Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP)

Nucleic Acids Research

Volumn 33, Issue 21, 2005, Pages

  Hoskins, Roger A ^a   Stapleton, Mark ^a   George, Reed A ^a   Yu, Charles ^a   Wan, Kenneth H ^a   Carlson, Joseph W ^a   Celniker, Susan E ^a  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; TRANSCRIPTION FACTOR;

ARTICLE; DNA LIBRARY; DNA SCREENING; DNA SEQUENCE; DROSOPHILA; INVERSE POLYMERASE CHAIN REACTION; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

ANIMALS; DNA, COMPLEMENTARY; DROSOPHILA MELANOGASTER; EXPRESSED SEQUENCE TAGS; GENE LIBRARY; GENES, INSECT; PLASMIDS; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; TIME FACTORS; TRANSCRIPTION FACTORS;

EUKARYOTA;

EID: 29244482245     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gni184     Document Type: Article

References (41)

1. Haas,B.J., Volfovsky,N., Town,C.D., Troukhan,M., Alexandrov,N., Feldmann,K.A., Flavell,R.B., White,O. and Salzberg,S.L. (2002) Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol., 3, RESEARCH0029.
2. Misra,S., Crosby,M.A., Mungall,C.J., Matthews,B.B., Campbell,K.S., Hradecky,P., Huang,Y., Kaminker,J.S., Millburn,G.H., Prochnik,S.E. et al. (2002) Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol., 3, RESEARCH0083.
3. Schena,M., Shalon,D., Davis,R.W. and Brown,P.O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270, 467-470.
4. Uetz,P., Giot,L., Cagney,G., Mansfield,T.A., Judson,R.S., Knight,J.R., Lockshon,D., Narayan,V., Srinivasan,M., Pochart,P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.
5. Ito,T., Chiba,T., Ozawa,R., Yoshida,M., Hattori,M. and Sakaki,Y. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA, 98, 4569-4574.
6. Hui,R. and Edwards,A. (2003) High-throughput protein crystallization. J. Struct. Biol., 142, 154-161.
7. Strausberg,R.L., Feingold,E.A., Klausner,R.D. and Collins,F.S. (1999) The mammalian gene collection. Science, 286, 455-457.
8. Gerhard,D.S., Wagner,L., Feingold,E.A., Shenmen,C.M., Grouse,L.H., Schuler,G., Klein,S.L., Old,S., Rasooly,R., Good,P. et al. (2004) The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res., 14, 2121-2127.
9. Adams,M.D., Kelley,J.M., Gocayne,J.D., Dubnick,M., Polymeropoulos,M., Xiao,H., Merril,C.R., Wu,A., Olde,B. and Moreno,R.F. (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science, 252, 1651-1656.
10. McCombie,W.R., Adams,M.D., Kelley,J.M., FitzGerald,M.G., Utterback,T.R., Khan,M., Dubnick,M., Kerlavage,A.R., Venter,J.C. and Fields,C. (1992) Caenorhabditis elegans expressed sequence tags identify gene families and potential disease gene homologues. Nature Genet., 1, 124-131.
11. Delseny,M., Cooke,R., Raynal,M. and Grellet,F. (1997) The Arabidopsis thaliana cDNA sequencing projects. FEBS Lett., 405, 129-132.
12. Rubin,G.M., Hong,L., Brokstein,P., Evans-Holm,M., Frise,E., Stapleton,M. and Harvey,D.A. (2000) A Drosophila complementary DNA resource. Science, 287, 2222-2224.
13. Stapleton,M., Carlson,J., Brokstein,P., Yu,C., Champe,M., George,R., Guarin,H., Kronmiller,B., Pacleb,J., Park,S. et al. (2002) A Drosophila full-length cDNA resource. Genome Biol., 3, RESEARCH0080.
14. Okazaki,Y., Furuno,M., Kasukawa,T., Adachi,J., Bono,H., Kondo,S., Nikaido,I., Osato,N., Saito,R., Suzuki,H. et al. (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 420, 563-573.
15. Imanishi,T., Itoh,T., Suzuki,Y., O'Donovan,C., Fukuchi,S., Koyanagi,K.O., Barrero,R.A., Tamura,T., Yamaguchi-Kabata,Y., Tanino,M. et al. (2004) Integrative annotation of 21 037 human genes validated by full-length cDNA clones. PLoS. Biol., 2, e162.
16. Stapleton,M., Liao,G., Brokstein,P., Hong,L., Carninci,P., Shiraki,T., Hayashizaki,Y., Champe,M., Pacleb,J., Wan,K. et al. (2002) The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes. Genome Res., 12, 1294-1300.
17. Maniatis,T., Fritsch,E.F. and Sambrook,J. (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Planview, NY.
18. Munroe,D.J., Loebbert,R., Bric,E., Whitton,T., Prawitt,D., Vu,D., Buckler,A., Winterpacht,A., Zabel,B. and Housman,D.E. (1995) Systematic screening of an arrayed cDNA library by PCR. Proc. Natl Acad. Sci. USA, 92, 2209-2213.
19. Mocharla,H., Mocharla,R. and Hodes,M.E. (1990) Coupled reverse transcription-polymerase chain reaction (RT-PCR) as a sensitive and rapid method for isozyme genotyping. Gene, 93, 271-275.
20. Frohman,M.A., Dush,M.K. and Martin,G.R. (1988) Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc. Natl Acad. Sci. USA, 85, 8998-9002.
21. Huang,S.H., Chen,S.H. and Jong,A.Y. (2003) Use of inverse PCR to clone cDNA ends. Methods Mol. Biol., 221, 51-58.
22. Ochman,H., Gerber,A.S. and Hartl,D.L. (1988) Genetic applications of an inverse polymerase chain reaction. Genetics, 120, 621-623.
23. Triglia,T., Peterson,M.G. and Kemp,D.J. (1988) A procedure for in vitro amplification of DNA segments that lie outside the boundaries of known sequences. Nucleic Acids Res., 16, 8186.
24. Green,I.R. and Sargan,D.R. (1991) Sequence of the cDNA encoding ovine tumor necrosis factor-alpha: problems with cloning by inverse PCR. Gene, 109, 203-210.
25. Haerry,T.E. and O'Connor,M.B. (2002) Isolation of Drosophila activin and follistatin cDNAs using novel MACH amplification protocols. Gene, 291, 85-93.
26. Jones,K.R. and Rubin,G.M. (1990) Molecular analysis of no-on-transient A, a gene required for normal vision in Drosophila. Neuron, 4, 711-723.
27. Rozen,S. and Skaletsky,H. (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol., 132, 365-386.
28. Ewing,B., Hillier,L., Wendl,M.C. and Green,P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res., 8, 175-185.
29. Ewing,B. and Green,P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res., 8, 186-194.
30. Gordon,D., Desmarais,C. and Green,P. (2001) Automated finishing with autofinish. Genome Res., 11, 614-625.
31. Florea,L., Hartzell,G., Zhang,Z., Rubin,G.M. and Miller,W. (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res., 8, 967-974.
32. Chao,K.M., Zhang,J., Ostell,J. and Miller,W. (1997) A tool for aligning very similar DNA sequences. Comput. Appl. Biosci., 13, 75-80.
33. Harris,M.A., Clark,J., Ireland,A., Lomax,J., Ashburner,M., Foulger,R., Eilbeck,K., Lewis,S., Marshall,B., Mungall,C. et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res., 32 (Database issue), D258-D261.
34. Shendure,J. and Church,G.M. (2002) Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biol., 3, RESEARCH0044.
35. Cheng,S., Fockler,C., Barnes,W.M. and Higuchi,R. (1994) Effective amplification of long targets from cloned inserts and human genomic DNA. Proc. Natl Acad. Sci. USA, 91, 5695-5699.
36. Carninci,P., Shibata,Y., Hayatsu,N., Itoh,M., Shiraki,T., Hirozane,T., Watahiki,A., Shibata,K., Konno,H., Muramatsu,M. and Hayashizaki,Y. (2001) Balanced-size and long-size cloning of full-length, cap-trapped cDNAs into vectors of the novel lambda-FLC family allows enhanced gene discovery rate and functional analysis. Genomics, 77, 79-90.
37. Baross,A., Butterfield,Y.S., Coughlin,S.M., Zeng,T., Griffith,M., Griffith,O.L., Petrescu,A.S., Smailus,D.E., Khattra,J., McDonald,H.L. et al. (2004) Systematic recovery and analysis of full-ORF human cDNA clones. Genome Res., 14, 2083-2092.
38. Arbeitman,M.N., Furlong,E.E., Imam,F., Johnson,E., Null,B.H., Baker,B.S., Krasnow,M.A., Scott,M.P., Davis,R.W. and White,K.P. (2002) Gene expression during the life cycle of Drosophila melanogaster. Science, 297, 2270-2275.
39. Stolc,V., Gauhar,Z., Mason,C., Halasz,G., van Batenburg,M.F., Rifkin,S.A., Hua,S., Herreman,T., Tongprasit,W., Barbano,P.E. et al. (2004) A gene expression map for the euchromatic genome of Drosophila melanogaster. Science, 306, 655-660.
40. Tomancak,P., Beaton,A., Weiszmann,R., Kwan,E., Shu,S., Lewis,S.E., Richards,S., Ashburner,M., Hartenstein,V., Celniker,S.E. and Rubin,G.M. (2002) Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol., 3, RESEARCH0088.
41. Scheetz,T.E., Laffin,J.J., Berger,B., Holte,S., Baumes,S.A., Brown,R., 2nd, Chang,S., Coco,J., Conklin,J., Crouch,K. et al. (2004) High-throughput gene discovery in the rat. Genome Res., 14, 733-741.