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PRINS and In Situ PCR 421 6. Koch, J., Kölvraa, S., Petersen, K. B., Gregersen, N., and Bolund, L. (1989) Oligonucleotidepriming methods for the chromosome-specific labelling of alpha satellite DNA in situ. Chromosoma 98, 259–265. 7. Haase, A. T., Retzel, E. F., and Staskus, K. A. (1990) Amplification and detection of lentiviral DNA inside cells. Proc. Natl. Acad. Sci. USA 87, 4971– 4975. 8. Gosden, J. R., ed. (1997) PRINS and In Situ PCR protocols. Methods in Molecular Biology, Vol. 71, Humana Press, Totowa, NJ. 9. Long, A. A. and Komminoth, P. (1997) In situ PCR, in PRINS and in situ PCR protocols. Methods in Molecular Biology, Vol. 71 (Gosden, J. R., ed.), Humana Press, Totowa, NJ, pp. 141–161. 10. Nuovo, G. J. (1997) PCR in situ hybridization, protocols and applications, 3rd ed., Lippincott-Raven, New York. 11. Totos, G., Tbakhi, A., Hauser-Kronberger, C., and Tubbs, R. R. (1997) Catalyzed reporter deposition: a new era in molecular and immunomorphology—Nanogold-silver staining and colorimetric detection and protocols. Cell Vision 4, 433– 442. 12. Wilkens, L., Tchinda, J., Komminoth, P., and Werner, M. (1997) Single- and double-color oligonucleotide primed in situ labeling (PRINS): applications in pathology. Histochem. Cell Biol. 108, 439– 446. 13. Herrington, C. S. and O’Leary, J. J. (1998) PCR In Situ Hybridization: A Practical Approach, Oxford University Press, Oxford, U.K. 14. Speel, E. J. M., Hopman, A. H. N., and Komminoth, P. (1999) Amplification methods to increase the sensitivity of in situ hybridization. Play card(s). J. Histochem. Cytochem. 47, 281–288. 15. Darby, I. A. (2000) In Situ Hybridization Protocols. Methods in Molecular Biology, Vol. 123, Humana Press, Totowa, NJ. 16. Coullin, P., Roy, L., Pellestor, F., Candelier, J.-J., Bed”hom, B., Guillier-Gencik, Z., et al. (2002) PRINS, the other in situ DNA labeling method that is useful in cellular biology. Am. J. Med. Genet., in press. 17. Hindkjœr, J., Bolund, L., and Kolvraa, S. (2001) Primed in situ labeling, in Methods in Cell Biology, Vol. 63–64, Academic Press, San Diego, pp. 55–68. 18. Speel, E. J. M., Lawson, D., Ramaekers, F. C. S., Gosden, J. R., and Hopman, A. H. N. (1996) Rapid brightfield detection of oligonucleotide primed in situ (PRINS)-labeled DNA in chromosome preparations and frozen tissue sections. BioTechniques 20, 226–234. 19. Ramael, M., Van Steelandt, H., Stuyven, G., Van Steenkiste, M., and Degroote, J. (1999) Detection of human papilloma virus (HPV) genomes by the primed in situ labelling technique. Pathol. Res. Pract. 195, 801–807. 20. Gosden, J. and Lawson, D. (1994) Rapid chromosome identification by oligonucleotideprimed in situ DNA synthesis (PRINS). Hum. Mol. Genet. 3, 931–936. 21. Koch, J., Hindkjœr, J., Kolvraa, S., and Bolund, L. (1995) Construction of a panel of chromosome-specific oligonucleotide probes (PRINS-primers) useful for the identification of individual human chromosomes in situ. Cytogenet. Cell. Genet. 71, 142–147. 22. Pellestor, F., Girardet, A., Lefort, G., Andréo, B., and Charlieu, J.-P. (1995) Selection of chromosome specific primers and their use in simple and double PRINS technique for rapid in situ identification of human chromosomes. Cytogenet. Cell. Genet. 70, 138–142. 23. Roguel-Gaillard, C., Hayes, H., Coullin, P., Chardon, P., and Vaiman, M. (1997) Swine centromeric DNA repeats revealed by primed in situ (PRINS) labeling. Cytogenet. Cell Genet. 79, 79–84. 24. Gosden, J., Hanratty, D., Starling, J., Fantes, J., Mitchell, A., and Porteous, D. (1991) Oligonucleotide-primed in situ DNA synthesis (PRINS): A method for chromosome mapping, banding, and investigation of sequence organization. Cytogenet. Cell. Genet. 57, 100–104.
422 Speel, Ramaekers, and Hopman 25. Krejci, K. and Koch, J. (1999) An in situ study of variant telomeric repeats in human chromosomes. Genomics 58, 202–206. 26. Go, Y., Rakotoarisoa, G., Kawamoto, Y., Randrianjafy, A., Koyama, N., and Hirai, H. (2000) PRINS analysis of telomeric sequence in seven lemurs. Chrom. Res. 8, 57–65. 27. Cinti, C., Santi, S., and Maraldi, N. M. (1993) Localization of a single copy gene by PRINS technique. Nucleic Acids Res. 21, 5799–5800. 28. Kadandale, J. S., Tunca, Y., and Tharapel, A. T. (2000) Chromosomal localization of single copy genes SRY and SOX3 by primed in situ labeling (PRINS). Microbial. Comparative Genomics 5, 71–74. 29. Harrer, T., Schwinger, E., and Mennicke, K. (2001) A new technique for cyclic in situ amplification and a case report about amplification of a single copy gene sequence in human metaphase chromosomes through PCR-PRINS. Hum. Mutat. 17, 131–140. 30. Pellestor, F. (2002) PRINS and cycling PRINS on chromosomes and sperm cells, in Chromosome Analysis Protocols, 2nd ed, Methods in Molecular Biology (Speel, E. J. M., and Hopman, A. H. N., eds.), Humana Press, Totowa, NJ, in press. 31. Volpi, E. V. and Baldini, A. (1993) MultiPRINS: A method for multicolor primed in situ labeling. Chrom. Res. 1, 257–260. 32. Hindkjœr, J., Koch, J., Terkelsen, C., Brandt, C. A., Kolvraa, S., and Bolund, L. (1994) Fast, sensitive multicolor detection of nucleic acids in situ by primed in situ labeling (PRINS). Cytogenet. Cell. Genet. 66, 152–154. 33. Speel, E. J. M., Lawson, D., Hopman, A. H. N., and Gosden, J. (1995) Multi-PRINS: multiple sequential oligonucleotide primed in situ DNA synthesis reactions label specific chromosomes and produce bands. Hum. Genet. 95, 29–33. 34. Schröck, E., Du Manoir, S., Veldman, T., Schoell, B., Wienberg, J., Ferguson-Smith, M. A., et al. (1996) Multicolor spectral karyotyping of human chromosomes. Science 273, 494– 497. 35. Speicher, M. R., Ballard, S. G., and Ward, D. C. (1996) Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat. Genet. 12, 368–375. 36. Schriml, L. M., Padilla-Nash, H. M., Coleman, A., Moen, P., Nash, W. G., Menninger, J., et al. (1999) Tyramide signal amplification (TSA)-FISH applied to mapping PCR-labeled probes less than 1 kb in size. BioTechniques 27, 608–613. 37. Terkelsen, C., Koch, J., Kolvraa, S., Hindkjœr, J., Pedersen, S., and Bolund, L. (1993) Repeated primed in situ labeling: formation and labeling of specific DNA sequences in chromosomes and nuclei. Cytogenet. Cell Genet. 63, 235–237. 38. Troyer, D. L., Goad, D. W., Xie, H., Rohrer, G. A., Alexander, L. J., and Beattle, C. W. (1994) Use of direct in situ single-copy (DISC) PCR to physically map five porcine microsatellites. Cytogenet. Cell Genet. 67, 199–204. 39. Tharapel, S. A. and Kadandale, J. S. (2002) Primed in situ labeling (PRINS) for evaluation of gene deletions in cancer. Am. J. Med. Genet., in press. 40. Paskins, L., Brownie, J., and Bull, J. (1999) In situ polymerase chain reaction and cycling primed in situ amplification: improvements and adaptations. Histochem. Cell Biol. 111, 411– 416. 41. Jonveaux, J. (1991) PCR amplification of specific DNA sequences from routinely fixed chromosomal spreads. Nucleic Acids Res. 19, 1946. 42. Höfler, H. (1993) In situ polymerase chain reaction: toy or tool? Histochemistry 99, 103–104. 43. Teo, I. A. and Shaunak, S. (1995) Polymerase chain reaction in situ: An appraisal of an emerging technique. Histochem. J. 27, 647–659. 44. Hopman, A. H. N. and Ramaekers, F. C. S. (1998) Processing and staining of cell and tissue material for interphase cytogenetics, in Current Protocols in Cytometry (Robinson, J. P., ed.), John Wiley & Sons, New York, pp. 8.5.1–8.5.22.
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63. Primed In Situ Nucleic Acid Lab
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44 Pearson 7. Add 60 µL of chlorof
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82 Hyndman and Mitsuhashi 3.1. Effi
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106 Wang and Young full-length cDNA
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124 Iannone et al. Fig. 1. Diagram
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Table 1 Oligonucleotides Descriptio
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130 Iannone et al. 4. To adjust for
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140 Benjamin, Smith, and Waites 2.2
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152 Olmos et al. Fig. 1. RT-hemines
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154 Olmos et al. This nested RT-PCR
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156 Olmos et al. Table 2 Volume and
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158 Olmos et al. 8. The sensitivity
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160 Olmos et al.
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162 Abe 5. Moloney murine leukemia
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164 Abe Table 2 Detection Rate of H
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166 Abe 4. For HBV, nested PCR usin
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168 Tellier et al. of Pfu (and ther
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170 Tellier et al. 2. Cline, J., Br
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172 Tellier et al. 38. Tamiya, S.,
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174 Tellier et al. 13. Thin-wall PC
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176 Tellier et al. 13 min for the l
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198 McDonagh the dilution method is
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200 McDonagh 2.2. Basic PCR 1. dNTP
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202 McDonagh Fig. 2. Quantitative P
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206 Bartlett Table 1 Example Assay
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208 Bartlett 3.4. Calculation of Re
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212 Kerr Fig. 1. Fluorescent probes
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224 Bartlett
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226 Dominguez et al. Table 1 Primer
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232 Dominguez et al. 3.4. Gel Elect
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236 Dominguez et al. 11. Joshi, C.
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238 Khalturin, Kuznetsov, and Bosch
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256 Case-Green, Pritchard, and Sout
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276 Oien 2. Purify polyA + mRNA fro
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278 Oien 50-mL conical tubes. Resus
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280 Oien Forward Primer, and then r
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282 Oien 8. PCR. With SAGE, achievi
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284 Oien
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288 Edwards and Bartlett technology
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290 Edwards and Bartlett ing less p
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292 Edwards and Bartlett Stepwise m
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294 Edwards and Bartlett
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296 Rithidech and Dunn 11. Ethidium
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312 Schmerer References 1. Kunkel,
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316 Aubele and Smida 2.2. Chemicals
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318 Aubele and Smida References 1.
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320 Nakashima, Akahoshi, and Tanaka
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326 Stirling
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332 Han and Robinson 4. Notes 1. PC
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334 Han and Robinson
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338 Stirling of simple and improved
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340 Stirling concentrations interfe
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342 Daniels to sequence a 500-bp PC
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344 Daniels 4. Load all of the samp
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346 Daniels References 1. Orita, M.
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348 Kösel et al. Fig. 1. Schematic
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350 Kösel et al. 3. Methods 3.1. P
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352 Kösel et al. Fig. 2. Sequencin
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354 Kösel et al. 5. Kwok, S. and H
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356 Mazars and Theillet Fig. 1. Sch
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358 Mazars and Theillet of genomic
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360 Mazars and Theillet
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362 Suomalainen and Syvänen Fig. 1
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364 Suomalainen and Syvänen detect
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366 Suomalainen and Syvänen temper
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474 Wang
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476 Horton, Raju, and Conti-Fine Fi
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478 Horton, Raju, and Conti-Fine th
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480 Horton, Raju, and Conti-Fine 1.
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482 Horton, Raju, and Conti-Fine ot
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484 Horton, Raju, and Conti-Fine
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486 Preston amplification approach
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488 Preston 1. 10× PCR buffer: 100
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490 Preston Fig. 1. Design of degen
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492 Preston 2. Remove the AmpliTaq
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494 Preston 3.3. Cloning and DNA Se
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496 Preston MgCl 2 concentrations b
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498 Preston 21. Hung, T., Mak, K.,
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500 Ravassard et al. Fig. 1. Constr
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502 Ravassard et al. size dispersio
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504 Ravassard et al. 9. ddH 2 O. 10
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506 Ravassard et al. 3.2.2. RNA Mix
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508 Ravassard et al. 4. Wash twice
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510 Ravassard et al.
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512 Pont-Kingdon Fig. 1. Constructi
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514 Pont-Kingdon 9. Invert tube and
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516 Pont-Kingdon
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518 Jones and Winistorfer Fig. 1. D
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520 Jones and Winistorfer Fig. 2. D
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522 Jones and Winistorfer The yield
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524 Jones and Winistorfer 7. Goulde
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526 Burke and Barik Fig. 1. The bas
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528 Burke and Barik concentration o
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530 Burke and Barik purified mutant
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532 Burke and Barik
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