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Volumn 8, Issue 1, 2012, Pages

Evaluation of alternative RNA labeling protocols for transcript profiling with Arabidopsis AGRONOMICS1 tiling arrays

Author keywords

AGRONOMICS1; Arabidopsis; Microarray; RNA labeling; Tiling array; Transcript profiling

Indexed keywords

ARABIDOPSIS;

EID: 84862206083     PISSN: None     EISSN: 17464811     Source Type: Journal    
DOI: 10.1186/1746-4811-8-18     Document Type: Article
Times cited : (7)

References (42)
  • 1
    • 4043153341 scopus 로고    scopus 로고
    • Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications
    • 10.1101/gr.2544504, 528935, 15489341
    • Hilson P, Allemeersch J, Altmann T, Aubourg S, Avon A, Beynon J, Bhalerao RP, Bitton F, Caboche M, Cannoot B, et al. Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Genome Res 2004, 14:2176-2189. 10.1101/gr.2544504, 528935, 15489341.
    • (2004) Genome Res , vol.14 , pp. 2176-2189
    • Hilson, P.1    Allemeersch, J.2    Altmann, T.3    Aubourg, S.4    Avon, A.5    Beynon, J.6    Bhalerao, R.P.7    Bitton, F.8    Caboche, M.9    Cannoot, B.10
  • 2
    • 2342501846 scopus 로고    scopus 로고
    • Development and evaluation of an Arabidopsis whole genome Affymetrix probe array
    • 10.1111/j.1365-313X.2004.02061.x, 15086809
    • Redman JC, Haas BJ, Tanimoto G, Town CD. Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Plant J 2004, 38:545-561. 10.1111/j.1365-313X.2004.02061.x, 15086809.
    • (2004) Plant J , vol.38 , pp. 545-561
    • Redman, J.C.1    Haas, B.J.2    Tanimoto, G.3    Town, C.D.4
  • 3
    • 24344508130 scopus 로고    scopus 로고
    • A microarray analysis of the rice transcriptome and its comparison to Arabidopsis
    • 10.1101/gr.3657405, 1199542, 16140994
    • Ma L, Chen C, Liu X, Jiao Y, Su N, Li L, Wang X, Cao M, Sun N, Zhang X, et al. A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res 2005, 15:1274-1283. 10.1101/gr.3657405, 1199542, 16140994.
    • (2005) Genome Res , vol.15 , pp. 1274-1283
    • Ma, L.1    Chen, C.2    Liu, X.3    Jiao, Y.4    Su, N.5    Li, L.6    Wang, X.7    Cao, M.8    Sun, N.9    Zhang, X.10
  • 4
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • 10.1126/science.270.5235.467, 7569999
    • Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270:467-470. 10.1126/science.270.5235.467, 7569999.
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 5
    • 0034119379 scopus 로고    scopus 로고
    • Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis
    • 139922, 10810145
    • Reymond P, Weber H, Damond M, Farmer EE. Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis. Plant Cell 2000, 12:707-720. 139922, 10810145.
    • (2000) Plant Cell , vol.12 , pp. 707-720
    • Reymond, P.1    Weber, H.2    Damond, M.3    Farmer, E.E.4
  • 7
    • 0034353112 scopus 로고    scopus 로고
    • Arabidopsis microarray service facilities
    • 10.1104/pp.124.4.1468, 1539298, 11115861
    • Wisman E, Ohlrogge J. Arabidopsis microarray service facilities. Plant Physiol 2000, 124:1468-1471. 10.1104/pp.124.4.1468, 1539298, 11115861.
    • (2000) Plant Physiol , vol.124 , pp. 1468-1471
    • Wisman, E.1    Ohlrogge, J.2
  • 8
    • 1542475839 scopus 로고    scopus 로고
    • Arabidopsis transcript profiling on Affymetrix genechip arrays
    • Hennig L, Menges M, Murray JAH, Gruissem W. Arabidopsis transcript profiling on Affymetrix genechip arrays. Plant Mol Biol 2003, 53:457-465.
    • (2003) Plant Mol Biol , vol.53 , pp. 457-465
    • Hennig, L.1    Menges, M.2    Murray, J.A.H.3    Gruissem, W.4
  • 9
    • 13444264729 scopus 로고    scopus 로고
    • Genevestigator. Arabidopsis microarray database and analysis toolbox
    • 10.1104/pp.104.046367, 523327, 15375207
    • Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W. Genevestigator. Arabidopsis microarray database and analysis toolbox. Plant Physiol 2004, 136:2621-2632. 10.1104/pp.104.046367, 523327, 15375207.
    • (2004) Plant Physiol , vol.136 , pp. 2621-2632
    • Zimmermann, P.1    Hirsch-Hoffmann, M.2    Hennig, L.3    Gruissem, W.4
  • 10
    • 70350142925 scopus 로고    scopus 로고
    • Global analysis of allele-specific expression in Arabidopsis thaliana
    • 10.1534/genetics.109.103499, 2728882, 19474198
    • Zhang X, Borevitz JO. Global analysis of allele-specific expression in Arabidopsis thaliana. Genetics 2009, 182:943-954. 10.1534/genetics.109.103499, 2728882, 19474198.
    • (2009) Genetics , vol.182 , pp. 943-954
    • Zhang, X.1    Borevitz, J.O.2
  • 12
    • 47249089938 scopus 로고    scopus 로고
    • Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana
    • 10.1073/pnas.0802493105, 2426964, 18550839
    • Laubinger S, Sachsenberg T, Zeller G, Busch W, Lohmann JU, Ratsch G, Weigel D. Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2008, 105:8795-8800. 10.1073/pnas.0802493105, 2426964, 18550839.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 8795-8800
    • Laubinger, S.1    Sachsenberg, T.2    Zeller, G.3    Busch, W.4    Lohmann, J.U.5    Ratsch, G.6    Weigel, D.7
  • 13
    • 48249130774 scopus 로고    scopus 로고
    • At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana
    • 10.1186/gb-2008-9-7-r112, 2530869, 18613972
    • Laubinger S, Zeller G, Henz SR, Sachsenberg T, Widmer CK, Naouar N, Vuylsteke M, Scholkopf B, Ratsch G, Weigel D, et al. At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Genome Biol 2008, 9:R112. 10.1186/gb-2008-9-7-r112, 2530869, 18613972.
    • (2008) Genome Biol , vol.9
    • Laubinger, S.1    Zeller, G.2    Henz, S.R.3    Sachsenberg, T.4    Widmer, C.K.5    Naouar, N.6    Vuylsteke, M.7    Scholkopf, B.8    Ratsch, G.9    Weigel, D.10
  • 15
    • 41949131536 scopus 로고    scopus 로고
    • Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays
    • 10.1371/journal.pgen.1000032, 2265482, 18369451
    • Zhang X, Shiu S, Cal A, Borevitz JO. Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays. PLoS Genet 2008, 4:e1000032. 10.1371/journal.pgen.1000032, 2265482, 18369451.
    • (2008) PLoS Genet , vol.4
    • Zhang, X.1    Shiu, S.2    Cal, A.3    Borevitz, J.O.4
  • 16
    • 62349089764 scopus 로고    scopus 로고
    • Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays
    • 10.1186/gb-2009-10-2-r17, 2688271, 19210792
    • Hazen SP, Naef F, Quisel T, Gendron JM, Chen H, Ecker JR, Borevitz JO, Kay SA. Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. Genome Biol 2009, 10:R17. 10.1186/gb-2009-10-2-r17, 2688271, 19210792.
    • (2009) Genome Biol , vol.10
    • Hazen, S.P.1    Naef, F.2    Quisel, T.3    Gendron, J.M.4    Chen, H.5    Ecker, J.R.6    Borevitz, J.O.7    Kay, S.A.8
  • 17
    • 79955592294 scopus 로고    scopus 로고
    • The epigenome and plant development
    • 10.1146/annurev-arplant-042110-103806, 21438682
    • He G, Elling AA, Deng XW. The epigenome and plant development. Annu Rev Plant Biol 2011, 62:411-435. 10.1146/annurev-arplant-042110-103806, 21438682.
    • (2011) Annu Rev Plant Biol , vol.62 , pp. 411-435
    • He, G.1    Elling, A.A.2    Deng, X.W.3
  • 18
    • 57549116153 scopus 로고    scopus 로고
    • AtMap1: a DNA microarray for genomic deletion mapping in Arabidopsis thaliana
    • 10.1111/j.1365-313X.2008.03656.x, 18702675
    • Nagano AJ, Fukazawa M, Hayashi M, Ikeuchi M, Tsukaya H, Nishimura M, Hara-Nishimura I. AtMap1: a DNA microarray for genomic deletion mapping in Arabidopsis thaliana. Plant J 2008, 56:1058-1065. 10.1111/j.1365-313X.2008.03656.x, 18702675.
    • (2008) Plant J , vol.56 , pp. 1058-1065
    • Nagano, A.J.1    Fukazawa, M.2    Hayashi, M.3    Ikeuchi, M.4    Tsukaya, H.5    Nishimura, M.6    Hara-Nishimura, I.7
  • 19
    • 35948958253 scopus 로고    scopus 로고
    • Genome-wide expression profiling of the Arabidopsis female gametophyte identifies families of small, secreted proteins
    • 2014789, 17937500
    • Jones-Rhoades MW, Borevitz JO, Preuss D. Genome-wide expression profiling of the Arabidopsis female gametophyte identifies families of small, secreted proteins. PLoS Genet 2007, 3:1848-1861. 2014789, 17937500.
    • (2007) PLoS Genet , vol.3 , pp. 1848-1861
    • Jones-Rhoades, M.W.1    Borevitz, J.O.2    Preuss, D.3
  • 20
    • 77956525856 scopus 로고    scopus 로고
    • Analysis of antisense expression by whole genome tiling microarrays and siRNAs suggests mis-annotation of Arabidopsis orphan protein-coding genes
    • 10.1371/journal.pone.0010710, 2877095, 20520764
    • Richardson CR, Luo QJ, Gontcharova V, Jiang YW, Samanta M, Youn E, Rock CD. Analysis of antisense expression by whole genome tiling microarrays and siRNAs suggests mis-annotation of Arabidopsis orphan protein-coding genes. PLoS One 2010, 5:e10710. 10.1371/journal.pone.0010710, 2877095, 20520764.
    • (2010) PLoS One , vol.5
    • Richardson, C.R.1    Luo, Q.J.2    Gontcharova, V.3    Jiang, Y.W.4    Samanta, M.5    Youn, E.6    Rock, C.D.7
  • 21
    • 50849112729 scopus 로고    scopus 로고
    • Genic and global functions for Paf1C in chromatin modification and gene expression in Arabidopsis
    • 10.1371/journal.pgen.1000077, 2515192, 18725930
    • Oh S, Park S, van Nocker S. Genic and global functions for Paf1C in chromatin modification and gene expression in Arabidopsis. PLoS Genet 2008, 4:e1000077. 10.1371/journal.pgen.1000077, 2515192, 18725930.
    • (2008) PLoS Genet , vol.4
    • Oh, S.1    Park, S.2    van Nocker, S.3
  • 22
    • 65949090511 scopus 로고    scopus 로고
    • Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower
    • 2671559, 19385720
    • Kaufmann K, Muino JM, Jauregui R, Airoldi CA, Smaczniak C, Krajewski P, Angenent GC. Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower. PLoS Biol 2009, 7:e1000090. 2671559, 19385720.
    • (2009) PLoS Biol , vol.7
    • Kaufmann, K.1    Muino, J.M.2    Jauregui, R.3    Airoldi, C.A.4    Smaczniak, C.5    Krajewski, P.6    Angenent, G.C.7
  • 25
    • 77950547216 scopus 로고    scopus 로고
    • Probing the reproducibility of leaf growth and molecular phenotypes: a comparison of three Arabidopsis accessions cultivated in ten laboratories
    • 10.1104/pp.109.148338, 2850010, 20200072
    • Massonnet C, Vile D, Fabre J, Hannah MA, Caldana C, Lisec J, Beemster GT, Meyer RC, Messerli G, Gronlund JT, et al. Probing the reproducibility of leaf growth and molecular phenotypes: a comparison of three Arabidopsis accessions cultivated in ten laboratories. Plant Physiol 2010, 152:2142-2157. 10.1104/pp.109.148338, 2850010, 20200072.
    • (2010) Plant Physiol , vol.152 , pp. 2142-2157
    • Massonnet, C.1    Vile, D.2    Fabre, J.3    Hannah, M.A.4    Caldana, C.5    Lisec, J.6    Beemster, G.T.7    Meyer, R.C.8    Messerli, G.9    Gronlund, J.T.10
  • 26
    • 78449265382 scopus 로고    scopus 로고
    • H3K27me3 profiling of the endosperm implies exclusion of Polycomb group protein targeting by DNA methylation
    • 10.1371/journal.pgen.1001152, 2951372, 20949070
    • Weinhofer I, Hehenberger E, Roszak P, Hennig L, Köhler C. H3K27me3 profiling of the endosperm implies exclusion of Polycomb group protein targeting by DNA methylation. PLoS Genet 2010, 6:e1001152. 10.1371/journal.pgen.1001152, 2951372, 20949070.
    • (2010) PLoS Genet , vol.6
    • Weinhofer, I.1    Hehenberger, E.2    Roszak, P.3    Hennig, L.4    Köhler, C.5
  • 27
    • 84855182246 scopus 로고    scopus 로고
    • Plastid proteome assembly without Toc159: Photosynthetic protein import and accumulation of n-acetylated plastid precursor proteins
    • 10.1105/tpc.111.092882, 22128122
    • Bischof S, Baerenfaller K, Wildhaber T, Troesch R, Vidi PA, Roschitzki B, Hirsch-Hoffmann M, Hennig L, Kessler F, Gruissem W, et al. Plastid proteome assembly without Toc159: Photosynthetic protein import and accumulation of n-acetylated plastid precursor proteins. Plant Cell 2011, 23:3911-3928. 10.1105/tpc.111.092882, 22128122.
    • (2011) Plant Cell , vol.23 , pp. 3911-3928
    • Bischof, S.1    Baerenfaller, K.2    Wildhaber, T.3    Troesch, R.4    Vidi, P.A.5    Roschitzki, B.6    Hirsch-Hoffmann, M.7    Hennig, L.8    Kessler, F.9    Gruissem, W.10
  • 28
    • 30344450374 scopus 로고    scopus 로고
    • RNA Polyadenylation in prokaryotes and organelles; Different tails tell different tales
    • Slomovic S, Portnoy V, Schuster G. RNA Polyadenylation in prokaryotes and organelles; Different tails tell different tales. Crit Rev Plant Sci 2006, 25:65-77.
    • (2006) Crit Rev Plant Sci , vol.25 , pp. 65-77
    • Slomovic, S.1    Portnoy, V.2    Schuster, G.3
  • 29
    • 34447274090 scopus 로고    scopus 로고
    • Identification of an in vitro transcription-based artifact affecting oligonucleotide microarrays
    • 10.1016/j.febslet.2007.06.033, 17604026
    • Nelson DC, Wohlbach DJ, Rodesch MJ, Stolc V, Sussman MR, Samanta MP. Identification of an in vitro transcription-based artifact affecting oligonucleotide microarrays. FEBS Lett 2007, 581:3363-3370. 10.1016/j.febslet.2007.06.033, 17604026.
    • (2007) FEBS Lett , vol.581 , pp. 3363-3370
    • Nelson, D.C.1    Wohlbach, D.J.2    Rodesch, M.J.3    Stolc, V.4    Sussman, M.R.5    Samanta, M.P.6
  • 31
    • 77953005066 scopus 로고    scopus 로고
    • Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer
    • 10.1186/1471-2164-11-352, 2889901, 20525254
    • Pio R, Blanco D, Pajares MJ, Aibar E, Durany O, Ezponda T, Agorreta J, Gomez-Roman J, Anton MA, Rubio A, et al. Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer. BMC Genomics 2010, 11:352. 10.1186/1471-2164-11-352, 2889901, 20525254.
    • (2010) BMC Genomics , vol.11 , pp. 352
    • Pio, R.1    Blanco, D.2    Pajares, M.J.3    Aibar, E.4    Durany, O.5    Ezponda, T.6    Agorreta, J.7    Gomez-Roman, J.8    Anton, M.A.9    Rubio, A.10
  • 32
    • 77951226966 scopus 로고    scopus 로고
    • G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration
    • Fasold M, Stadler PF, Binder H. G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration. BMC Bioinforma 2010, 11:207.
    • (2010) BMC Bioinforma , vol.11 , pp. 207
    • Fasold, M.1    Stadler, P.F.2    Binder, H.3
  • 33
    • 33645520538 scopus 로고    scopus 로고
    • Analysis of Affymetrix GeneChip data using amplified RNA
    • 10.2144/000112057, 16526405
    • Cope L, Hartman SM, Gohlmann HW, Tiesman JP, Irizarry RA. Analysis of Affymetrix GeneChip data using amplified RNA. Biotechniques 2006, 40:165-170. 10.2144/000112057, 16526405.
    • (2006) Biotechniques , vol.40 , pp. 165-170
    • Cope, L.1    Hartman, S.M.2    Gohlmann, H.W.3    Tiesman, J.P.4    Irizarry, R.A.5
  • 34
    • 33745482592 scopus 로고    scopus 로고
    • Reverse transcription using random pentadecamer primers increases yield and quality of resulting cDNA
    • 10.2144/000112153, 16708763
    • Stangegaard M, Dufva IH, Dufva M. Reverse transcription using random pentadecamer primers increases yield and quality of resulting cDNA. Biotechniques 2006, 40:649-657. 10.2144/000112153, 16708763.
    • (2006) Biotechniques , vol.40 , pp. 649-657
    • Stangegaard, M.1    Dufva, I.H.2    Dufva, M.3
  • 35
    • 67649096971 scopus 로고    scopus 로고
    • Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array
    • 10.1186/1471-2164-10-253, 2694213, 19480707
    • Coram TE, Settles ML, Chen X. Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array. BMC Genomics 2009, 10:253. 10.1186/1471-2164-10-253, 2694213, 19480707.
    • (2009) BMC Genomics , vol.10 , pp. 253
    • Coram, T.E.1    Settles, M.L.2    Chen, X.3
  • 36
    • 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, 22:1963-1970. 10.1093/bioinformatics/btl289, 16787969.
    • (2006) Bioinformatics , vol.22 , pp. 1963-1970
    • Huber, W.1    Toedling, J.2    Steinmetz, L.M.3
  • 37
    • 3042513378 scopus 로고    scopus 로고
    • Spearman's footrule as a measure of cDNA microarray reproducibility
    • 10.1016/j.ygeno.2004.02.015, 15234007
    • Kim BS, Rha SY, Cho GB, Chung HC. Spearman's footrule as a measure of cDNA microarray reproducibility. Genomics 2004, 84:441-448. 10.1016/j.ygeno.2004.02.015, 15234007.
    • (2004) Genomics , vol.84 , pp. 441-448
    • Kim, B.S.1    Rha, S.Y.2    Cho, G.B.3    Chung, H.C.4
  • 38
    • 79951480123 scopus 로고    scopus 로고
    • R Foundation for Statistical Computing, Vienna, Austria, R Development Core Team
    • R Development Core Team R: A language and environment for statistical computing 2010, R Foundation for Statistical Computing, Vienna, Austria, R Development Core Team.
    • (2010) R: A language and environment for statistical computing
  • 39
    • 70349739736 scopus 로고    scopus 로고
    • The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets
    • 10.1093/bioinformatics/btp472, 2759552, 19654113
    • Nicol JW, Helt GA, Blanchard SG, Raja A, Loraine AE. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 2009, 25:2730-2731. 10.1093/bioinformatics/btp472, 2759552, 19654113.
    • (2009) Bioinformatics , vol.25 , pp. 2730-2731
    • Nicol, J.W.1    Helt, G.A.2    Blanchard, S.G.3    Raja, A.4    Loraine, A.E.5
  • 42
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
    • Smyth GK. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3:1-26.
    • (2004) Stat Appl Genet Mol Biol , vol.3 , pp. 1-26
    • Smyth, G.K.1


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