1. The A-like Faker Assay for Measuring Yeast Chromosome III Stability
Carolina A. Novoa, J. Sidney Ang, and Peter C. Stirling
2. The Chromosome Transmission Fidelity Assay for Measuring Chromosome Loss in Yeast
Supipi Duffy and Philip Hieter
3. Measuring Mutation Rates using the Luria-Delbrück Fluctuation Assay
Gregory I. Lang
4. Molecular Genetic Characterization of Mutagenesis Using a Highly Sensitized Single-Stranded DNA Reporter System in Budding Yeast
Kin Chan
5. Analyzing Genome Rearrangements in Saccharomyces cerevisiae
Anjana Srivatsan, Christopher D. Putnam, and Richard D. Kolodner
6. High Resolution Mapping of Modified DNA Nucleobases using Excision Repair Enzymes
Monica Ransom, D. Suzi Bryan and Jay R. Hesselberth
7. Integrated Microarray-based Tools for Detection of Genomic DNA Damage and Repair Mechanisms
Patrick van Eijk, Yumin Teng, Mark R. Bennet, Katie E. Evans, James R. Powell, Richard M. Webster, and Simon H. Reed
8. Study of UV-induced DNA Repair Factor Recruitment: Kinetics and Dynamics
Sertic S., Roma S., Plevani P., Lazzaro F., and Muzi-Falconi M.
9. Inserting Site-specific DNA Lesions into Whole Genomes
Vincent Pagès and Robert P Fuchs
10. A qPCR-based Protocol to Quantify DSB Resection
Matteo Ferrari, Shyam Twayana, Federica Marini, and Achille Pellicioli
11. Alkaline Denaturing Southern Blot Analysis to Monitor Double-strand Break Processing
Chiara Vittoria Colombo, Luca Menin, and Michela Clerici
12. Single Molecule Analysis of Resection Tracks
Pablo Huertas and Andrés Cruz-García
13. Mapping DNA Breaks by Next-generation Sequencing
Laura Baranello, Fedor Kouzine, Damian Wojtowicz, Kairong Cui, Keji Zhao, Teresa M Przytycka, Giovanni Capranico, and David Levens 14. Genome-wide Profiling of DNA Double-strand Breaks by the BLESS and BLISS Methods
Reza Mirzazadeh, Tomasz Kallas, Magda Bienko, and Nicola Crosetto
15. DNA Replication Profiling using Deep Sequencing
Xanita Saayman, Cristina Ramos-Pérez, and Grant W Brown
16. Quantitative Bromodeoxyuridine Immunoprecipitation Analyzed by High-Throughput Sequencing (qBrdU-seq or QBU)
Joanna E. Haye-Bertolozzi and Oscar M. Aparicio
17. Strand-specific Analysis of DNA Synthesis and Proteins Association with DNA Replication Forks in Budding Yeast
Chuanhe Yu, Haiyun Gan, and Zhiguo Zhang
18. Analysis of Replicative Polymerase Usage by Ribonucleotide Incorporation
Andrea Keszthelyi, Izumi Miyabe, Katie Ptasińska, Yasukazu Daigaku, Karel Naiman, and Antony M. Carr
19. Dynamic Architecture of Eukaryotic DNA Replication Forks in vivo, Visualized by Electron Microscopy
Ralph Zellweger and Massimo Lopes
20. A Molecular Toolbox to Engineer Site-Specific DNA Replication Perturbation
Nicolai B. Larsen, Ian D. Hickson, and Hocine W. Mankouri
21. Single Cell Gel Electrophoresis for the Detection of Genomic Ribonucleotides Barbara Kind, Christine Wolf, Kerstin Engel, Alexander Rapp, M. Cristina Cardoso, and Min Ae Lee-Kirsch
22. Measuring the Levels of Ribonucleotides Embedded in Genomic DNA
Meroni A., Nava G.M., Sertic S., Plevani P., Muzi-Falconi M. and Lazzaro F.
23. Mapping Ribonucleotides Incorporated into DNA by Hydrolytic End-Sequencing
Clinton D. Orebaugh, Scott A. Lujan, Adam B. Burkholder, Anders R Clausen, and Thomas A. Kunkel
