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Methods: Decoding Randomly Ordered DNA Arrays
- Kevin L. Gunderson,
- Semyon Kruglyak,
- Michael S. Graige,
- Francisco Garcia,
- Bahram G. Kermani,
- Chanfeng Zhao,
- Diping Che,
- Todd Dickinson,
- Eliza Wickham,
- Jim Bierle,
- Dennis Doucet,
- Monika Milewski,
- Robert Yang,
- Chris Siegmund,
- Juergen Haas,
- Lixin Zhou,
- Arnold Oliphant,
- Jian-Bing Fan,
- Steven Barnard,
- and Mark S. Chee
Genome Res. May 2004 14: 870-877; Published in Advance April 12, 2004, doi:10.1101/gr.2255804
....J. and Winzeler, E.A. 2000 . Genomics, gene expression and DNA arrays. Nature 405 : 827 -836. ↵ Lockhart, D.J., Dong, H., Byrne, M.C., Follettie, M.T., Gallo, M.V., Chee, M.S., Mittmann, M., Wang, C., Kobayashi, M., Horton, H., et al. 1996 . Expression monitoring by hybridization to high-density oligonucleotide...
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Methods: Design optimization methods for genomic DNA tiling arrays
- Paul Bertone,
- Valery Trifonov,
- Joel S. Rozowsky,
- Falk Schubert,
- Olof Emanuelsson,
- John Karro,
- Ming-Yang Kao,
- Michael Snyder,
- and Mark Gerstein
Genome Res. February 2006 16: 271-281; Published in Advance December 19, 2005, doi:10.1101/gr.4452906
...within annotated exons so that they will hybridize to the mature spliced transcript ( Wang and Seed 2003 ), and are typically positioned proximal to the 3′ end of the gene to increase the likelihood of detecting partially reverse-transcribed messages. Designing oligonucleotide tiling arrays constitutes...
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Methods: Microfabricated Fountain Pens for High-Density DNA Arrays
- Matthew O. Reese,
- R. Michae van Dam,
- Axel Scherer,
- and Stephen R. Quake
Genome Res. October 2003 13: 2348-2352; Published in Advance January 1, 2003, doi:10.1101/gr.623903
...al. 2002 . Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res. 12 : 1749 -1755. ↵ Okamoto, T., Suzuki, T., and Yamamoto, N. 2000 . Microarray fabrication with covalent attachment of DNA using bubble jet technology. Nat. Biotech. 18 : 438 -441...
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Methods: Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays
- Christopher W. Wong,
- Thomas J. Albert,
- Vinsensius B. Vega,
- Jason E. Norton,
- David J. Cutler,
- Todd A. Richmond,
- Lawrence W. Stanton,
- Edison T. Liu,
- and Lance D. Miller
Genome Res. March 2004 14: 398-405; doi:10.1101/gr.2141004
...produced by maskless photolithography. Genome Res. 12 : 1749 –1755. ↵ Pease, A.C., Solas, D., Sullivan, E.J., Cronin, M.T., Holmes, C.P., and Fodor, S.P. 1994 . Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl. Acad. Sci. 91 : 5022 –5026. ↵ Richterich, P. 1998 . Estimation...
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Methods: A Versatile Assay for High-Throughput Gene Expression Profiling on Universal Array Matrices
- Jian-Bing Fan,
- Joanne M. Yeakley,
- Marina Bibikova,
- Eugene Chudin,
- Eliza Wickham,
- Jing Chen,
- Dennis Doucet,
- Philippe Rigault,
- Baohong Zhang,
- Richard Shen,
- Celeste McBride,
- Hai-Ri Li,
- Xiang-Dong Fu,
- Arnold Oliphant,
- David L. Barker,
- and Mark S. Chee
Genome Res. May 2004 14: 878-885; doi:10.1101/gr.2167504
...gene, for 96 samples in parallel. The c D NA-mediated a nnealing, s election, extension and l igation (DASL) assay targets specific transcripts, using oligonucleotides containing unique address sequences that can hybridize to universal arrays. Cell-specific gene expression profiles were obtained...
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Methods: Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements
- Josée Dostie,
- Todd A. Richmond,
- Ramy A. Arnaout,
- Rebecca R. Selzer,
- William L. Lee,
- Tracey A. Honan,
- Eric D. Rubio,
- Anton Krumm,
- Justin Lamb,
- Chad Nusbaum,
- Roland D. Green,
- and Job Dekker
Genome Res. October 2006 16: 1299-1309; Published in Advance September 5, 2006, doi:10.1101/gr.5571506
..., Tracey A. Honan 3 , Eric D. Rubio 6 , Anton Krumm 6 , Justin Lamb 3 , Chad Nusbaum 3 , Roland D. Green 2 , and Job Dekker 1 , 7 1Program in Gene Function and Expression and Department of Biochemistry and Molecular...
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Methods: Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies
- Ghia M. Euskirchen,
- Joel S. Rozowsky,
- Chia-Lin Wei,
- Wah Heng Lee,
- Zhengdong D. Zhang,
- Stephen Hartman,
- Olof Emanuelsson,
- Viktor Stolc,
- Sherman Weissman,
- Mark B. Gerstein,
- Yijun Ruan,
- and Michael Snyder
Genome Res. June 2007 17: 898-909; doi:10.1101/gr.5583007
...regions using ChIP-based methods. Results Exploring ChIP-chip performance: Longer oligonucleotides yield better signals In the first phase of these studies, we investigated ChIP-chip performance on oligonucleotide arrays synthesized by maskless photolithography ( Nuwaysir et al. 2002 ). For these studies...
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Methods: Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
- Olof Emanuelsson,
- Ugrappa Nagalakshmi,
- Deyou Zheng,
- Joel S. Rozowsky,
- Alexander E. Urban,
- Jiang Du,
- Zheng Lian,
- Viktor Stolc,
- Sherman Weissman,
- Michael Snyder,
- and Mark B. Gerstein
Genome Res. June 2007 17: 886-897; Published in Advance November 21, 2006, doi:10.1101/gr.5014606
...of the nonrepetitive sequence of the ENCODE regions end-to-end (allowing some positional shifts to reduce self-complementarity) was prepared using maskless photolithography, MAS (maskless array synthesis). The MAS arrays cover both strands of the ENCODE regions ENm001–ENm011 (11.6 Mb). An Affymetrix ENCODE array...
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Resource: Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment
- Martin Ebeling,
- Erich Küng,
- Angela See,
- Clemens Broger,
- Guido Steiner,
- Marco Berrera,
- Tobias Heckel,
- Leonardo Iniguez,
- Thomas Albert,
- Roland Schmucki,
- Hermann Biller,
- Thomas Singer,
- and Ulrich Certa
Genome Res. October 2011 21: 1746-1756; Published in Advance August 23, 2011, doi:10.1101/gr.123117.111
...). Expression profiling in M. fascicularis liver samples To profile gene expression, we used the protein-coding transcripts predicted from the draft to produce aM. fascicularis-specific microarray bymaskless photolithography (Singh-Gasson et al. 1999). We created a multiplex format with 12 arrays each...
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Methods: Comparative isoschizomer profiling of cytosine methylation: The HELP assay
- Batbayar Khulan,
- Reid F. Thompson,
- Kenny Ye,
- Melissa J. Fazzari,
- Masako Suzuki,
- Edyta Stasiek,
- Maria E. Figueroa,
- Jacob L. Glass,
- Quan Chen,
- Cristina Montagna,
- Eli Hatchwell,
- Rebecca R. Selzer,
- Todd A. Richmond,
- Roland D. Green,
- Ari Melnick,
- and John M. Greally
Genome Res. August 2006 16: 1046-1055; Published in Advance June 29, 2006, doi:10.1101/gr.5273806
...distribution of subsequent oligos along the length of the fragment. A microarray of ∼13,500 oligonucleotides was used to represent the ∼6.2 Mb of the mouse in this study. These were printed using maskless array synthesis ( Nuwaysir et al. 2002 ) in the NimbleScreen 12 format (NimbleGen Systems Inc). The LM...

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