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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
...-CoV , the iterative design flexibility and high density of probes makes this a highly attractive platform for gene expression analysis, comparative genomic hybridization, SNP discovery, and other genomic applications. METHODS Amplification of SARS Viral RNA A detailed protocol is published on our Web site. Briefly...
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Research: Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis
- Huan Wang,
- Pil Joong Chung,
- Jun Liu,
- In-Cheol Jang,
- Michelle J. Kean,
- Jun Xu,
- and Nam-Hai Chua
Genome Res. March 2014 24: 444-453; Published in Advance January 8, 2014, doi:10.1101/gr.165555.113
...transcription regulation and the generation of cellular complexity. Depending on their genomic origins, lncRNAs can be transcribed from intergenic or intragenic regions or from introns of protein-coding genes. We have recently reported more than 6000 intergenic lncRNAs in Arabidopsis . Here, we systematically...
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LETTER: Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)
- Yijun Ruan,
- Hong Sain Ooi,
- Siew Woh Choo,
- Kuo Ping Chiu,
- Xiao Dong Zhao,
- K.G. Srinivasan,
- Fei Yao,
- Chiou Yu Choo,
- Jun Liu,
- Pramila Ariyaratne,
- Wilson G.W. Bin,
- Vladimir A. Kuznetsov,
- Atif Shahab,
- Wing-Kin Sung,
- Guillaume Bourque,
- Nallasivam Palanisamy,
- and Chia-Lin Wei
Genome Res. June 2007 17: 828-838; doi:10.1101/gr.6018607
...units. Furthermore, the tiling array approach suffers from cross hybridization noise when it is used to detect transcripts expressed in highly homologous genomic regions, and it is incapable of uncovering unconventional transcripts, such as fusion transcripts, multi-cistronic transcripts that give rise...
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RESOURCE: An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
- Vardhman K. Rakyan,
- Thomas A. Down,
- Natalie P. Thorne,
- Paul Flicek,
- Eugene Kulesha,
- Stefan Gräf,
- Eleni M. Tomazou,
- Liselotte Bäckdahl,
- Nathan Johnson,
- Marlis Herberth,
- Kevin L. Howe,
- David K. Jackson,
- Marcos M. Miretti,
- Heike Fiegler,
- John C. Marioni,
- Ewan Birney,
- Tim J.P. Hubbard,
- Nigel P. Carter,
- Simon Tavaré,
- and Stephan Beck
Genome Res. September 2008 18: 1518-1529; Published in Advance June 24, 2008, doi:10.1101/gr.077479.108
...for DNA methylation in any organism. Using a combination of methylated DNA immunoprecipitation (MeDIP) ( Weber et al. 2005 ; Keshet et al. 2006 ), custom high-density microarrays, and novel bioinformatic analytical tools, we have generated reference human -wide DNA methylation profiles for 13 normal...
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Resource: Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
- Wen Huang,
- Andreas Massouras,
- Yutaka Inoue,
- Jason Peiffer,
- Miquel Ràmia,
- Aaron M. Tarone,
- Lavanya Turlapati,
- Thomas Zichner,
- Dianhui Zhu,
- Richard F. Lyman,
- Michael M. Magwire,
- Kerstin Blankenburg,
- Mary Anna Carbone,
- Kyle Chang,
- Lisa L. Ellis,
- Sonia Fernandez,
- Yi Han,
- Gareth Highnam,
- Carl E. Hjelmen,
- John R. Jack,
- Mehwish Javaid,
- Joy Jayaseelan,
- Divya Kalra,
- Sandy Lee,
- Lora Lewis,
- Mala Munidasa,
- Fiona Ongeri,
- Shohba Patel,
- Lora Perales,
- Agapito Perez,
- LingLing Pu,
- Stephanie M. Rollmann,
- Robert Ruth,
- Nehad Saada,
- Crystal Warner,
- Aneisa Williams,
- Yuan-Qing Wu,
- Akihiko Yamamoto,
- Yiqing Zhang,
- Yiming Zhu,
- Robert R.H. Anholt,
- Jan O. Korbel,
- David Mittelman,
- Donna M. Muzny,
- Richard A. Gibbs,
- Antonio Barbadilla,
- J. Spencer Johnston,
- Eric A. Stone,
- Stephen Richards,
- Bart Deplancke,
- and Trudy F.C. Mackay
Genome Res. July 2014 24: 1193-1208; Published in Advance April 8, 2014, doi:10.1101/gr.171546.113
..., 1458 (99.66%) and 1872 (99.79%), respectively, were concordant (Supplemental Data Files S2, S3). Second, we performed high-density tiling microarray-based validation experiments using published data for six DGRP lines Figure 1. Flowchart of the integrated genotyping procedure used to call SNP and non...
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Methods: Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays
- Georg Zeller,
- Richard M. Clark,
- Korbinian Schneeberger,
- Anja Bohlen,
- Detlef Weigel,
- and Gunnar Rätsch
Genome Res. June 2008 18: 918-929; Published in Advance March 6, 2008, doi:10.1101/gr.070169.107
...sciences ( Shendure et al. 2004 ). Toward this goal, the generation of high-density, oligonucleotide microarrays suitable for whole- variation detection was a major technological breakthrough (e.g., Chee et al. 1996 ; Patil et al. 2001 ; Hinds et al. 2005 ). Such microarrays, hereafter referred...
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LETTER: Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution
- Deyou Zheng,
- Adam Frankish,
- Robert Baertsch,
- Philipp Kapranov,
- Alexandre Reymond,
- Siew Woh Choo,
- Yontao Lu,
- France Denoeud,
- Stylianos E. Antonarakis,
- Michael Snyder,
- Yijun Ruan,
- Chia-Lin Wei,
- Thomas R. Gingeras,
- Roderic Guigó,
- Jennifer Harrow,
- and Mark B. Gerstein
Genome Res. June 2007 17: 839-851; doi:10.1101/gr.5586307
...the transcriptional activity of the ENCODE pseudogenes. We performed systematic series of pseudogene-specific RACE analyses. These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one...
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Methods: Identification of higher-order functional domains in the human ENCODE regions
- Robert E. Thurman,
- Nathan Day,
- William S. Noble,
- and John A. Stamatoyannopoulos
Genome Res. June 2007 17: 917-927; doi:10.1101/gr.6081407
...a high density of evolutionarily conserved noncoding sequences; indeed, this entire domain displays conserved synteny with the chicken OLIG1 and OLIG2 locus. This region was readily delineated by the HMM and assigned to state 0. The OLIG1/2 domain replicates late during the S phase, has low levels of H3...
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Research: Extensive relationship between antisense transcription and alternative splicing in the human genome
- A. Sorana Morrissy,
- Malachi Griffith,
- and Marco A. Marra
Genome Res. August 2011 21: 1203-1212; Published in Advance June 30, 2011, doi:10.1101/gr.113431.110
...exons or introns. (B) A novel SAS sense gene. Since the structure of the transcribed antisense RNA is unknown, an antisense construct (dashed-line box) spans the genomic coordinates of the sense gene and approximates antisense expression. All antisense probesets encompassed by that region are used...
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ARTICLE: Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions
- France Denoeud,
- Philipp Kapranov,
- Catherine Ucla,
- Adam Frankish,
- Robert Castelo,
- Jorg Drenkow,
- Julien Lagarde,
- Tyler Alioto,
- Caroline Manzano,
- Jacqueline Chrast,
- Sujit Dike,
- Carine Wyss,
- Charlotte N. Henrichsen,
- Nancy Holroyd,
- Mark C. Dickson,
- Ruth Taylor,
- Zahra Hance,
- Sylvain Foissac,
- Richard M. Myers,
- Jane Rogers,
- Tim Hubbard,
- Jennifer Harrow,
- Roderic Guigó,
- Thomas R. Gingeras,
- Stylianos E. Antonarakis,
- and Alexandre Reymond
Genome Res. June 2007 17: 746-759; doi:10.1101/gr.5660607
...presents systematic empirical annotation of transcript products from 399 annotated protein-coding loci across the 1% of the human genome targeted by the Encyclopedia of DNA elements (ENCODE) pilot project using a combination of 5′ rapid amplification of cDNA ends (RACE) and high-density resolution tiling...
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