Target Discovery and Validation Reviews and Protocols

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RNAi Libraries 141 12. Paddison, P. J., Caudy, A. A., Bernstein, E., Hannon, G. J., and Conklin, D. S. (2002) Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev. 16, 948–958. 13. Paul, C. P., Good, P. D., Winer, I., and Engelke, D. R. (2002) Effective expression of small interfering RNA in human cells. Nat. Biotechnol. 20, 505–508. 14. Sui, G., Soohoo, C., Affar el, B., Gay, F., Shi, Y., and Forrester, W. C. (2002) A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc. Natl. Acad. Sci. USA 99, 5515–5520. 15. Fraser, A. G., Kamath, R. S., Zipperlen, P., Martinez-Campos, M., Sohrmann, M., and Ahringer, J. (2000) Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408, 325–330. 16. Gonczy, P., Echeverri, C., Oegema, K., et al. (2000) Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature 408, 331–336. 17. Aza-Blanc, P., Cooper, C. L., Wagner, K., Batalov, S., Deveraux, Q. L., and Cooke, M. P. (2003) Identification of modulators of TRAIL-induced apoptosis via RNAibased phenotypic screening. Mol. Cell 12, 627–637. 18. Miyagishi, M. and Taira, K. (2003) Strategies for generation of an siRNA expression library directed against the human genome. Oligonucleotides 13, 325–333. 19. Berns, K., Hijmans, E. M., Mullenders, J., et al. (2004) A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 428, 431–437. 20. Paddison, P. J., Silva, J. M., Conklin, D. S., et al. (2004) A resource for large-scale RNA-interference-based screens in mammals. Nature 428, 427–431 21. Sen, G., Wehrman, T. S., Myers, J. W., and Blau, H. M. (2004) Restriction enzyme-generated siRNA (REGS) vectors and libraries. Nat. Genet. 36, 183–189. 22. Shirane, D., Sugao, K., Namiki, S., Tanabe, M., Iino, M., and Hirose, K. (2004) Enzymatic production of RNAi libraries from cDNAs. Nat. Genet. 36, 190–196. 23. Hsieh, A. C., Bo, R., Manola, J., et al. (2004) A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: determinants of gene silencing for use in cell-based screens. Nucleic Acids Res. 32, 893–901. 24. Kaykas, A. and Moon, R. T. (2004) A plasmid-based system for expressing small interfering RNA libraries in mammalian cells. BMC Cell Biol. 5, 16. 25. Colland, F., Jacq, X., Trouplin, V., et al. (2004) Functional proteomics mapping of a human signaling pathway. Genome Res. 14, 1324–1332. 26. Luo, B., Heard, A. D., and Lodish, H. F. (2004) Small interfering RNA production by enzymatic engineering of DNA (SPEED) Proc. Natl. Acad. Sci. USA 101, 5494–5499. 27. Zheng, L., Liu, J., Batalov, S., et al. (2004) An approach to genomewide screens of expressed small interfering RNAs in mammalian cells. Proc. Natl. Acad. Sci. USA 101, 135–140. 28. Futami, T., Miyagishi, M., and Taira, K. (2004) Identification of a network involved in thapsigargin-induced apoptosis using a library of siRNA-expression vectors. J. Biol. Chem. 280, 826–831.
142 Matsumoto, Miyagishi, and Taira 29. Miyagishi, M., Matsumoto, S., and Taira, K. (2004) Generation of an shRNAi expression library against the whole human transcripts. Virus Res. 102, 117–124. 30. Matsumoto, S., Miyagishi, M., Akashi, H., Nagai, R., and Taira, K. (2005) Analysis of double-stranded RNA-induced apoptosis pathways using interferon-response noninducible small interfering RNA expression vector library. J. Biol. Chem 280, 25,687–25,696. 31. Westbrook, T. F., Martin, E. S., Schlabach, M. R., et al. (2005) A genetic screen for candidate tumor suppressors identifies REST. Cell 121, 837–848. 32. Kolfschoten, I. G., van Leeuwen, B., Berns, K., et al. (2005) A genetic screen identifies PITX1 as a suppressor of RAS activity and tumorigenicity. Cell 121, 849–858. 33. Jackson, A. L., Bartz, S. R., Schelter, J., et al. (2003) Expression profiling reveals off-target gene regulation by RNAi. Nat. Biotechnol. 21, 635–637. 34. Curran, S. P., Leverich, E. P., Koehler, C. M., and Larsen, P. L. (2004) Defective mitochondrial protein translocation precludes normal Caenorhabditis elegans development. J. Biol. Chem. 279, 52,655–52,662. 35. Miyagishi, M. and Taira, K. (2005) siRNA becomes smart and intelligent. Nat. Biotechnol. 23, (8): 946–947.
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METHODS IN MOLECULAR BIOLOGY 360 T
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M E T H O D S I N M O L E C U L A R
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© 2007 Humana Press Inc. 999 River
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vi Preface get. Approaches to targe
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viii Contents 10 Transgenic Animal
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x Contributors SAHOHIME MATSUMOTO
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xii Contents of Volume 2 12 Validat
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2 Sioud disease pathogenesis and pe
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4 Sioud A more fruitful approach fo
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6 Sioud both transient and permanen
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8 Sioud serum biomarkers. This syne
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10 Sioud Fig. 2. Schematic of targe
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12 Sioud 13. Magin, T. M. (1998) Le
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Harnessing the Human Genome 15 The
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Harnessing the Human Genome 17 Fig.
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Harnessing the Human Genome 23 The
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Harnessing the Human Genome 27 repr
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Harnessing the Human Genome 29 14.
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Harnessing the Human Genome 31 45.
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34 Imoto et al. (4,5), and Bayesian
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36 Imoto et al. 2. Materials Two ty
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38 Imoto et al. Fig. 3. Graphical v
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40 Imoto et al. Fig. 5. Result of t
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42 Imoto et al. p(D |G) = ∫ p(D,
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44 Imoto et al. β k (k = 1,…,q j
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46 Imoto et al. Fig. 7. Partial res
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48 Imoto et al. Fig. 8. Strategy to
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50 Imoto et al. Fig. 9. (continued)
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52 Imoto et al. Table 3 List of Roo
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54 Imoto et al. 5. De Hoon, M. J. L
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56 Imoto et al. 39. Kamimura, T., S
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58 Beaty et al. cytotoxic drugs and
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60 Beaty et al. Fig. 1. Principles
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62 Beaty et al. oligonucleotide mic
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64 Beaty et al. 3. The 12% polyacry
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66 Beaty et al. 2.3.3. Protein Stai
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68 Beaty et al. 3.1.3. Labeling of
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70 Beaty et al. 1 µL of the anneal
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72 Beaty et al. 4. Phenol:cholorfor
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74 Beaty et al. 19. Wash twice with
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76 Beaty et al. The Following Volum
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78 Beaty et al. using a protein ass
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80 Beaty et al. 6. Shake the gel fo
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82 Beaty et al. Fig. 2. Preparation
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84 Beaty et al. search in. A widely
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86 Beaty et al. 3. Kern, S. E., Hru
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88 Beaty et al. 34. Peters, D. G.,
Page 104 and 105: 5 Molecular Classification of Breas
Page 106 and 107: Molecular Profiling of Breast Cance
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Page 130 and 131: Gene Target Discovery 117 In the fi
Page 132 and 133: Gene Target Discovery 119 sequences
Page 134 and 135: Gene Target Discovery 121 There is
Page 136 and 137: Gene Target Discovery 123 digestion
Page 138 and 139: Gene Target Discovery 125 Fig. 1. P
Page 140 and 141: Gene Target Discovery 127 5. Sargen
Page 142: Gene Target Discovery 129 41. Berry
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Page 157 and 158: 144 Fig. 1. The ribozyme-expression
Page 159 and 160: 146 Sano and Taira 5. 10X L (low-sa
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Page 163 and 164: 150 Fig. 3. A system for the identi
Page 165 and 166: 152 Sano and Taira 4. Notes 1. We r
Page 168 and 169: 9 Production of siRNA- and cDNA-Tra
Page 170 and 171: Transfected Cell Arrays 157 Fig. 1.
Page 172 and 173: Transfected Cell Arrays 159 2. The
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Page 177 and 178: 164 Houdebine Fig. 1. Different met
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Page 181 and 182: 168 Houdebine Fig. 2. Major methods
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Page 185 and 186: 172 Houdebine 2.2.3. Knock-In Into
Page 187 and 188: 174 Houdebine as insulators. The co
Page 189 and 190: 176 Houdebine Fig. 5. Different met
Page 191 and 192: 178 Houdebine systems. Moreover, st
Page 193 and 194: 180 Houdebine contribute to generat
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Page 197 and 198: 184 Houdebine more extensively. Tra
Page 199 and 200: 186 Houdebine and stroma. Several o
Page 201 and 202: 188 Houdebine explained at the mole
Page 203 and 204: 190 Houdebine of the intestinal epi
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192 Houdebine interference of the g
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194 Houdebine 17. Whitelaw, C. B. A
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196 Houdebine 51. Bell, A. C., West
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198 Houdebine 86. Carmichael, G. G.
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200 Houdebine 121. Pailhoux, E., Vi
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202 Houdebine 156. Auerbach, A. B.,
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204 Vijayaraj, Söhl, and Magin 1.
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206 Vijayaraj, Söhl, and Magin Fig
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208 Vijayaraj, Söhl, and Magin fil
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210 Table 1 Orthologous Human and M
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212 Table 2 Orthologous Human and M
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214 Vijayaraj, Söhl, and Magin ulc
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216 Vijayaraj, Söhl, and Magin of
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218 Vijayaraj, Söhl, and Magin sug
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220 Vijayaraj, Söhl, and Magin abs
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222 Vijayaraj, Söhl, and Magin 1.2
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224 Vijayaraj, Söhl, and Magin Fig
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226 Vijayaraj, Söhl, and Magin gen
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228 Vijayaraj, Söhl, and Magin the
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230 Vijayaraj, Söhl, and Magin f.
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234 Vijayaraj, Söhl, and Magin b.
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240 Vijayaraj, Söhl, and Magin alt
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242 Table 3 Time Schedule For Aggre
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250 Vijayaraj, Söhl, and Magin 101
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12 The HUVEC/Matrigel Assay An In V
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256 Skovseth, Küchler, and Haralds
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270 Iversen and Sørensen witnessed
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272 Iversen and Sørensen Fig. 1. P
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274 Iversen and Sørensen the core
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14 An Overview of the Immune System
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Overview of Immune System 279 diffe
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Overview of Immune System 281 Fig.
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Overview of Immune System 283 then
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Overview of Immune System 285 expre
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Overview of Immune System 287 Once
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Overview of Immune System 289 solub
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Overview of Immune System 291 amino
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Overview of Immune System 293 (unre
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Overview of Immune System 297 the c
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Overview of Immune System 299 (44).
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Overview of Immune System 301 demon
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Overview of Immune System 307 some
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Overview of Immune System 309 sera
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Overview of Immune System 313 measu
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Overview of Immune System 315 42. H
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Overview of Immune System 317 74. D
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15 Potential Target Antigens for Im
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Tumor Antigen Discovery 321 develop
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Tumor Antigen Discovery 323 panel b
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Tumor Antigen Discovery 325 16. Joc
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16 Identification of Tumor Antigens
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Immunoproteomics 329 by “shot gun
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Immunoproteomics 331 isoelectric fo
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Immunoproteomics 333 3. 2D-PAGE is
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17 Protein Arrays A Versatile Toolb
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Protein Arrays 337 Table 1 Classifi
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Protein Arrays 339 fractions from c
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Protein Arrays 341 combinatorial sc
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Protein Arrays 343 The ideal proteo
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Protein Arrays 345 18. Cekaite, H.
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Protein Arrays 347 49. Yuko Kawahas
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Index 349 Index A Acetyl-CoA carbox
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Index 351 conditional by using FRT
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Index 353 Recombinant tumor antigen
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