Identification of an in vitro transcription-based artifact affecting oligonucleotide microarrays

FEBS Letters

Volumn 581, Issue 18, 2007, Pages 3363-3370

  Nelson, David C ^a   Wohlbach, Dana J ^a   Rodesch, Matthew J ^a   Stolc, Viktor ^b   Sussman, Michael R ^a   Samanta, Manoj P ^c  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b UARC   (United States)

^c Systemix Institute   (United States)

Author keywords

Chips; DNA; Expression; Genes; Microarrays; RNA

Indexed keywords

ARABIDOPSIS; ARTICLE; ARTIFACT; DNA MICROARRAY; EUKARYOTE; GENE EXPRESSION; GENE PROBE; GENETIC TRANSCRIPTION; GENOME ANALYSIS; HYBRIDIZATION; MATHEMATICAL MODEL; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN MOTIF;

ARTIFACTS; BASE SEQUENCE; NUCLEOTIDES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TRANSCRIPTION, GENETIC;

ARABIDOPSIS THALIANA; EUKARYOTA;

EID: 34447274090     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2007.06.033     Document Type: Article

References (27)

1. Shoemaker D.D., Schadt E.E., Armour C.D., He Y.D., Garrett-Engele P., McDonagh P.D., Loerch P.M., Leonardson A., Lum P.Y., Cavet G., Wu L.F., Altschuler S.J., Edwards S., King J., Tsang J.S., Schimmack G., Schelter J.M., Koch J., Ziman M., Marton M.J., Li B., Cundiff P., Ward T., Castle J., Krolewski M., Meyer M.R., Mao M., Burchard J., Kidd M.J., Dai H., Phillips J.W., Linsley P.S., Stoughton R., Scherer S., and Boguski M.S. Experimental annotation of the human genome using microarray technology. Nature 409 (2001) 922-927
2. Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C., Nguyen M., Pham P., Cheuk R., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., and Ecker J.R. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302 (2003) 842-846
3. Bertone P., Stolc V., Royce T.E., Rozowsky J.S., Urban A.E., Zhu X., Rinn J.L., Tongprasit W., Samanta M., Weissman S., Gerstein M., and Snyder M. Global identification of human transcribed sequences with genome tiling arrays. Science 306 (2004) 2242-2246
4. Stolc V., Samanta M.P., Tongprasit W., Sethi H., Liang S., Nelson D.C., Hegeman A., Nelson C., Rancour D., Bednarek S., Ulrich E.L., Zhao Q., Wrobel R.L., Newman C.S., Fox B.G., Phillips Jr. G.N., Markley J.L., and Sussman M.R. Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc. Natl. Acad. Sci. USA 102 (2005) 4453-4458
5. Samanta M.P., Tongprasit W., Sethi H., Chin C.S., and Stolc V. Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway. Proc. Natl. Acad. Sci. USA 103 (2006) 4192-4197
6. Cheng J., Kapranov P., Drenkow J., Dike S., Brubaker S., Patel S., Long J., Stern D., Tammana H., Helt G., Sementchenko V., Piccolboni A., Bekiranov S., Bailey D.K., Ganesh M., Ghosh S., Bell I., Gerhard D.S., and Gingeras T.R. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308 (2005) 1149-1154
7. Li L., Wang X., Stolc V., Li X., Zhang D., Su N., Tongprasit W., Li S., Cheng Z., Wang J., and Deng X.W. Genome-wide transcription analyses in rice using tiling microarrays. Nat. Genet. 38 (2006) 124-129
8. Selinger D.W., Cheung K.J., Mei R., Johansson E.M., Richmond C.S., Blattner F.R., Lockhart D.J., and Church G.M. RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat. Biotechnol. 18 (2000) 1262-1268
9. Samanta, M.P., Maleszka, R., Tongprasit, W., Newman, T., Elsik, C., Nelson, D.C., Sussman, M.R., Robinson, G. and Stolc, V. (unpublished).
10. Amburst, G. et al. (unpublished).
11. Samanta, M.P., Tongprasit, W., Istrail, S., Cameron, A., Tu, Q., Davidson E.H. and Stolc, V. (unpublished).
12. Royce T.E., Rozowsky J.S., Bertone P., Samanta M., Stolc V., Weissman S., Snyder M., and Gerstein M. Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet. 21 (2005) 466-475
13. Johnson J.M., Edwards S., Shoemaker D., and Schadt E.E. Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet. 21 (2005) 93-102
14. Mockler T.C., Chan S., Sundaresan A., Chen H., Jacobsen S.E., and Ecker J.R. Applications of DNA tiling arrays for whole-genome analysis. Genomics 85 (2005) 1-15
15. Nuwaysir E.F., Huang W., Albert T.J., Singh J., Nuwaysir K., Pitas A., Richmond T., Gorski T., Berg J.P., Ballin J., McCormick M., Norton J., Pollock T., Sumwalt T., Butcher L., Porter D., Molla M., Hall C., Blattner F., Sussman M.R., Wallace R.L., Cerrina F., and Green R.D. Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res. 12 (2002) 1749-1755
16. Stolc V., Samanta M.P., Tongprasit W., and Marshall W.F. Genome-wide transcriptional analysis of flagellar regeneration in Chlamydomonas reinhardtii identifies orthologs of ciliary disease genes. Proc. Natl. Acad. Sci. USA 102 (2005) 3703-3707
17. Stolc V., Gauhar Z., Mason C., Halasz G., van Batenburg M.F., Rifkin S.A., Hua S., Herreman T., Tongprasit W., Barbano P.E., Bussemaker H.J., and White K.P. A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 306 (2004) 655-660
18. Pleiss J.A., Derrick M.L., and Uhlenbeck O.C. T7 RNA polymerase produces 5′ end heterogeneity during in vitro transcription from certain templates. RNA 4 (1998) 1313-1317
19. Martin C.T., Muller D.K., and Coleman J.E. Processivity in early stages of transcription by T7 RNA polymerase. Biochemistry 27 (1988) 3966-3974
20. Imburgio D., Rong M., Ma K., and McAllister W.T. Studies of promoter recognition and start site selection by T7 RNA polymerase using a comprehensive collection of promoter variants. Biochemistry 39 (2000) 10419-10430
21. Milligan J.F., Groebe D.R., Witherell G.W., and Uhlenbeck O.C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15 (1987) 8783-8798
22. Kuzmine I., Gottlieb P.A., and Martin C.T. Structure in nascent RNA leads to termination of slippage transcription by T7 RNA polymerase. Nucleic Acids Res. 29 (2001) 2601-2606
23. Richmond K.E., Li M.H., Rodesch M.J., Patel M., Lowe A.M., Kim C., Chu L.L., Venkataramaian N., Flickinger S.F., Kaysen J., Belshaw P.J., Sussman M.R., and Cerrina F. Amplification and assembly of chip-eluted DNA (AACED): a method for high-throughput gene synthesis. Nucleic Acids Res. 32 (2004) 5011-5018
24. Irizarry R.A., Hobbs B., Collin F., Beazer-Barclay Y.D., Antonellis K.J., Scherf U., and Speed T.P. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4 (2003) 249-264
25. Wu Z., Irizarry R.A., Gentleman R., Martinez-Murillo F., and Spencer F. A model based background adjustment for oligonucleotide expression arrays. J. Am. Stat. Assoc. 99 (2004) 909-917
26. Bioconductor. .
27. Gentleman R.C., Carey V.J., Bates D.M., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y., Gentry J., Hornik K., Hothorn T., Huber W., Iacus S., Irizarry R., Leisch F., Li C., Maechler M., Rossini A.J., Sawitzki G., Smith C., Smyth G., Tierney L., Yang J.Y., and Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5 (2004) R80