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Volumn 12, Issue , 2011, Pages

Strand-specific transcriptome profiling with directly labeled RNA on genomic tiling microarrays

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; RNA; TRANSCRIPTOME; BACTERIAL RNA; COMPLEMENTARY RNA;

EID: 78651372031     PISSN: None     EISSN: 14712199     Source Type: Journal    
DOI: 10.1186/1471-2199-12-3     Document Type: Article
Times cited : (12)

References (33)
  • 2
    • 1542328972 scopus 로고    scopus 로고
    • Properties of the reverse transcription reaction in mRNA quantification
    • 10.1373/clinchem.2003.026161, 14726469
    • Stahlberg A, Hakansson J, Xian X, Semb H, Kubista M. Properties of the reverse transcription reaction in mRNA quantification. Clin Chem 2004, 50(3):509-515. 10.1373/clinchem.2003.026161, 14726469.
    • (2004) Clin Chem , vol.50 , Issue.3 , pp. 509-515
    • Stahlberg, A.1    Hakansson, J.2    Xian, X.3    Semb, H.4    Kubista, M.5
  • 3
    • 67349200276 scopus 로고    scopus 로고
    • Antisense transcripts of V(D)J rearrangements; artifacts caused by false priming?
    • 10.1016/j.molimm.2009.03.020, 19403175
    • Zhao Y, Dunn-Walters DK, Barone F, Spencer J. Antisense transcripts of V(D)J rearrangements; artifacts caused by false priming?. Mol Immunol 2009, 46(11-12):2357-2362. 10.1016/j.molimm.2009.03.020, 19403175.
    • (2009) Mol Immunol , vol.46 , Issue.11-12 , pp. 2357-2362
    • Zhao, Y.1    Dunn-Walters, D.K.2    Barone, F.3    Spencer, J.4
  • 4
    • 34548400808 scopus 로고    scopus 로고
    • Sense or antisense? False priming reverse transcription controls are required for determining sequence orientation by reverse transcription-PCR
    • 10.1016/j.ab.2007.06.044, 17698025
    • Beiter T, Reich E, Weigert C, Niess AM, Simon P. Sense or antisense? False priming reverse transcription controls are required for determining sequence orientation by reverse transcription-PCR. Anal Biochem 2007, 369(2):258-261. 10.1016/j.ab.2007.06.044, 17698025.
    • (2007) Anal Biochem , vol.369 , Issue.2 , pp. 258-261
    • Beiter, T.1    Reich, E.2    Weigert, C.3    Niess, A.M.4    Simon, P.5
  • 5
    • 33746683274 scopus 로고    scopus 로고
    • Reverse transcriptase template switching and false alternative transcripts
    • 10.1016/j.ygeno.2005.12.013, 16457984
    • Cocquet J, Chong A, Zhang G, Veitia RA. Reverse transcriptase template switching and false alternative transcripts. Genomics 2006, 88(1):127-131. 10.1016/j.ygeno.2005.12.013, 16457984.
    • (2006) Genomics , vol.88 , Issue.1 , pp. 127-131
    • Cocquet, J.1    Chong, A.2    Zhang, G.3    Veitia, R.A.4
  • 7
    • 34249326541 scopus 로고    scopus 로고
    • Potential pitfalls in the accuracy of analysis of natural sense-antisense RNA pairs by reverse transcription-PCR
    • 10.1186/1472-6750-7-21, 1876213, 17480233
    • Haddad F, Qin AX, Giger JM, Guo H, Baldwin KM. Potential pitfalls in the accuracy of analysis of natural sense-antisense RNA pairs by reverse transcription-PCR. BMC Biotechnol 2007, 7:21. 10.1186/1472-6750-7-21, 1876213, 17480233.
    • (2007) BMC Biotechnol , vol.7 , pp. 21
    • Haddad, F.1    Qin, A.X.2    Giger, J.M.3    Guo, H.4    Baldwin, K.M.5
  • 8
    • 0024531983 scopus 로고
    • Fidelity of two retroviral reverse transcriptases during DNA-dependent DNA synthesis in vitro
    • 362622, 2469002
    • Roberts JD, Preston BD, Johnston LA, Soni A, Loeb LA, Kunkel TA. Fidelity of two retroviral reverse transcriptases during DNA-dependent DNA synthesis in vitro. Mol Cell Biol 1989, 9(2):469-476. 362622, 2469002.
    • (1989) Mol Cell Biol , vol.9 , Issue.2 , pp. 469-476
    • Roberts, J.D.1    Preston, B.D.2    Johnston, L.A.3    Soni, A.4    Loeb, L.A.5    Kunkel, T.A.6
  • 9
    • 36148972085 scopus 로고    scopus 로고
    • Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D
    • 10.1093/nar/gkm683, 2095812, 17897965
    • Perocchi F, Xu Z, Clauder-Munster S, Steinmetz LM. Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res 2007, 35(19):e128. 10.1093/nar/gkm683, 2095812, 17897965.
    • (2007) Nucleic Acids Res , vol.35 , Issue.19
    • Perocchi, F.1    Xu, Z.2    Clauder-Munster, S.3    Steinmetz, L.M.4
  • 10
    • 33645805622 scopus 로고    scopus 로고
    • An antibody-based microarray assay for small RNA detection
    • 10.1093/nar/gkl142, 1435976, 16614443
    • Hu Z, Zhang A, Storz G, Gottesman S, Leppla SH. An antibody-based microarray assay for small RNA detection. Nucleic Acids Res 2006, 34(7):e52. 10.1093/nar/gkl142, 1435976, 16614443.
    • (2006) Nucleic Acids Res , vol.34 , Issue.7
    • Hu, Z.1    Zhang, A.2    Storz, G.3    Gottesman, S.4    Leppla, S.H.5
  • 11
    • 48249146397 scopus 로고    scopus 로고
    • Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping
    • 10.1038/ng.196, 2538488, 18641648
    • Dutrow N, Nix DA, Holt D, Milash B, Dalley B, Westbroek E, Parnell TJ, Cairns BR. Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping. Nat Genet 2008, 40(8):977-986. 10.1038/ng.196, 2538488, 18641648.
    • (2008) Nat Genet , vol.40 , Issue.8 , pp. 977-986
    • Dutrow, N.1    Nix, D.A.2    Holt, D.3    Milash, B.4    Dalley, B.5    Westbroek, E.6    Parnell, T.J.7    Cairns, B.R.8
  • 12
    • 19544379844 scopus 로고    scopus 로고
    • Gold nanoparticle probe-based gene expression analysis with unamplified total human RNA
    • 10.1093/nar/gnh133, 524311, 15475384
    • Huber M, Wei TF, Muller UR, Lefebvre PA, Marla SS, Bao YP. Gold nanoparticle probe-based gene expression analysis with unamplified total human RNA. Nucleic Acids Res 2004, 32(18):e137. 10.1093/nar/gnh133, 524311, 15475384.
    • (2004) Nucleic Acids Res , vol.32 , Issue.18
    • Huber, M.1    Wei, T.F.2    Muller, U.R.3    Lefebvre, P.A.4    Marla, S.S.5    Bao, Y.P.6
  • 13
    • 18144442663 scopus 로고    scopus 로고
    • Direct labeling of RNA with multiple biotins allows sensitive expression profiling of acute leukemia class predictor genes
    • 10.1093/nar/gnh085, 443553, 15205470
    • Cole K, Truong V, Barone D, McGall G. Direct labeling of RNA with multiple biotins allows sensitive expression profiling of acute leukemia class predictor genes. Nucleic Acids Res 2004, 32(11):e86. 10.1093/nar/gnh085, 443553, 15205470.
    • (2004) Nucleic Acids Res , vol.32 , Issue.11
    • Cole, K.1    Truong, V.2    Barone, D.3    McGall, G.4
  • 14
    • 33845876339 scopus 로고    scopus 로고
    • Direct and sensitive miRNA profiling from low-input total RNA
    • 10.1261/rna.234507, 1705746, 17105992
    • Wang H, Ach RA, Curry B. Direct and sensitive miRNA profiling from low-input total RNA. RNA 2007, 13(1):151-159. 10.1261/rna.234507, 1705746, 17105992.
    • (2007) RNA , vol.13 , Issue.1 , pp. 151-159
    • Wang, H.1    Ach, R.A.2    Curry, B.3
  • 15
    • 0028817281 scopus 로고
    • Nonradioactive 3'-end-labeling of RNA molecules of different lengths by terminal deoxynucleotidyltransferase
    • 10.1006/abio.1995.1068, 7535988
    • Rosemeyer V, Laubrock A, Seibl R. Nonradioactive 3'-end-labeling of RNA molecules of different lengths by terminal deoxynucleotidyltransferase. Anal Biochem 1995, 224(1):446-449. 10.1006/abio.1995.1068, 7535988.
    • (1995) Anal Biochem , vol.224 , Issue.1 , pp. 446-449
    • Rosemeyer, V.1    Laubrock, A.2    Seibl, R.3
  • 17
    • 0037441669 scopus 로고    scopus 로고
    • Directly labeled mRNA produces highly precise and unbiased differential gene expression data
    • 10.1093/nar/gng013, 150245, 12582258
    • Gupta V, Cherkassky A, Chatis P, Joseph R, Johnson AL, Broadbent J, Erickson T, DiMeo J. Directly labeled mRNA produces highly precise and unbiased differential gene expression data. Nucleic Acids Res 2003, 31(4):e13. 10.1093/nar/gng013, 150245, 12582258.
    • (2003) Nucleic Acids Res , vol.31 , Issue.4
    • Gupta, V.1    Cherkassky, A.2    Chatis, P.3    Joseph, R.4    Johnson, A.L.5    Broadbent, J.6    Erickson, T.7    DiMeo, J.8
  • 19
    • 57049101718 scopus 로고    scopus 로고
    • Comparative genomics of wild type yeast strains unveils important genome diversity
    • 10.1186/1471-2164-9-524, 2588607, 18983662
    • Carreto L, Eiriz MF, Gomes AC, Pereira PM, Schuller D, Santos MA. Comparative genomics of wild type yeast strains unveils important genome diversity. BMC Genomics 2008, 9:524. 10.1186/1471-2164-9-524, 2588607, 18983662.
    • (2008) BMC Genomics , vol.9 , pp. 524
    • Carreto, L.1    Eiriz, M.F.2    Gomes, A.C.3    Pereira, P.M.4    Schuller, D.5    Santos, M.A.6
  • 20
    • 38349081518 scopus 로고    scopus 로고
    • MicroRNA Labeling Methods Directly Influence the Accuracy of Expression Profiling Detection
    • Enos JM, Duzeski JL, Roesch PL, Hagstrom JE, Watt MAV. MicroRNA Labeling Methods Directly Influence the Accuracy of Expression Profiling Detection. Biotechniques 2007, 42:378.
    • (2007) Biotechniques , vol.42 , pp. 378
    • Enos, J.M.1    Duzeski, J.L.2    Roesch, P.L.3    Hagstrom, J.E.4    Watt, M.A.V.5
  • 21
    • 77949895526 scopus 로고    scopus 로고
    • Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays
    • 10.1186/1471-2105-11-82, 2836303, 20144223
    • Hovik H, Chen T. Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays. BMC Bioinformatics 2010, 11(1):82. 10.1186/1471-2105-11-82, 2836303, 20144223.
    • (2010) BMC Bioinformatics , vol.11 , Issue.1 , pp. 82
    • Hovik, H.1    Chen, T.2
  • 22
    • 0027214848 scopus 로고
    • Interactions of Porphyromonas gingivalis with epithelial cells
    • 280837, 8386706
    • Duncan MJ, Nakao S, Skobe Z, Xie H. Interactions of Porphyromonas gingivalis with epithelial cells. Infect Immun 1993, 61(5):2260-2265. 280837, 8386706.
    • (1993) Infect Immun , vol.61 , Issue.5 , pp. 2260-2265
    • Duncan, M.J.1    Nakao, S.2    Skobe, Z.3    Xie, H.4
  • 23
    • 33747856481 scopus 로고    scopus 로고
    • Transcript mapping with high-density oligonucleotide tiling arrays
    • 10.1093/bioinformatics/btl289, 16787969
    • Huber W, Toedling J, Steinmetz LM. Transcript mapping with high-density oligonucleotide tiling arrays. Bioinformatics 2006, 22(16):1963-1970. 10.1093/bioinformatics/btl289, 16787969.
    • (2006) Bioinformatics , vol.22 , Issue.16 , pp. 1963-1970
    • Huber, W.1    Toedling, J.2    Steinmetz, L.M.3
  • 24
    • 32344445935 scopus 로고    scopus 로고
    • Strand-specific, real-time RT-PCR assays for quantification of genomic and positive-sense RNAs of the fish rhabdovirus, Infectious hematopoietic necrosis virus
    • 10.1016/j.jviromet.2005.08.017, 16199097
    • Purcell MK, Hart SA, Kurath G, Winton JR. Strand-specific, real-time RT-PCR assays for quantification of genomic and positive-sense RNAs of the fish rhabdovirus, Infectious hematopoietic necrosis virus. J Virol Methods 2006, 132(1-2):18-24. 10.1016/j.jviromet.2005.08.017, 16199097.
    • (2006) J Virol Methods , vol.132 , Issue.1-2 , pp. 18-24
    • Purcell, M.K.1    Hart, S.A.2    Kurath, G.3    Winton, J.R.4
  • 25
    • 25444509247 scopus 로고    scopus 로고
    • Secondary structure in the target as a confounding factor in synthetic oligomer microarray design
    • 10.1186/1471-2164-6-31, 555549, 15755320
    • Ratushna VG, Weller JW, Gibas CJ. Secondary structure in the target as a confounding factor in synthetic oligomer microarray design. BMC Genomics 2005, 6(1):31. 10.1186/1471-2164-6-31, 555549, 15755320.
    • (2005) BMC Genomics , vol.6 , Issue.1 , pp. 31
    • Ratushna, V.G.1    Weller, J.W.2    Gibas, C.J.3
  • 27
    • 71749111302 scopus 로고    scopus 로고
    • Effects of formamide on the thermal stability of DNA duplexes on biochips
    • 10.1016/j.ab.2009.09.044, 19796625
    • Fuchs J, Dell'Atti D, Buhot A, Calemczuk R, Mascini M, Livache T. Effects of formamide on the thermal stability of DNA duplexes on biochips. Anal Biochem 2010, 397(1):132-134. 10.1016/j.ab.2009.09.044, 19796625.
    • (2010) Anal Biochem , vol.397 , Issue.1 , pp. 132-134
    • Fuchs, J.1    Dell'Atti, D.2    Buhot, A.3    Calemczuk, R.4    Mascini, M.5    Livache, T.6
  • 28
    • 33747880641 scopus 로고    scopus 로고
    • Troubleshooting microarray hybridizations
    • 10.1016/S0076-6879(06)11003-4, 16939784
    • Eads B, Cash A, Bogart K, Costello J, Andrews J. Troubleshooting microarray hybridizations. Methods Enzymol 2006, 411:34-49. 10.1016/S0076-6879(06)11003-4, 16939784.
    • (2006) Methods Enzymol , vol.411 , pp. 34-49
    • Eads, B.1    Cash, A.2    Bogart, K.3    Costello, J.4    Andrews, J.5
  • 29
    • 1842571774 scopus 로고    scopus 로고
    • Impact of surface chemistry and blocking strategies on DNA microarrays
    • 10.1093/nar/gng086, 169979, 12907739
    • Taylor S, Smith S, Windle B, Guiseppi-Elie A. Impact of surface chemistry and blocking strategies on DNA microarrays. Nucleic Acids Res 2003, 31(16):e87. 10.1093/nar/gng086, 169979, 12907739.
    • (2003) Nucleic Acids Res , vol.31 , Issue.16
    • Taylor, S.1    Smith, S.2    Windle, B.3    Guiseppi-Elie, A.4
  • 30
    • 0000912747 scopus 로고
    • Basis of actinomycin action. I. DNA binding and inhibition of RNA-polymerase synthetic reactions by actinomycin
    • 10.1073/pnas.48.12.2094, 221129, 13948669
    • Goldberg IH, Rabinowitz M, Reich E. Basis of actinomycin action. I. DNA binding and inhibition of RNA-polymerase synthetic reactions by actinomycin. Proc Natl Acad Sci USA 1962, 48:2094-2101. 10.1073/pnas.48.12.2094, 221129, 13948669.
    • (1962) Proc Natl Acad Sci USA , vol.48 , pp. 2094-2101
    • Goldberg, I.H.1    Rabinowitz, M.2    Reich, E.3
  • 31
    • 22144467302 scopus 로고    scopus 로고
    • Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping
    • 10.1016/j.tig.2005.06.007, 1855044, 15979196
    • Royce TE, Rozowsky JS, Bertone P, Samanta M, Stolc V, Weissman S, Snyder M, Gerstein M. Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet 2005, 21(8):466-475. 10.1016/j.tig.2005.06.007, 1855044, 15979196.
    • (2005) Trends Genet , vol.21 , Issue.8 , pp. 466-475
    • Royce, T.E.1    Rozowsky, J.S.2    Bertone, P.3    Samanta, M.4    Stolc, V.5    Weissman, S.6    Snyder, M.7    Gerstein, M.8
  • 32
    • 0037440012 scopus 로고    scopus 로고
    • Prioritized selection of oligodeoxyribonucleotide probes for efficient hybridization to RNA transcripts
    • 10.1093/nar/gkg133, 140499, 12527785
    • Luebke KJ, Balog RP, Garner HR. Prioritized selection of oligodeoxyribonucleotide probes for efficient hybridization to RNA transcripts. Nucleic Acids Res 2003, 31(2):750-758. 10.1093/nar/gkg133, 140499, 12527785.
    • (2003) Nucleic Acids Res , vol.31 , Issue.2 , pp. 750-758
    • Luebke, K.J.1    Balog, R.P.2    Garner, H.R.3
  • 33
    • 77953901913 scopus 로고    scopus 로고
    • A hidden Markov support vector machine framework incorporating profile geometry learning for identifying microbial RNA in tiling array data
    • 10.1093/bioinformatics/btq162, 20395286
    • Yu WH, Hovik H, Chen T. A hidden Markov support vector machine framework incorporating profile geometry learning for identifying microbial RNA in tiling array data. Bioinformatics 2010, 26(11):1423-1430. 10.1093/bioinformatics/btq162, 20395286.
    • (2010) Bioinformatics , vol.26 , Issue.11 , pp. 1423-1430
    • Yu, W.H.1    Hovik, H.2    Chen, T.3


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