanna L.A. Paijmans, Gloria Gonzalez-Fortes, and Daniel W. Förster

 

15. Targeted PCR Amplification and Multiplex Sequencing of Ancient DNA for SNP Analysis

            Saskia Wutke and Arne Ludwig

 

16. Targeted Amplification and Sequencing of Ancient Environmental and Sedimentary DNA

            Ruth V. Nichols, Emily Curd, Peter D. Heintzman, and Beth Shapiro

 

17. Authentication and Assessment of Contamination in Ancient DNA

            Gabriel Renaud, Mikkel Schubert, Susanna Sawyer, and Ludovic Orlando

 

18. Assembly of Ancient Mitochondrial Genomes without a Closely Related Reference Sequence

            Christoph Hahn

Blurb

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.