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RESOURCE: EagleView: A genome assembly viewer for next-generation sequencing technologies
- Weichun Huang and
- Gabor Marth
Genome Res. September 2008 18: 1538-1543; Published in Advance June 11, 2008, doi:10.1101/gr.076067.108
....J. , Ooi, H.S. , Lee, Y.L. , Chiu, K.P. , Fullwood, M.J. , Srinivasan, K.G. , Perbost, C. , Du, L. , Sung, W.K. , et al. ( 2006 ) Multiplex sequencing of paired-end ditags (MS-PET): A strategy for the ultra-high-throughput analysis of transcriptomes and s . Nucleic Acids Res. 34 : e84 , doi: 10.1093/nar...
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Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
- Christine R. Keenan,
- Hannah D. Coughlan,
- Nadia Iannarella,
- Andres Tapia del Fierro,
- Andrew Keniry,
- Timothy M. Johanson,
- Wing Fuk Chan,
- Alexandra L. Garnham,
- Lachlan W. Whitehead,
- Marnie E. Blewitt,
- Gordon K. Smyth,
- and Rhys S. Allan
Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
...(D5205), and sequencing libraries were prepared using an Illumina TruSeq DNA sample prep kit using half volumes of all reagents. Libraries were sequenced on an Illumina NextSeq 500 to produce 81-base-length paired-end reads. Independent biological duplicates were prepared for each condition...
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Research: Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes
- Axel M. Hillmer,
- Fei Yao,
- Koichiro Inaki,
- Wah Heng Lee,
- Pramila N. Ariyaratne,
- Audrey S.M. Teo,
- Xing Yi Woo,
- Zhenshui Zhang,
- Hao Zhao,
- Leena Ukil,
- Jieqi P. Chen,
- Feng Zhu,
- Jimmy B.Y. So,
- Manuel Salto-Tellez,
- Wan Ting Poh,
- Kelson F.B. Zawack,
- Niranjan Nagarajan,
- Song Gao,
- Guoliang Li,
- Vikrant Kumar,
- Hui Ping J. Lim,
- Yee Yen Sia,
- Chee Seng Chan,
- See Ting Leong,
- Say Chuan Neo,
- Poh Sum D. Choi,
- Hervé Thoreau,
- Patrick B.O. Tan,
- Atif Shahab,
- Xiaoan Ruan,
- Jonas Bergh,
- Per Hall,
- Valère Cacheux-Rataboul,
- Chia-Lin Wei,
- Khay Guan Yeoh,
- Wing-Kin Sung,
- Guillaume Bourque,
- Edison T. Liu,
- and Yijun Ruan
Genome Res. May 2011 21: 665-675; Published in Advance April 5, 2011, doi:10.1101/gr.113555.110
...contributed equally to this work. Abstract Somatic genome rearrangements are thought to play important roles in cancer development. We optimized a long-span paired-end-tag (PET) sequencing approach using 10-Kb genomic DNA inserts to study human genome structural variations (SVs). The use of a 10-Kb...
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Method: High-confidence coding and noncoding transcriptome maps
- Bo-Hyun You,
- Sang-Ho Yoon,
- and Jin-Wu Nam
Genome Res. June 2017 27: 1050-1062; Published in Advance April 10, 2017, doi:10.1101/gr.214288.116
...provide biologically relevant isoforms directly. One approach is to integrate paired-end ditag (PET) data that contain both 5′ and 3′ end sequence tags of transcripts (Djebali et al. 2012), and an alternative is to sequence full-length RNAs using third-generation sequencing methods such as Iso-seq (Sharon...
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Research: Diploid genome architecture revealed by multi-omic data of hybrid mice
- Zhijun Han,
- Kairong Cui,
- Katarzyna Placek,
- Ni Hong,
- Chengqi Lin,
- Wei Chen,
- Keji Zhao,
- and Wenfei Jin
Genome Res. August 2020 30: 1097-1106; Published in Advance August 5, 2020, doi:10.1101/gr.257568.119
...inherited from B6 and Cast were called Fb6 and Fcast, respectively. The length distribution of paired-end tags (PETs) in Fb6 and Fcast are similar to that in B6 or Cast Hi-C libraries (Supplemental Fig. S1; Supplemental Table S2).View larger version: In this window In a new window Figure 1. Homologous...
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Perspective: Epigenomics and the structure of the living genome
- Nir Friedman and
- Oliver J. Rando
Genome Res. October 2015 25: 1482-1490; doi:10.1101/gr.190165.115
...measurement to characterize chromatin state and DNA modifications in eukaryotes. Such -wide measurements involve comprehensive analysis of nucleic acid populations, whether DNA or RNA, using DNA microarrays or so-called “deep sequencing” methods. The key differences between most epigenomic analyses thus...
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Research: Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq
- Tingting Lu,
- Guojun Lu,
- Danlin Fan,
- Chuanrang Zhu,
- Wei Li,
- Qiang Zhao,
- Qi Feng,
- Yan Zhao,
- Yunli Guo,
- Wenjun Li,
- Xuehui Huang,
- and Bin Han
Genome Res. September 2010 20: 1238-1249; Published in Advance July 13, 2010, doi:10.1101/gr.106120.110
...CL, Liu ET, Ruan Y. 2009. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and analyses. Genome Res 19: 521–532. Furutani I, Sukegawa S, Kyozuka J. 2006. Genome-wide analysis of spatial and temporal gene expression in rice panicle development. Plant J 46: 503–511. Lu et al...
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Methods: Scanning the human genome at kilobase resolution
- Jun Chen,
- Yeong C. Kim,
- Yong-Chul Jung,
- Zhenyu Xuan,
- Geoff Dworkin,
- Yanming Zhang,
- Michael Q. Zhang,
- and San Ming Wang
Genome Res. May 2008 18: 751-762; Published in Advance February 21, 2008, doi:10.1101/gr.068304.107
...sequencing used in BAC and fosmid sequencing for structural analysis ( International Human Genome Study Consortium 2004 ; Volik et al. 2006 ), ditag sequencing used in ChIP-PET for detecting protein-bound DNA fragments ( Wei et al. 2006 ; Dunn et al. 2007 ), 454 sequencing technology for massive sequencing...
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Research: Systems consequences of amplicon formation in human breast cancer
- Koichiro Inaki,
- Francesca Menghi,
- Xing Yi Woo,
- Joel P. Wagner,
- Pierre-Étienne Jacques,
- Yi Fang Lee,
- Phung Trang Shreckengast,
- Wendy WeiJia Soon,
- Ankit Malhotra,
- Audrey S.M. Teo,
- Axel M. Hillmer,
- Alexis Jiaying Khng,
- Xiaoan Ruan,
- Swee Hoe Ong,
- Denis Bertrand,
- Niranjan Nagarajan,
- R. Krishna Murthy Karuturi,
- Alfredo Hidalgo Miranda,
- and Edison T. Liu
Genome Res. October 2014 24: 1559-1571; Published in Advance September 3, 2014, doi:10.1101/gr.164871.113
...an important role in determining the transcriptional landscape of human breast cancers. To assess the nature of these structural variations, we analyzed eight breast tumor samples with a focus on regions of gene amplification using mate-pair sequencing of long-insert genomic DNA with matched transcriptome...
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Research: Binding of nuclear factor κB to noncanonical consensus sites reveals its multimodal role during the early inflammatory response
- Petros Kolovos,
- Theodore Georgomanolis,
- Anna Koeferle,
- Joshua D. Larkin,
- Lilija Brant,
- Miloš Nikolicć,
- Eduardo G. Gusmao,
- Anne Zirkel,
- Tobias A. Knoch,
- Wilfred F. van Ijcken,
- Peter R. Cook,
- Ivan G. Costa,
- Frank G. Grosveld,
- and Argyris Papantonis
Genome Res. November 2016 26: 1478-1489; Published in Advance September 15, 2016, doi:10.1101/gr.210005.116
...conformation capture and genome editing uncovers how NF-κΒ that has just entered the nucleus exploits pre-existing chromatin looping to exert its multimodal role. This work highlights the involvement of topology in cis -regulatory element function during acute transcriptional responses, where primary DNA...

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