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Genomics Protocols - Michael P. Starkey , Ramnath Elaswarapu


Contents


1 Construction of Microsatellite-Based, High-Resolution
Genetic Maps in the Mouse
Paul A. Lyons ................................................................................ 1
2 Genetic Analysis of Complex Traits
Stephen P. Bryant and Mathias N. Chiano .............................. 11
3 Sequence-Based Detection
of Single Nucleotide Polymorphisms
Deborah A. Nickerson, Natali Kolker, Scott L. Taylor,
and Mark J. Rieder................................................................ 29
4 Genomic Mismatch Scanning for the Mapping of Genetic Traits
Farideh Mirzayans and Michael A. Walter ............................... 37
5 Detection of Chromosomal Abnormalities by Comparative
Genomic Hybridization
Mario A. J. A. Hermsen, Marjan M. Weiss, Gerrit A. Meijer,
and Jan P. A. Baak ............................................................... 47
6 Construction of a Bacterial Artificial Chromosome Library
Sangdun Choi and Ung-Jin Kim ............................................... 57
7 Contiguation of Bacterial Clones
Sean J. Humphray, Susan J. Knaggs,
and Ioannis Ragoussis ........................................................ 69

8 Mapping of Genomic Clones by Fluorescence In Situ
Hybridization
Margaret A. Leversha ............................................................... 109
9 Map Integration: From a Genetic Map to a Physical Gene Map
and Ultimately to the Sequence Map
Panagiotis Deloukas ................................................................ 129
10 Construction of Full-Length–Enriched cDNA Libraries:
The Oligo-Capping Method
Yutaka Suzuki and Sumio Sugano ......................................... 143

11 Construction of Transcript Maps by Somatic Cell/Radiation
Hybrid Mapping: The Human Gene Map
Panagiotis Deloukas ................................................................ 155
12 Preparation and Screening of High-Density cDNA Arrays
with Genomic Clones
Günther Zehetner, Maria Pack, and Katja Schäfer............... 169
13 Direct Selection of cDNAs by Genomic Clones
Daniela Toniolo ......................................................................... 189
14 Exon Trapping: Application of a Large-Insert
Multiple-Exon-Trapping System
Martin C. Wapenaar and Johan T. Den Dunnen ................... 201
15 Sequencing Bacterial Artificial Chromosomes
David E. Harris and Lee Murphy ............................................. 217
16 Finding Genes in Genomic Nucleotide Sequences
by Using Bioinformatics
Yvonne J. K. Edwards and Simon M. Brocklehurst ............. 235
17 Gene Identification Using the Pufferfish, Fugu rubripes,
by Sequence Scanning
Greg Elgar ................................................................................. 249
18 Isolation of Differentially Expressed Genes
Through Subtractive Suppression Hybridization
Oliver Dorian von Stein ........................................................... 263
19 Isolation of Differentially Expressed Genes
by Representational Difference Analysis
Christine Wallrapp and Thomas M. Gress ............................ 279
20 Expression Profiling and the Isolation of Differentially
Expressed Genes by Indexing-Based Differential Display
Michael P. Starkey .................................................................... 295
21 Expression Profiling by Systematic High-Throughput In Situ
Hybridization to Whole-Mount Embryos
Nicolas Pollet and Christof Niehrs......................................... 309
22 Expression Monitoring Using cDNA Microarrays:
A General Protocol
Xing Jian Lou, Mark Schena, Frank T. Horrigan,
Richard M. Lawn, and Ronald W. Davis .......................... 323
23 Prediction of Protein Structure and Function
by Using Bioinformatics
Yvonne J. K. Edwards and Amanda Cottage ........................ 341

24 Identification of Novel Genes by Gene Trap Mutagenesis
Anne K. Voss and Tim Thomas .............................................. 377
25 Determination of Gene Function by Homologous Recombination
Using Embryonic Stem Cells and Knockout Mice
Ahmed Mansouri ...................................................................... 397
26 Genomic Analysis Utilizing the Yeast Two-Hybrid System
Ilya G. Serebriiskii, Garabet G. Toby, Russell L. FInley, Jr.,
and Erica A. Golemis ........................................................... 415
27 Methods for Adeno-Associated Virus–Mediated
Gene Transfer into Muscle
Terry J. Amiss and Richard Jude Samulski.......................... 455
28 Retroviral-Mediated Gene Transduction
Donald S. Anson ....................................................................... 471
29 Gene Therapy Approaches to Sensitization of Human Prostate
Carcinoma to Cisplatin by Adenoviral Expression of p53
and by Antisense Jun Kinase Oligonucleotide Methods
Ruth Gjerset, Ali Haghighi, Svetlana Lebedeva,
and Dan Mercola ................................................................. 495
30 Ribozyme Gene Therapy
Leonidas A. Phylactou............................................................. 521
Index .................................................................................................531

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