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RESOURCE: A Whole-Genome Mouse BAC Microarray With 1-Mb Resolution for Analysis of DNA Copy Number Changes by Array Comparative Genomic Hybridization
- Yeun-Jun Chung,
- Jos Jonkers,
- Hannah Kitson,
- Heike Fiegler,
- Sean Humphray,
- Carol Scott,
- Sarah Hunt,
- Yuejin Yu,
- Ichiko Nishijima,
- Arno Velds,
- Henne Holstege,
- Nigel Carter,
- and Allan Bradley
Genome Res. January 2004 14: 188-196; doi:10.1101/gr.1878804
...microarray. As a first step, we performed sex-matched normal versus normal hybridizations to determine the hybridization variation in normal genomic DNA ( Fig. 2A ). We performed all CGH experiments in fluorochrome-reversed pairs of two-color hybridizations. For all data points, we obtained quadruple...
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LETTER: Representational Oligonucleotide Microarray Analysis: A High-Resolution Method to Detect Genome Copy Number Variation
- Robert Lucito,
- John Healy,
- Joan Alexander,
- Andrew Reiner,
- Diane Esposito,
- Maoyen Chi,
- Linda Rodgers,
- Amy Brady,
- Jonathan Sebat,
- Jennifer Troge,
- Joseph A. West,
- Seth Rostan,
- Ken C.Q. Nguyen,
- Scott Powers,
- Kenneth Q. Ye,
- Adam Olshen,
- Ennapadam Venkatraman,
- Larry Norton,
- and Michael Wigler
Genome Res. October 2003 13: 2291-2305; Published in Advance January 1, 2003, doi:10.1101/gr.1349003
...'t Veer et al. 2002 ), and three groups, including ours, have adapted microarrays to detect genomic deletions and amplifications in tumors. Pinkel et al. ( 1998 ) have used arrays of BAC DNAs as hybridization probes; Pollack et al. ( 1999 ) have used cDNA fragments as probes; and in our first...
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METHODS: Methylation-Specific Oligonucleotide Microarray: A New Potential for High-Throughput Methylation Analysis
- Raad S. Gitan,
- Huidong Shi,
- Chuan-Mu Chen,
- Pearlly S. Yan,
- and Tim Hui-Ming Huang
Genome Res. January 1, 2002 12: 158-164; Published in Advance December 14, 2001, doi:10.1101/gr.202801
...of methylation is determined by two-color fluorescence analysis. This microarray-based analysis of DNA methylation is expected to provide new tools for research in this field. Until recently, most methylation assays have been limited to analyzing CpG islands of a few known genes and are restricted in throughput...
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RESOURCE: Argus—A New Database System for Web-Based Analysis of Multiple Microarray Data Sets
- Jason Comander,
- Griffin M. Weber,
- Michael A. Gimbrone, Jr.,
- and Guillermo García-Cardeña
Genome Res. September 1, 2001 11: 1603-1610; doi:10.1101/gr.186601
...” and “Cells plus drug”.) Microarrays with labeled cDNA from each condition were quantified using Pathways 3.0 (Research Genetics) and imported into Argus for creation of the analysis Web site (see Methods). A set of three separate nylon arrays was probed for each condition. Figure 2 A displays a query...
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Research: Pluripotent stem cells escape from senescence-associated DNA methylation changes
- Carmen M. Koch,
- Kristina Reck,
- Kaifeng Shao,
- Qiong Lin,
- Sylvia Joussen,
- Patrick Ziegler,
- Gudrun Walenda,
- Wolf Drescher,
- Bertram Opalka,
- Tobias May,
- Tim Brümmendorf,
- Martin Zenke,
- Tomo Šarić,
- and Wolfgang Wagner
Genome Res. February 2013 23: 248-259; Published in Advance October 18, 2012, doi:10.1101/gr.141945.112
...was isolated from 106 cells using the QIAGEN DNA Blood Midi-Kit. Bisulfite-converted DNA (EZ DNA Methylation Kit; Zymo) was prepared and then analyzed using the InfiniumHumanMethylation450 BeadChip (Illumina) according to the manufacturer’s instructions. DNAm is provided as beta-values for each of the 485...
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LETTER: Microarray Expression Profiling Identifies Genes with Altered Expression in HDL-Deficient Mice
- Matthew J. Callow,
- Sandrine Dudoit,
- Elaine L. Gong,
- Terence P. Speed,
- and Edward M. Rubin
Genome Res. December 1, 2000 10: 2022-2029; doi:10.1101/gr.147200
.... 93 : 10614 – 10619 . ↵ Shaffer J.P. ( 1995 ) Multiple hypothesis testing. Annu. Rev. Psychol. 46 : 561 – 584 . ↵ Shalon D. , Smith S.J. , Brown P.O. ( 1996 ) A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6 : 639 – 645...
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Methods: A genotyping system capable of simultaneously analyzing >1000 single nucleotide polymorphisms in a haploid genome
- Hui-Yun Wang,
- Minjie Luo,
- Irina V. Tereshchenko,
- Danielle M. Frikker,
- Xiangfeng Cui,
- James Y. Li,
- Guohong Hu,
- Yi Chu,
- Marco A. Azaro,
- Yong Lin,
- Li Shen,
- Qifeng Yang,
- Manousos E. Kambouris,
- Richeng Gao,
- Weichung Shih,
- and Honghua Li
Genome Res. February 2005 15: 276-283; doi:10.1101/gr.2885205
...NTP) conjugated to a fluorescent chromophore (Cy3 or Cy5). In this way, probes hybridizing to different allelic sequences were labeled with different fluorescent colors ( Fig. 1F ). After labeling, everything but the labeled probes was washed off, and the microarray was ready for scanning. Because DNA sequences...
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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
...of a large collection of DNA-linked objects through the use of hybridization, and have applied it to the manufacture of randomly assembled arrays of beads in wells. Once the algorithm has been used to determine the identity of each bead, the microarray can be used in a wide variety of applications, including...
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Resource: Mapping DNA structural variation in dogs
- Wei-Kang Chen,
- Joshua D. Swartz,
- Laura J. Rush,
- and Carlos E. Alvarez
Genome Res. March 2009 19: 500-509; Published in Advance November 17, 2008, doi:10.1101/gr.083741.108
...by hybridization to the NimbleGen Systems Inc. canFam2 WG CGH oligo array platform ( http://www.nimblegen.com ), designed from the NCBI canine build of May 2005 ( Lindblad-Toh et al. 2005 ). The array has 385,000 probes on a single slide, resulting in a median probe spacing of 4675 bp. Confident DNA CNV detection...
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Methods: Highly multiplexed molecular inversion probe genotyping: Over 10,000 targeted SNPs genotyped in a single tube assay
- Paul Hardenbol,
- Fuli Yu,
- John Belmont,
- Jennifer MacKenzie,
- Carsten Bruckner,
- Tiffany Brundage,
- Andrew Boudreau,
- Steve Chow,
- Jim Eberle,
- Ayca Erbilgin,
- Mat Falkowski,
- Ron Fitzgerald,
- Sy Ghose,
- Oleg Iartchouk,
- Maneesh Jain,
- George Karlin-Neumann,
- Xiuhua Lu,
- Xin Miao,
- Bridget Moore,
- Martin Moorhead,
- Eugeni Namsaraev,
- Shiran Pasternak,
- Eunice Prakash,
- Karen Tran,
- Zhiyong Wang,
- Hywel B. Jones,
- Ronald W. Davis,
- Thomas D. Willis,
- and Richard A. Gibbs
Genome Res. February 2005 15: 269-275; doi:10.1101/gr.3185605
...( www.hapmap.org ). Each of the four MIP reactions was mixed with 500 ng of genomic DNA. Two-color assay execution After amplification and tag cleavage, the products were hybridized to two GeneChip Tag Arrays: TrueTag 5k or TrueTag 10k (Affymetrix) and stained using a two-color staining kit from Par...

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