Large‐Scale BAC Clone Restriction Digest Fingerprinting

Carrie A. Mathewson1, Jacqueline E. Schein1, Marco A. Marra1

1 Canada's Michael Smith Genome Sciences Center Vancouver, British Columbia, Canada
Publication Name:  Current Protocols in Human Genetics
Unit Number:  Unit 5.19
DOI:  10.1002/0471142905.hg0519s53
Online Posting Date:  April, 2007
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Abstract

Restriction digest fingerprinting is a common method for characterizing large insert genomic clones, e.g., bacterial artificial chromosome (BAC), P1 artificial chromosome (PAC) and Fosmid clones. This clone fingerprinting method has been widely applied in the construction of clone‐based physical maps, which have been used as positional cloning resources as well as to support directed and genome‐wide sequencing efforts. This unit describes a robust, large‐scale procedure for generation of agarose gel–based clone fingerprints from BAC clones.

Keywords: restriction digest fingerprint; bacterial artificial chromosome (BAC); BAC DNA isolation; agarose gel electrophoresis; BAC fingerprint map

     
 
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Table of Contents

  • Basic Protocol 1: Bacterial Clone Cell Culturing
  • Basic Protocol 2: BAC DNA Isolation
  • Basic Protocol 3: Restriction Enzyme Digestion of BAC DNA
  • Basic Protocol 4: Agarose Gel Preparation
  • Basic Protocol 5: Agarose Gel Loading and Electrophoresis
  • Basic Protocol 6: Post‐Electrophoresis Gel Staining and Imaging
  • Reagents and Solutions
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

Basic Protocol 1: Bacterial Clone Cell Culturing

  Materials
  • 70% (v/v) ethanol
  • 2× YT medium ( appendix 2D)
  • Appropriate antibiotic for selection
  • Glycerol stocks containing BAC clones of interest in 384‐well plates
  • 2% (v/v) Micro‐90 detergent
  • H 2O, sterile
  • 70% (v/v) ethanol: prepare fresh
  • Bleach
  • Graduated cylinder
  • Parafilm
  • 96‐well, square well culture block, 2 ml capacity (Beckman Coulter), autoclaved
  • Four‐reagent reservoirs
  • C‐fold paper towels
  • Fan
  • Multichannel pipettor (e.g., Biohit)
  • 96‐pin slotted pin replicator: 5‐µl slots, minimum length 22 mm (V & P Scientific)
  • Microporous tape sheets (Qiagen AirPore tape or similar)
  • 37°C platform shaker incubator capable of holding 96‐well blocks
  • Foil tape (Scotch No. 425)
  • Refrigerated centrifuge with adapator for 96‐well culture block (e.g., Sorvall)
CAUTION: Any material that has been in contact with E. coli should be disposed of as biohazardous waste.NOTE: All solutions and equipment coming into contact with cells must be sterile, and proper aseptic technique should be used accordingly.

Basic Protocol 2: BAC DNA Isolation

  Materials
  • Cell pellets in 96‐well block, frozen ( protocol 1)
  • DNase‐free RNase A (Qiagen)
  • GET buffer (see recipe)
  • 10% (w/v) sodium dodecyl sulfate (SDS)
  • 10 N NaOH
  • 3 M potassium acetate (KOAc; see recipe)
  • Isopropanol
  • 80% v/v ethanol: prepare fresh
  • TE (10:0.1) buffer (see recipe)
  • Multichannel pipettor (Biohit) or 96‐well robotic liquid handling device (e.g., Biomek FX)
  • Clear plastic sealing tape sheets (Edge Biosystems)
  • Multitube vortexer (VWR)
  • Microtiter plate shaker with 4‐mm orbital diameter (IKA Vibrax‐VXR, with microtiter plate attachment modified to hold 4 × 96‐well, deep‐well blocks)
  • Refrigerated centrifuge with adaptors for 96‐well culture blocks and 96‐well collection plates (e.g., Sorvall)
  • 96‐well collection plates with minimum 800‐µl capacity (e.g., 1.2‐ml square well plate; Ultident Scientific)
  • C‐fold towels
  • 96‐well, thin‐walled cycle plates (ABgene)
  • SpeedVac (Savant, Model SC210A without rotor) and GP110 vacuum pump
  • Foil tape (Scotch No. 425)
NOTE: Solutions can be added with either a multichannel pipettor or a 96‐well liquid handling device.

Basic Protocol 3: Restriction Enzyme Digestion of BAC DNA

  Materials
  • BAC DNA plates ( protocol 2)
  • H 2O, 4°C and sterile
  • 10× buffer appropriate for the restriction enzyme (typically supplied with the enzyme by manufacturer)
  • Restriction enzymes (e.g., NEB)
  • 5× (w/v) loading buffer (see recipe)
  • Multichannel pipettor (Biohit) or other 96‐well liquid handling device (Biomek FX)
  • 96‐well, thin‐walled cycle plates (Abgene)
  • Refrigerated centrifuge with adaptors for 96‐well plates (e.g., Sorvall)
  • Foil tape (Scotch No. 425)
NOTE: Solutions can be added with either a multichannel pipettor or a 96‐well liquid handling device.

Basic Protocol 4: Agarose Gel Preparation

  Materials
  • 0.5% (v/v) BacDown soap solution
  • SeaKem LE agarose (Cambrex)
  • 400 ml 1× TAE buffer (made fresh from 50× stock; appendix 2D)
  • Powder‐free gloves
  • 23 × 42.5–cm gel‐casting trays (e.g., for Gator A3‐1 electrophoresis apparatus; Owl Separation Systems)
  • Lint free tissues (e.g., Kimwipes)
  • Gel combs and spacers (2 combs and 1 spacer per casting tray)
  • 1‐liter screw‐top Erlenmeyer flask
  • 55°C water bath

Basic Protocol 5: Agarose Gel Loading and Electrophoresis

  Materials
  • 1× TAE buffer (diluted from 50× stock; appendix 2D)
  • Recirculating, refrigerated chiller (VWR Model 1173)
  • Large format gel electrophoresis apparatus with buffer recirculation ports (e.g., Gator A3‐1; Owl Separations)
  • Peristaltic pumps (e.g., Master Flex Easy Load L/S, Cole Parmer)
  • Peristaltic tubing (Tygon LFL L/S 17, Cole Parmer)
  • Gel ( protocol 4)
  • BAC DNA samples ( protocol 2)
  • Molecular weight marker mix (see recipe)
  • Multichannel loaders (8 and 12 channels; Hamilton)
  • Power supply

Basic Protocol 6: Post‐Electrophoresis Gel Staining and Imaging

  Materials
  • SYBR Green I DNA stain (Molecular Probes) diluted 1:10,000 in 1× TAE (see appendix 2D)
  • 70% (v/v) ethanol
  • Plastic gel staining containers large enough to hold one 23 × 21–cm gel
  • Light tight cabinet or chamber, capable of gentle agitation and with capacity to hold multiple staining containers
  • Fluorimager compatible with SYBR Green I excitation and emission spectra (e.g., Fluorimager 595, Molecular Dynamics)
  • Plexiglas, ∼23 × 43 cm (the size of the gel)
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Figures

Videos

Literature Cited

Literature Cited
   Adams, M.D., Celniker, S.E., Holt, R.A., Evans, C.A., Gocayne, J.D., Amanatides, P.G., Scherer, S.E., Li, P.W., Hoskins, R.A., Galle, R.F., George, R.A., Lewis, S.E., Richards, S., Ashburner, M., Henderson, S.N., Sutton, G.G., Wortman, J.R., Yandell, M.D., Zhang, Q., Chen, L.X., Brandon, R.C., Rogers, Y.H., Blazej, R.G., Champe, M., Pfeiffer, B.D., Wan, K.H., Doyle, C., Baxter, Helt, G., Nelson, C.R., Gabor, G.L., Abril, J.F., Agbayani, A., An, H.J., Andrews‐Pfannkoch, C., Baldwin, D., Ballew, R.M., Basu, A., Baxendale, J., Bayraktaroglu, L., Beasley, E.M., Beeson, K.Y., Benos, P.V., Berman, B.P., Bhandari, D., Bolshakov, S., Borkova, D., Botchan, M.R., Bouck, J., Brokstein, P., Brottier, P., Burtis, K.C., Busam, D.A., Butler, H., Cadieu, E., Center, A., Chandra, I., Cherry, J.M., Cawley, S., Dahlke, C., Davenport, L.B., Davies, P., de Pablos, B., Delcher, A., Deng, Z., Mays, A.D., Dew, I., Dietz, S.M., Dodson, K., Doup, L.E., Downes, M., Dugan‐Rocha, S., Dunkov, B.C., Dunn, P., Durbin, K.J., Evangelista, C.C., Ferraz, C., Ferriera, S., Fleischmann, W., Fosler, C., Gabrielian, A.E., Garg, N.S., Gelbart, W.M., Glasser, K., Glodek, A., Gong, F., Gorrell, J.H., Gu, Z., Guan, P., Harris, M., Harris, N.L., Harvey, D., Heiman, T.J., Hernandez, J.R., Houck, J., Hostin, D., Houston, K.A., Howland, T.J., Wei, M.H., Ibegwam, C., Jalali, M., Kalush, F., Karpen, G.H., Ke, Z., Kennison, J.A., Ketchum, K.A., Kimmel, B.E., Kodira, C.D., Kraft, C., Kravitz, S., Kulp, D., Lai, Z., Lasko, P., Lei, Y., Levitsky, A.A., Li, J., Li, Z., Liang, Y., Lin, X., Liu, X., Mattei, B., McIntosh, T.C., McLeod, M.P., McPherson, D., Merkulov, G., Milshina, N.V., Mobarry, C., Morris, J., Moshrefi, A., Mount, S.M., Moy, M., Murphy, B., Murphy, L., Muzny, D.M., Nelson, D.L., Nelson, D.R., Nelson, K.A., Nixon, K., Nusskern, D.R., Pacleb, J.M., Palazzolo, M., Pittman, G.S., Pan, S., Pollard, J., Puri, V., Reese, M.G., Reinert, K., Remington, K., Saunders, R.D., Scheeler, F., Shen, H., Shue, B.C., Siden‐Kiamos, I., Simpson, M., Skupski, M.P., Smith, T., Spier, E., Spradling, A.C., Stapleton, M., Strong, R., Sun, E., Svirskas, R., Tector, C., Turner, R., Venter, E., Wang, A.H., Wang, X., Wang, Z.Y., Wassarman, D.A., Weinstock, G.M., Weissenbach, J., Williams, S.M., Woodage, T., Worley, K.C., Wu, D., Yang, S., Yao, Q.A., Ye, J., Yeh, R.F., Zaveri, J.S., Zhan, M., Zhang, G., Zhao, Q., Zheng, L., Zheng, X.H., Zhong, F.N., Zhong, W., Zhou, X., Zhu, S., Zhu, X., Smith, H.O., Gibbs, R.A., Myers, E.W., Rubin, G.M., and Venter, J.C. 2000. The genome sequence of Drosophila melanogaster. Science 287:2185‐2195.
   Cone, K.C., McMullen, M.D. Bi, I.V., Davis, G.L., Yim, Y.S., Gardiner, J.M., Polacco, M.L., Sanchez‐Villeda, H., Fang, Z., Schroeder, S.G., Havermann, S.A., Bowers, J.E., Paterson, A.H., Soderlund, C.A., Engler, F.W., Wing, R.A., and Coe, E.H., Jr. 2002. Genetic, physical, and informatics resources for maize. On the road to an integrated map. Plant Physiol. 130:1598‐1605.
   Coulson, A. 1996. The Caenorhabditis elegans genome project. C. elegans Genome Consortium. Biochem. Soc. Trans. 24:289‐291.
   Coulson, A.R., Sulston, J., Brenner, S., and Karn, J. 1986. Towards a physical map of the genome of the nematode Caenorhabditis elegans. Proc. Natl. Acad. Sci. U.S.A. 83:7821‐7825.
   Ding, Y., Johnson, M.D., Colayco, R., Chen, Y.J., Melnyk, J., Schmitt, H., and Shizuya, H. 1999. Contig assembly of bacterial artificial chromosome clones through multiplexed fluorescence‐labeled fingerprinting. Genomics 56:237‐246.
   Fuhrmann, D.R., Krzywinski, M.I., Chiu, R., Saeedi, P., Schein, J.E., Bosdet, I.E., Chinwalla, A., Hillier, L.W., Waterston, R.H., McPherson, J.D., Jones, S.J., and Marra, M.A. 2003. Software for automated analysis of DNA fingerprinting gels. Genome Res. 13:940‐953.
   Gibbs, R.A. Weinstock, G.M., Metzker, M.L., Muzny, D.M., Sodergren, E.J., Scherer, S., Scott, G., Steffen, D., Worley, K.C., Burch, P.E., Okwuonu, G., Hines, S., Lewis, L., DeRamo, C., Delgado, O., Dugan‐Rocha, S., Miner, G., Morgan, M., Hawes, A., Gill, R., Celera, Holt, R.A., Adams, M.D., Amanatides, P.G., Baden‐Tillson, H., Barnstead, M., Chin, S., Evans, C.A., Ferriera, S., Fosler, C., Glodek, A., Gu, A., Jennings, D., Kraft, C.L., Nguyen, T., Pfannkoch, C.M., Sitter, C., Sutton, G.G., Venter, J.C., Woodage, T., Smith, D., Lee, H.M., Gustafson, E., Cahill, P., Kana, A., Doucette‐Stamm, L., Weinstock, K., Fechtel, K., Weiss, R.B., Dunn, D.M., Green, E.D., Blakesley, R.W., Bouffard, G.G., De Jong, P.J., Osoegawa, K., Zhu, B., Marra, M., Schein, J., Bosdet, I., Fjell, C., Jones, S., Krzywinski, M., Mathewson, C., Siddiqui, A., Wye, N., McPherson, J., Zhao, S., Fraser, C.M., Shetty, J., Shatsman, S., Geer, K., Chen, Y., Abramzon, S., Nierman, W.C., Havlak, P.H., Chen, R., Durbin, K.J., Egan, A., Ren, Y., Song, X.Z., Li, B., Liu, Y., Qin, X., Cawley, S., Cooney, A.J., D'Souza, L.M., Martin, K., Wu, J.Q., Gonzalez‐Garay, M.L., Jackson, A.R., Kalafus, K.J., McLeod, M.P., Milosavljevic, A., Virk, D., Volkov, A., Wheeler, D.A., Zhang, Z., Bailey, J.A., Eichler, E.E., Tuzun, E., Birney, E., Mongin, E., Ureta‐Vidal, A., Woodwark, C., Zdobnov, E., Bork, P., Suyama, M., Torrents, D., Alexandersson, M., Trask, B.J., Young, J.M., Huang, H., Wang, H., Xing, H., Daniels, S., Gietzen, D., Schmidt, J., Stevens, K., Vitt, U., Wingrove, J., Camara, F., Mar Alba, M., Abril, J.F., Guigo, R., Smit, A., Dubchak, I., Rubin, E.M., Couronne, O., Poliakov, A., Hubner, N., Ganten, D., Goesele, C., Hummel, O., Kreitler, T., Lee, Y.A., Monti, J., Schulz, H., Zimdahl, H., Himmelbauer, H., Lehrach, H., Jacob, H.J., Bromberg, S., Gullings‐Handley, J., Jensen‐Seaman, M.I., Kwitek, A.E., Lazar, J., Pasko, D., Tonellato, P.J., Twigger, S., Ponting, C.P., Duarte, J.M., Rice, S., Goodstadt, L., Beatson, S.A., Emes, R.D., Winter, E.E., Webber, C., Brandt, P., Nyakatura, G., Adetobi, M., Chiaromonte, F., Elnitski, L., Eswara, P., Hardison, R.C., Hou, M., Kolbe, D., Makova, K., Miller, W., Nekrutenko, A., Riemer, C., Schwartz, S., Taylor, J., Yang, S., Zhang, Y., Lindpaintner, K., Andrews, T.D., Caccamo, M., Clamp, M., Clarke, L., Curwen, V., Durbin, R., Eyras, E., Searle, S.M., Cooper, G.M., Batzoglou, S., Brudno, M., Sidow, A., Stone, E.A., Payseur, B.A., Bourque, G., Lopez‐Otin, C., Puente, X.S., Chakrabarti, K., Chatterji, S., Dewey, C., Pachter, L., Bray, N., Yap, V.B., Caspi, A., Tesler, G., Pevzner, P.A., Haussler, D., Roskin, K.M., Baertsch, R., Clawson, H., Furey, T.S., Hinrichs, A.S., Karolchik, D., Kent, W.J., Rosenbloom, K.R., Trumbower, H., Weirauch, M., Cooper, D.N., Stenson, P.D., Ma, B., Brent, M., Arumugam, M., Shteynberg, D., Copley, R.R., Taylor, M.S., Riethman, H., Mudunuri, U., Peterson, J., Guyer, M., Felsenfeld, A., Old, S., Mockrin, S., and Collins, S. 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428:493‐521.
   Gregory, S.G., Howell, G.R., and Bentley, D.R. 1997. Genome mapping by fluorescent fingerprinting. Genome Res. 7:1162‐1168.
   Gregory, S.G., Sekhon, M., Schein, J., Zhao, S., Osoegawa, K., Scott, C.E., Evans, R.S., Burridge, P.W., Cox, T.V., Fox, C.A., Hutton, R.D., Mullenger, I.R., Phillips, K.J., Smith, J., Stalker, J., Threadgold, G.J., Birney, E., Wylie, K., Chinwalla, A., Wallis, J., Hillier, L., Carter, J., Gaige, T., Jaeger, S., Kremitzki, C., Layman, D., Maas, J., McGrane, R., Mead, K., Walker, R., Jones, S., Smith, M., Asano, J., Bosdet, I., Chan, S., Chittaranjan, S., Chiu, R., Fjell, C., Fuhrmann, D., Girn, N., Gray, C., Guin, R., Hsiao, L., Krzywinski, M., Kutsche, R., Lee, S.S., Mathewson, C., McLeavy, C., Messervier, S., Ness, S., Pandoh, P., Prabhu, A.L., Saeedi, P., Smailus, D., Spence, L., Stott, J., Taylor, S., Terpstra, W., Tsai, M., Vardy, J., Wye, N., Yang, G., Shatsman, S., Ayodeji, B., Geer, K., Tsegaye, G., Shvartsbeyn, A., Gebregeorgis, E., Krol, M., Russell, D., Overton, L., Malek, J.A., Holmes, M., Heaney, M., Shetty, J., Feldblyum, T., Nierman, W.C., Catanese, J.J., Hubbard, T., Waterston, R.H., Rogers, J., de Jong, P.J., Fraser, Marra, M., McPherson, J.D., and Bentley, D.R. 2002. A physical map of the mouse genome. Nature 418:743‐750.
   Ioannou, P.A., Amemiya, C.T., Garnes, J., Kroisel, P.M., Shizuya, H., Chen, C., Batzer, M.A., and de Jong, P.J. 1994. A new bacteriophage P1‐derived vector for the propagation of large human DNA fragments. Nat. Genet. 6:84‐89.
   Kim, U.J., Shizuya, H., de Jong, P.J., Birren, B., and Simon, M.I. 1992. Stable propagation of cosmid sized human DNA inserts in an F factor based vector. Nucleic Acids Res. 20:1083‐1085.
   Krzywinski, M., Bosdet, I., Smailus, D., Chiu, R., Mathewson, C., Wye, N., Barber, S., Brown‐John, M., Chan, S., Chand, S., Cloutier, A., Girn, N., Lee, D., Masson, A., Mayo, M., Olson, T., Pandoh, P., Prabhu, A.L., Schoenmakers, E., Tsai, M., Albertson, D., Lam, W., Choy, C.O., Osoegawa, K., Zhao, S., de Jong, P.J., Schein, J., Jones, S., and Marra, M.A. 2004a. A set of BAC clones spanning the human genome. Nucleic Acids Res. 32:3651‐3660.
   Krzywinski, M., Wallis, J., Gosele, C., Bosdet, I., Chiu, R., Graves, T., Hummel, O., Layman, D., Mathewson, C., Wye, N., Zhu, B., Albracht, D., Asano, J., Barber, S., Brown‐John, M., Chan, S., Chand, S., Cloutier, A., Davito, J., Fjell, C., Gaige, T., Ganten, D., Girn, N., Guggenheimer, K., Himmelbauer, H., Kreitler, T., Leach, S., Lee, D., Lehrach, H., Mayo, M., Mead, K., Olson, T., Pandoh, P., Prabhu, A.L., Shin, H., Tanzer, S., Thompson, J., Tsai, M., Walker, J., Yang, G., Sekhon, M., Hillier, L., Zimdahl, H., Marziali, A., Osoegawa, K., Zhao, S., Siddiqui, A., de Jong, P.J., Warren, W., Mardis, E., McPherson, J.D., Wilson, R., Hubner, N., Jones, S., Marra, M., and Schein, J. 2004b. Integrated and sequence‐ordered BAC‐ and YAC‐based physical maps for the rat genome. Genome Res. 14:766‐779.
   Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., Funke, R., Gage, D., Harris, K., Heaford, A., Howland, J., Kann, L., Lehoczky, J., LeVine, R., McEwan, P., McKernan, K., Meldrim, J., Mesirov, J.P., Miranda, C., Morris, W., Naylor, J., Raymond, C., Rosetti, M., Santos, R., Sheridan, A., Sougnez, C., Stange‐Thomann, N., Stojanovic, N., Subramanian, A., Wyman, D., Rogers, J., Sulston, J., Ainscough, R., Beck, S., Bentley, D., Burton, J., Clee, C., Carter, N., Coulson, A., Deadman, R., Deloukas, P., Dunham, A., Dunham, I., Durbin, R., French, L., Grafham, D., Gregory, S., Hubbard, T., Humphray, S., Hunt, A., Jones, M., Lloyd, C., McMurray, A., Matthews, L., Mercer, S., Milne, S., Mullikin, J.C., Mungall, A., Plumb, R., Ross, M., Shownkeen, R., Sims, S., Waterston, R.H., Wilson, R.K., Hillier, L.W., McPherson, J.D., Marra, M.A., Mardis, E.R., Fulton, L.A., Chinwalla, A.T., Pepin, K.H., Gish, W.R., Chissoe, S.L., Wendl, M.C., Delehaunty, K.D., Miner, T.L., Delehaunty, A., Kramer, J.B., Cook, L.L., Fulton, R.S., Johnson, D.L., Minx, P.J., Clifton, S.W., Hawkins, T., Branscomb, E., Predki, P., Richardson, P., Wenning, S., Slezak, T., Doggett, N., Cheng, J.F., Olsen, A., Lucas, S., Elkin, C., Uberbacher, E., Frazier, M., Gibbs, R.A., Muzny, D.M., Scherer, S.E., Bouck, J.B., Sodergren, E.J., Worley, K.C., Rives, C.M., Gorrell, J.H., Metzker, M.L., Naylor, S.L., Kucherlapati, R.S., Nelson, D.L., Weinstock, G.M., Sakaki, Y., Fujiyama, A., Hattori, M., Yada, T., Toyoda, A., Itoh, T., Kawagoe, C., Watanabe, H., Totoki, Y., Taylor, T., Weissenbach, J., Heilig, R., Saurin, W., Artiguenave, F., Brottier, P., Bruls, T., Pelletier, E., Robert, C., Wincker, P., Smith, D.R., Doucette‐Stamm, L., Rubenfield, M., Weinstock, K., Lee, H.M., Dubois, J., Rosenthal, A., Platzer, M., Nyakatura, G., Taudien, S., Rump, A., Yang, H., Yu, J., Wang, J., Huang, G., Gu, J., Hood, L., Rowen, L., Madan, A., Qin, S., Davis, R.W., Federspiel, N.A., Abola, A.P., Proctor, M.J., Myers, R.M., Schmutz, J., Dickson, M., Grimwood, J., Cox, D.R., Olson, M.V., Kaul, R., Shimizu, N., Kawasaki, K., Minoshima, S., Evans, G.A., Athanasiou, M., Schultz, R., Roe, B.A., Chen, F., Pan, H., Ramser, J., Lehrach, H., Reinhardt, R., McCombie, W.R., de laBastide, M., Dedhia, N., Blocker, H., Hornischer, K., Nordsiek, G., Agarwala, R., Aravind, L., Bailey, J.A., Bateman, A., Batzoglou, S., Birney, E., Bork, P., Brown, D.G., Burge, C.B., Cerutti, L., Chen, H.C., Church, D., Clamp, M., Copley, R.R., Doerks, T., Eddy, S.R., Eichler, E.E., Furey, T.S., Galagan, J., Gilbert, J.G., Harmon, C., Hayashizaki, Y., Haussler, D., Hermjakob, H., Hokamp, K., Jang, W., Johnson, L.S., Jones, T.A., Kasif, S., Kaspryzk, A., Kennedy, S., Kent, W.J., Kitts, P., Koonin, E.V., Korf, I., Kulp, D., Lancet, D., Lowe, T.M., McLysaght, A., Mikkelsen, T., Moran, J.V., Mulder, N., Pollara, V.J., Ponting, C.P., Schuler, G., Schultz, J., Slater, G., Smit, A.F., Stupka, E., Szustakowski, J., Thierry‐Mieg, D., Thierry‐Mieg, J., Wagner, L., Wallis, J., Wheeler, R., William, A., Wolf, Y.I., Wolfe, K.H., Yang, S.P., Yeh, R.F., Collins, F., Guyer, M.S., Peterson, J., Felsenfeld, A., Wetterstrand, K.A., Patrinos, A., Morgan, M.J., de Jong, P., Catanese, J.J., Osoegawa, K., Shizuya, H., Choi, S., and Chen, Y.J. 2001. Initial sequencing and analysis of the human genome. Nature 409:860‐921.
   Link, A.J. and Olson, M.V. 1991. Physical map of the Saccharomyces cerevisiae genome at 110‐kilobase resolution. Genetics 127:681‐698.
   Luo, M.C., Thomas, C., You, F.M., Hsiao, J., Ouyang, S., Buell, C.R., Malandro, M., McGuire, P.E., Anderson, O.D., and Dvorak, J. 2003. High‐throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 82:378‐389.
   Marra, M.A., Kucaba, T.A., Dietrich, N.L., Green, E.D., Brownstein, B., Wilson, R.K., McDonald, K.M., Hillier, L.W., McPherson, J.D., and Waterston, R.H. 1997. High throughput fingerprint analysis of large‐insert clones. Genome Res. 7:1072‐1084.
   Marra, M., Kucaba, T., Sekhon, M., Hillier, L., Martienssen, R., Chinwalla, A., Crockett, J., Fedele, J., Grover, H., Gund, C., McCombie, W.R., McDonald, K., McPherson, J., Mudd, N., Parnell, L., Schein, J., Seim, R., Shelby, P., Waterston, R., and Wilson, R. 1999. zA map for sequence analysis of the Arabidopsis thaliana genome. Nat. Genet. 22:265‐270.
   McPherson, J.D., Marra, M., Hillier, L., Waterston, R.H., Chinwalla, A., Wallis, J., Sekhon, M., Wylie, K., Mardis, E.R., Wilson, R.K., Fulton, R., Kucaba, T.A., Wagner‐McPherson, C., Barbazuk, W.B., Gregory, S.G., Humphray, S.J., French, S.J., Evans, R.S., Bethel, G., Whittaker, A., Holden, J.L., McCann, O.T., Dunham, A., Soderlund, C., Scott, C.E., Bentley, D.R., Schuler, G., Chen, H.C., Jang, W., Green, E.D., Idol, J.R., Maduro, V.V. Montgomery, K.T., Lee, E., Miller, A., Emerling, S., Kucherlapati, Gibbs, R., Scherer, S., Gorrell, J.H., Sodergren, E., Clerc‐Blankenburg, K., Tabor, P., Naylor, S., Garcia, D., de Jong, P.J., Catanese, J.J., Nowak, N., Osoegawa, K., Qin, S., Rowen, L., Madan, A., Dors, M., Hood, L., Trask, B., Friedman, C., Massa, H., Cheung, V.G., Kirsch, I.R., Reid, T., Yonescu, R., Weissenbach, J., Bruls, T., Heilig, R., Branscomb, E., Olsen, A., Doggett, N, Cheng, J.F., Hawkins, T., Myers, R.M., Shang, J., Ramirez, L., Schmutz, J., Velasquez, O., Dixon, K., Stone, N.E., Cox, D.R., Haussler, D., Kent, W.J., Furey, T., Rogic, S., Kennedy, S., Jones, S., Rosenthal, A., Wen, G., Schilhabel, M., Gloeckner, G., Nyakatura, G., Siebert, R., Schlegelberger, B., Korenberg, J., Chen, X.N., Fujiyama, A., Hattori, M., Toyoda, A., Yada, T., Park, H.S., Sakaki, Y., Shimizu, N., Asakawa, S., Kawasaki, K., Sasaki, T., Shintani, A., Shimizu, A., Shibuya, K., Kudoh, J., Minoshima, S., Ramser, J., Seranski, P., Hoff, C., Poustka, A., Reinhardt, R., and Lehrach, H. 2001. A physical map of the human genome. Nature 409:934‐941.
   Meyers, B.C., Scalabrin, S., and Morgante, M. 2004. Mapping and sequencing complex genomes: Let's get physical! Nat. Rev. Genet. 5:578‐588.
   Nelson, W.M., Bharti, A.K., Butler, E., Wei, F., Fuks, G., Kim, H., Wing, R.A., Messing, J., and Soderlund, C. 2005. Whole‐genome validation of high‐information‐content fingerprinting. Plant Physiol. 139:27‐38.
   Olson, M.V., Dutchik, J.E., Graham, M.Y., Brodeur, G.M., Helms, C., Frank, M., MacCollin, M., Scheinman, R., and Frank, T. 1986. Random‐clone strategy for genomic restriction mapping in yeast. Proc. Natl. Acad. Sci. U.S.A. 83:7826‐7830.
   Schein, J.E., Tangen, K.L., Chiu, R., Shin, H., Lengeler, K.B., MacDonald, W.K., Bosdet, I., Heitman, J., Jones, S.J., Marra, M.A., and Kronstad, J.W. 2002. Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans. Genome Res. 12:1445‐1453.
   Schein, J.E. and Krzywinski, M.I. 2005. Fingerprint mapping. In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics (M.J. Dunn, L.B. Jorde, P.F.R. Little, and S. Subramaniam, eds). John Wiley & Sons, Hoboken, NJ.
   Shizuya, H., Birren, B., Kim, U.J., Mancino, V., Slepak, T., Tachiiri, Y., and Simon, M. 1992. Cloning and stable maintenance of 300‐kilobase‐pair fragments of human DNA in Escherichia coli using an F‐factor‐based vector. Proc. Natl. Acad. Sci. U.S.A. 89:8794‐8797.
   Smith, C.L., Econome, J.G., Schutt, A., Klco, S., and Cantor, C.R. 1987. A physical map of the Escherichia coli K12 genome. Science 236:1448‐1453.
   Soderlund, C., Longden, I., and Mott, R. 1997. FPC: A system for building contigs from restriction fingerprinted clones. Comput. Appl. Biosci. 13:523‐535.
   Soderlund, C., Humphray, S., Dunham, A, and French, L. 2000. Contigs built with fingerprints, markers, and FPC V4.7. Genome Res. 10:1772‐1787.
   Sulston, J., Mallett, F., Staden, R., Durbin, R., Horsnell, T., and Coulson, A. 1988. Software for genome mapping by fingerprinting techniques. Comput. Appl. Biosci. 4:125‐132.
   Tao, Q., Chang, Y.L., Wang, J., Chen, H., Islam‐Faridi, M.N., Scheuring, C., Wang, B., Stelly, D.M., and Zhang, H.B. 2001. Bacterial artificial chromosome‐based physical map of the rice genome constructed by restriction fingerprint analysis. Genetics 158:1711‐1724.
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