Oligonucleotide Không Khớp Trong Con Người Và Nấm Men: Hướng Dẫn Thiết Kế Đầu Nanh Trên Dàn Microarray Tiling
Tóm tắt
Các oligonucleotide không khớp được sử dụng rộng rãi trên các microarray để phân biệt sự lai ghép đặc hiệu từ không đặc hiệu. Trong khi nhiều thí nghiệm phụ thuộc vào các oligo như vậy, hành vi lai ghép của các cấu trúc sai lệch khác nhau chưa được nghiên cứu nhiều. Ở đây, chúng tôi trình bày kết quả của hai thí nghiệm microarray quy mô lớn trên
Từ khóa
#oligonucleotide #không khớp #microarray #lai ghép #DNA #S. cerevisiae #H. sapiensTài liệu tham khảo
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: 466-475. 10.1016/j.tig.2005.06.007.
Southern E, Mir K, Shchepinov M: Molecular interactions on microarrays. Nat Genet. 1999, 21: 5-9. 10.1038/4429.
Binder H, Preibisch S, Kirsten T: Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays. Langmuir. 2005, 21: 9287-9302. 10.1021/la051231s.
Naef F, Lim DA, Patil N, Magnasco M: DNA hybridization to mismatched templates: a chip study. Phys Rev E Stat Nonlin Soft Matter Phys. 2002, 65: 040902-
Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M: Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics. 2002, 18 (Suppl 1): S96-104.
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003, 4: 249-264. 10.1093/biostatistics/4.2.249.
Urakawa H, El Fantroussi S, Smidt H, Smoot JC, Tribou EH, Kelly JJ, Noble PA, Stahl DA: Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays. Appl Environ Microbiol. 2003, 69: 2848-2856. 10.1128/AEM.69.5.2848-2856.2003.
Lee I, Dombkowski AA, Athey BD: Guidelines for incorporating non-perfectly matched oligonucleotides into target-specific hybridization probes for a DNA microarray. Nucleic Acids Res. 2004, 32: 681-690. 10.1093/nar/gkh196.
Levicky R, Horgan A: Physicochemical perspectives on DNA microarray and biosensor technologies. Trends Biotechnol. 2005, 23: 143-149. 10.1016/j.tibtech.2005.01.004.
Hacia JG: Resequencing and mutational analysis using oligonucleotide microarrays. Nat Genet. 1999, 21 (Suppl): 42-7. 10.1038/4469.
Wu C, Carta R, Zhang L: Sequence dependence of cross-hybridization on short oligo microarrays. Nucleic Acids Res. 2005, 33: e84-10.1093/nar/gni082.
Letowski J, Brousseau R, Masson L: Designing better probes: effect of probe size, mismatch position and number on hybridization in DNA oligonucleotide microarrays. J Microbiol Methods. 2004, 57: 269-278. 10.1016/j.mimet.2004.02.002.
Li X, He Z, Zhou J: Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Res. 2005, 33: 6114-6123. 10.1093/nar/gki914.
Rouillard JM, Herbert CJ, Zuker M: OligoArray: genome-scale oligonucleotide design for microarrays. Bioinformatics. 2002, 18: 486-487. 10.1093/bioinformatics/18.3.486.
Rouillard JM, Zuker M, Gulari E: OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res. 2003, 31: 3057-3062. 10.1093/nar/gkg426.
Wang X, Seed B: Selection of oligonucleotide probes for protein coding sequences. Bioinformatics. 2003, 19: 796-802. 10.1093/bioinformatics/btg086.
Bozdech Z, Zhu J, Joachimiak MP, Cohen FE, Pulliam B, DeRisi JL: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol. 2003, 4: R9-10.1186/gb-2003-4-2-r9.
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 (18): 3363-70. 10.1016/j.febslet.2007.06.033.
Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ, University of California Santa Cruz: The UCSC Genome Browser Database. Nucleic Acids Res. 2003, 31: 51-54. 10.1093/nar/gkg129.
Urban AE, Korbel JO, Selzer R, Richmond T, Hacker A, Popescu GV, Cubells JF, Green R, Emanuel BS, Gerstein MB, Weissman SM, Snyder M: High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc Natl Acad Sci USA. 2006, 103: 4534-4539. 10.1073/pnas.0511340103.
Emanuelsson O, Nagalakshmi U, Zheng D, Rozowsky JS, Urban AE, Du J, Lian Z, Stolc V, Weissman S, Snyder M, Gerstein MB: Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. Genome Res. 2007, 17 (6): 886-97. 10.1101/gr.5014606.