Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer - PubMed (original) (raw)
M Mao, A R Jones, J Burchard, M J Marton, K W Shannon, S M Lefkowitz, M Ziman, J M Schelter, M R Meyer, S Kobayashi, C Davis, H Dai, Y D He, S B Stephaniants, G Cavet, W L Walker, A West, E Coffey, D D Shoemaker, R Stoughton, A P Blanchard, S H Friend, P S Linsley
Affiliations
- PMID: 11283592
- DOI: 10.1038/86730
Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer
T R Hughes et al. Nat Biotechnol. 2001 Apr.
Abstract
We describe a flexible system for gene expression profiling using arrays of tens of thousands of oligonucleotides synthesized in situ by an ink-jet printing method employing standard phosphoramidite chemistry. We have characterized the dependence of hybridization specificity and sensitivity on parameters including oligonucleotide length, hybridization stringency, sequence identity, sample abundance, and sample preparation method. We find that 60-mer oligonucleotides reliably detect transcript ratios at one copy per cell in complex biological samples, and that ink-jet arrays are compatible with several different sample amplification and labeling techniques. Furthermore, results using only a single carefully selected oligonucleotide per gene correlate closely with those obtained using complementary DNA (cDNA) arrays. Most of the genes for which measurements differ are members of gene families that can only be distinguished by oligonucleotides. Because different oligonucleotide sequences can be specified for each array, we anticipate that ink-jet oligonucleotide array technology will be useful in a wide variety of DNA microarray applications.
Similar articles
- Three microarray platforms: an analysis of their concordance in profiling gene expression.
Petersen D, Chandramouli GV, Geoghegan J, Hilburn J, Paarlberg J, Kim CH, Munroe D, Gangi L, Han J, Puri R, Staudt L, Weinstein J, Barrett JC, Green J, Kawasaki ES. Petersen D, et al. BMC Genomics. 2005 May 5;6:63. doi: 10.1186/1471-2164-6-63. BMC Genomics. 2005. PMID: 15876355 Free PMC article. - Technological platforms for microarray gene expression profiling.
Mandruzzato S. Mandruzzato S. Adv Exp Med Biol. 2007;593:12-8. doi: 10.1007/978-0-387-39978-2_2. Adv Exp Med Biol. 2007. PMID: 17265712 Review. - A microarray platform comparison for neuroscience applications.
Parrish ML, Wei N, Duenwald S, Tokiwa GY, Wang Y, Holder D, Dai H, Zhang X, Wright C, Hodor P, Cavet G, Phillips RL, Sun BI, Fare TL. Parrish ML, et al. J Neurosci Methods. 2004 Jan 15;132(1):57-68. doi: 10.1016/j.jneumeth.2003.09.013. J Neurosci Methods. 2004. PMID: 14687675 - Increased DNA microarray hybridization specificity using sscDNA targets.
Barker CS, Griffin C, Dolganov GM, Hanspers K, Yang JY, Erle DJ. Barker CS, et al. BMC Genomics. 2005 Apr 22;6:57. doi: 10.1186/1471-2164-6-57. BMC Genomics. 2005. PMID: 15847692 Free PMC article. - Improving reliability and performance of DNA microarrays.
Sievertzon M, Nilsson P, Lundeberg J. Sievertzon M, et al. Expert Rev Mol Diagn. 2006 May;6(3):481-92. doi: 10.1586/14737159.6.3.481. Expert Rev Mol Diagn. 2006. PMID: 16706748 Review.
Cited by
- Recent progress in DNA data storage based on high-throughput DNA synthesis.
Jo S, Shin H, Joe SY, Baek D, Park C, Chun H. Jo S, et al. Biomed Eng Lett. 2024 May 3;14(5):993-1009. doi: 10.1007/s13534-024-00386-z. eCollection 2024 Sep. Biomed Eng Lett. 2024. PMID: 39220021 Review. - Solid and Suspension Microarrays for Microbial Diagnostics.
Miller S, Karaoz U, Brodie E, Dunbar S. Miller S, et al. Methods Microbiol. 2015;42:395-431. doi: 10.1016/bs.mim.2015.04.002. Epub 2015 May 14. Methods Microbiol. 2015. PMID: 38620236 Free PMC article. - Automated high-throughput DNA synthesis and assembly.
Ma Y, Zhang Z, Jia B, Yuan Y. Ma Y, et al. Heliyon. 2024 Feb 25;10(6):e26967. doi: 10.1016/j.heliyon.2024.e26967. eCollection 2024 Mar 30. Heliyon. 2024. PMID: 38500977 Free PMC article. Review. - An open-source, 3D printed inkjet DNA synthesizer.
Kim J, Kim H, Bang D. Kim J, et al. Sci Rep. 2024 Feb 14;14(1):3773. doi: 10.1038/s41598-024-53944-x. Sci Rep. 2024. PMID: 38355610 Free PMC article. - Multiplex enzymatic synthesis of DNA with single-base resolution.
Verardo D, Adelizzi B, Rodriguez-Pinzon DA, Moghaddam N, Thomée E, Loman T, Godron X, Horgan A. Verardo D, et al. Sci Adv. 2023 Jul 7;9(27):eadi0263. doi: 10.1126/sciadv.adi0263. Epub 2023 Jul 7. Sci Adv. 2023. PMID: 37418522 Free PMC article.
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Miscellaneous