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Method: Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase
- Maria Grazia Mendoza-Ferri,
- Gwendoline Lozachmeur,
- Maximilien Duvina,
- Laetitia Perret,
- Didier Merciris,
- Anne Gigout,
- and Marco Antonio Mendoza-Parra
Genome Res. July 2025 35: 1633-1645; Published in Advance May 13, 2025, doi:10.1101/gr.280305.124
...) a modified version of double-barcoded DNA arrays for capturing cleaved chromatin with the CUT&Tag chemistry (Kaya-Okur et al. 2019); (2) a modified bioinformatics pipeline allowing us to demultiplex spatial read-counts retrieved around gene promoter regions and their visualization within our tool MULTILAYER...
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METHODS: Gene Expression Analysis Using Oligonucleotide Arrays Produced by Maskless Photolithography
- Emile F. Nuwaysir,
- Wei Huang,
- Thomas J. Albert,
- Jaz Singh,
- Kate Nuwaysir,
- Alan Pitas,
- Todd Richmond,
- Tom Gorski,
- James P. Berg,
- Jeff Ballin,
- Mark McCormick,
- Jason Norton,
- Tim Pollock,
- Terry Sumwalt,
- Lawrence Butcher,
- DeAnn Porter,
- Michael Molla,
- Christine Hall,
- Fred Blattner,
- Michael R. Sussman,
- Rodney L. Wallace,
- Franco Cerrina,
- and Roland D. Green
Genome Res. November 1, 2002 12: 1749-1755; doi:10.1101/gr.362402
...Gene Expression Analysis Using Oligonucleotide Arrays Produced by Maskless Photolithography Emile F. Nuwaysir 1 , Wei Huang 2 , Thomas J. Albert 1 , Jaz Singh 1 , Kate Nuwaysir 1 , Alan Pitas 1 , Todd Richmond 1 , Tom...
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METHODS: Arrays of Arrays for High-Throughput Gene Expression Profiling
- Patrick P. Zarrinkar,
- James K. Mainquist,
- Matthew Zamora,
- David Stern,
- John B. Welsh,
- Lisa M. Sapinoso,
- Garret M. Hampton,
- and David J. Lockhart
Genome Res. July 1, 2001 11: 1256-1261; Published in Advance June 12, 2001, doi:10.1101/gr.174801
...format using glass wafers that contain 49 individual high-density oligonucleotide arrays. This arrays of arrays concept is generalizable and can be adapted readily to other types of arrays, including spotted cDNA microarrays. It is also scalable for use with hundreds and even thousands of smaller arrays...
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Research: Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions
- Kyuha Choi,
- Xiaohui Zhao,
- Andrew J. Tock,
- Christophe Lambing,
- Charles J. Underwood,
- Thomas J. Hardcastle,
- Heïdi Serra,
- Juhyun Kim,
- Hyun Seob Cho,
- Jaeil Kim,
- Piotr A. Ziolkowski,
- Nataliya E. Yelina,
- Ildoo Hwang,
- Robert A. Martienssen,
- and Ian R. Henderson
Genome Res. April 2018 28: 532-546; Published in Advance March 12, 2018, doi:10.1101/gr.225599.117
..., with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant , we purified and sequenced Arabidopsis thaliana SPO11-1-oligonucleotides. SPO11-1-oligos are elevated in gene promoters, terminators, and introns, which is driven by AT-sequence richness that excludes nucleosomes...
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Method: High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow
- Xue Dong,
- Mengzhu Hu,
- Xiaonan Cui,
- Wenjian Zhou,
- Jingtao Cai,
- Guangyao Mao,
- and Weiyang Shi
Genome Res. September 2025 35: 2052-2063; Published in Advance August 5, 2025, doi:10.1101/gr.279906.124
...photocleavable oligonucleotides and ligation adapters to construct transcriptional profiles of specific regions of interest (ROIs) designated via microscopically controlled photo-illumination. In frozen mouse embryos, PCL-seq generates spatially aligned gene expression matrices and produces high-quality data...
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Method: Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes
- Alexandre Lomsadze,
- Karl Gemayel,
- Shiyuyun Tang,
- and Mark Borodovsky
Genome Res. July 2018 28: 1079-1089; Published in Advance May 17, 2018, doi:10.1101/gr.230615.117
...initio algorithm that uses a model derived by self-training for finding species-specific (native) genes, along with an array of precomputed “heuristic” models designed to identify harder-to-detect genes (likely horizontally transferred). Importantly, we designed GeneMarkS-2 to identify several types...
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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: Gene Expression Analysis with Universal n-mer Arrays
- R. Michael van Dam and
- Stephen R. Quake
Genome Res. January 1, 2002 12: 145-152; doi:10.1101/gr.198901
...to facilitate sensitivity comparisons. Therefore, we address the question of whether one can extract useful gene expression information from combinatorial arrays of short (i.e., n ⩽ 16) oligonucleotides. We first develop an analytical model to predict, for a given value of n and a particular , the average...
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METHODS: Oligonucleotide Arrays for High-Throughput SNPs Detection in the MHC Class I Genes: HLA-B as a Model System
- Zhen Guo,
- Mark S. Gatterman,
- Lee Hood,
- John A. Hansen,
- and Effie W. Petersdorf
Genome Res. March 1, 2002 12: 447-457; Published in Advance February 15, 2002, doi:10.1101/gr.206402
...Oligonucleotide Arrays for High-Throughput SNPs Detection in the MHC Class I Genes: HLA-B as a Model System Zhen Guo 1 , Mark S. Gatterman 3 , Lee Hood 1 , John A. Hansen 2 , 3 , and Effie W. Petersdorf 2 , 3 , 4 1...
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Research: Evidence for the fixation of gene duplications by positive selection in Drosophila
- Margarida Cardoso-Moreira,
- J. Roman Arguello,
- Srikanth Gottipati,
- L.G. Harshman,
- Jennifer K. Grenier,
- and Andrew G. Clark
Genome Res. June 2016 26: 787-798; Published in Advance April 12, 2016, doi:10.1101/gr.199323.115
.... We generated gene expression profiles for whole adult male flies for 83 of the 84 GDL using microarrays (Methods). Out of the 491 genes completely duplicated in our data set, we have expression profiles for 288 (59%). The remaining genes either were not represented on the arrays or did not have...

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