Part I. Characterizing the Genome
1. Genome Size Determination using Flow Cytometry of Propidium Iodide-stained Nuclei
Emily E. Hare and J. Spencer Johnston
2. Chromosome Analysis in Invertebrates and Vertebrates
David M. Rowell, Shu Ly Lim and Frank Grutzner
3. Genomic Libraries. I. Construction and Screening of Fosmid Genomic Libraries
Mike A. Quail, Lucy Matthews, Sarah Sims, Christine Lloyd, Helen Beasley, and Simon W. Baxter
4. Genomic Libraries. II. Subcloning, Sequencing, and Assembling Large-insert Genomic DNA Clones
Mike A. Quail, Lucy Matthews, Sarah Sims, Christine Lloyd, Helen Beasley, and Simon W. Baxter
Part II. Targeting Regions of the Genome
5. Reduced Representation Methods for Sub-genomic Enrichment and Next-generation Sequencing
Jeffrey M. Good
6. Accessing the Transcriptome: How to Normalize mRNA Pools
Heiko Vogel and Christopher W. Wheat
7. Transcriptome Sequencing Goals, Assembly, and Assessment
Christopher W. Wheat and Heiko Vogel
8. Rapid Retrieval of DNA Target Sequences by Primer Extension Capture
Adrian W. Briggs
Part III. Measuring Genetic Diversity
9. SNP Discovery and Genotyping for Evolutionary Genetics using RAD Sequencing
Paul D. Etter, Susan Bassham, Paul A. Hohenlohe, Eric Johnson, and William A. Cresko
10. DNA Microarray-based Mutation Discovery and Genotyping
David Gresham
11. Genotyping with Sequenom
Martina Bradic, João Costa, and Ivo M. Chelo
12. Isolating Microsatellite Loci: Looking Back, Looking Ahead
José A. Andrés and Steven M. Bogdanowicz
13. Design of Custom Oligonucleotide Microarrays for Single Species or Interspecies Hybrids using Array Oligo Selector
Amy A. Caudy
Part IV. Obtaining Candidate Gene Sequences
14. Identification of Homologous Gene Sequences by PCR with Degenerate Primers
Michael Lang and Virginie Orgogozo
15. Characterizing cDNA Ends by Circular RACE
Patrick T. McGrath
16. Identification of DNA Sequences that Flank a Known Region by Inverse PCR
Anastasios Pavlopoulos
Part V. Analyzing Candidate Gene Transcripts
17. Quantification of Transcript Levels with Quantitative RT-PCR
Karen L. Carleton
18. Using Pyrosequencing to Measure Allele-specific mRNA Abundance and Infer the Effects of Cis- and Trans-regulatory Differences
Patricia J. Wittkopp
19. Whole Mount In situ Hybridization of Sectioned Tissues of Species Hybrids to Detect Cis-Regulatory Changes in Gene Expression Pattern
Ryo Futahashi
20. Identifying Fluorescently Labeled Single Molecules in Image Stacks using Machine Learning
Scott Rifkin
Part VI. Testing Candidate Genes and Candidate Mutations
21. Experimental Approaches to Evaluate the Contributions of Candidate Cis-regulatory Mutations to Phenotypic Evolution
Mark Rebeiz and Thomas M. Williams
22. Experimental Approaches to Evaluate the Contributions of Candidate Protein-coding Mutations to Phenotypic Evolution
Jay F. Storz and Anthony J. Zera
23. Making Reporter Gene Constructs to Analyze Cis-regulatory Elements
José Bessa and José Luis Gómez-Skarmeta
24. PCR-directed In vivo Plasmid Construction using Homologous Recombination in Baker's Yeast
Erik C. Andersen
25. Pr
