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Method: Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing
- Hideya Kawaji,
- Marina Lizio,
- Masayoshi Itoh,
- Mutsumi Kanamori-Katayama,
- Ai Kaiho,
- Hiromi Nishiyori-Sueki,
- Jay W. Shin,
- Miki Kojima-Ishiyama,
- Mitsuoki Kawano,
- Mitsuyoshi Murata,
- Noriko Ninomiya-Fukuda,
- Sachi Ishikawa-Kato,
- Sayaka Nagao-Sato,
- Shohei Noma,
- Yoshihide Hayashizaki,
- Alistair R.R. Forrest,
- Piero Carninci,
- and The FANTOM Consortium
Genome Res. April 2014 24: 708-717; Published in Advance March 27, 2014, doi:10.1101/gr.156232.113
...DNA sequencing of a viral . Science 320: 106–109. Itoh M, Kojima M, Nagao-Sato S, Saijo E, Lassmann T, Kanamori-Katayama M, Kaiho A, Lizio M, Kawaji H, Carninci P, et al. 2012. Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer. PLoS ONE 7: e...
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Resource: Comparative validation of the D. melanogaster modENCODE transcriptome annotation
- Zhen-Xia Chen,
- David Sturgill,
- Jiaxin Qu,
- Huaiyang Jiang,
- Soo Park,
- Nathan Boley,
- Ana Maria Suzuki,
- Anthony R. Fletcher,
- David C. Plachetzki,
- Peter C. FitzGerald,
- Carlo G. Artieri,
- Joel Atallah,
- Olga Barmina,
- James B. Brown,
- Kerstin P. Blankenburg,
- Emily Clough,
- Abhijit Dasgupta,
- Sai Gubbala,
- Yi Han,
- Joy C. Jayaseelan,
- Divya Kalra,
- Yoo-Ah Kim,
- Christie L. Kovar,
- Sandra L. Lee,
- Mingmei Li,
- James D. Malley,
- John H. Malone,
- Tittu Mathew,
- Nicolas R. Mattiuzzo,
- Mala Munidasa,
- Donna M. Muzny,
- Fiona Ongeri,
- Lora Perales,
- Teresa M. Przytycka,
- Ling-Ling Pu,
- Garrett Robinson,
- Rebecca L. Thornton,
- Nehad Saada,
- Steven E. Scherer,
- Harold E. Smith,
- Charles Vinson,
- Crystal B. Warner,
- Kim C. Worley,
- Yuan-Qing Wu,
- Xiaoyan Zou,
- Peter Cherbas,
- Manolis Kellis,
- Michael B. Eisen,
- Fabio Piano,
- Karin Kionte,
- David H. Fitch,
- Paul W. Sternberg,
- Asher D. Cutter,
- Michael O. Duff,
- Roger A. Hoskins,
- Brenton R. Graveley,
- Richard A. Gibbs,
- Peter J. Bickel,
- Artyom Kopp,
- Piero Carninci,
- Susan E. Celniker,
- Brian Oliver,
- and Stephen Richards
Genome Res. July 2014 24: 1209-1223; Published in Advance July 1, 2014, doi:10.1101/gr.159384.113
...junction spanning reads in those RNA-seq profiles revealed a much richer set of processed transcripts. Additional RNA-seq data sets, along with cap analysis of gene expression (CAGE-seq) and full-insert cDNA sequencing, have been used to generate the modENCODE D. melanogaster transcriptome annotation...
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Research: Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome
- Cai Li,
- Boris Lenhard,
- and Nicholas M. Luscombe
Genome Res. May 2018 28: 676-688; Published in Advance April 4, 2018, doi:10.1101/gr.231449.117
...TSSs and their subsequent evolution.ResultsIdentifying evolutionarily young TSSs in the human Using the Cap Analysis of Gene Expression (CAGE) sequencing technology, the FANTOM5 project (The FANTOM Consortium 2014) generated the most comprehensive TSS annotation for the human to date, covering major...
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Research: Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing
- Joshua A. Arribere and
- Wendy V. Gilbert
Genome Res. June 2013 23: 977-987; Published in Advance April 11, 2013, doi:10.1101/gr.150342.112
...-seq), a technique combining enzymatic capture of m7G-capped mRNA 5′ ends with high-throughput sequencing. TL-seq identified mRNA start sites for the majority of yeast genes and revealed many examples of intragenic TL heterogeneity. Surprisingly, TL-seq identified transcription initiation sites within 6% of protein...
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Methods: Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding
- Kevin Judd McKernan,
- Heather E. Peckham,
- Gina L. Costa,
- Stephen F. McLaughlin,
- Yutao Fu,
- Eric F. Tsung,
- Christopher R. Clouser,
- Cisyla Duncan,
- Jeffrey K. Ichikawa,
- Clarence C. Lee,
- Zheng Zhang,
- Swati S. Ranade,
- Eileen T. Dimalanta,
- Fiona C. Hyland,
- Tanya D. Sokolsky,
- Lei Zhang,
- Andrew Sheridan,
- Haoning Fu,
- Cynthia L. Hendrickson,
- Bin Li,
- Lev Kotler,
- Jeremy R. Stuart,
- Joel A. Malek,
- Jonathan M. Manning,
- Alena A. Antipova,
- Damon S. Perez,
- Michael P. Moore,
- Kathleen C. Hayashibara,
- Michael R. Lyons,
- Robert E. Beaudoin,
- Brittany E. Coleman,
- Michael W. Laptewicz,
- Adam E. Sannicandro,
- Michael D. Rhodes,
- Rajesh K. Gottimukkala,
- Shan Yang,
- Vineet Bafna,
- Ali Bashir,
- Andrew MacBride,
- Can Alkan,
- Jeffrey M. Kidd,
- Evan E. Eichler,
- Martin G. Reese,
- Francisco M. De La Vega,
- and Alan P. Blanchard
Genome Res. September 2009 19: 1527-1541; Published in Advance June 22, 2009, doi:10.1101/gr.091868.109
...- or ligase-based) and two detection categories (‘‘asynchronous single molecule’’ and ‘‘synchronous multi-molecule,’’ often referred to as ‘‘ensemble’’ readouts). SOLiD (sequencing by oligo ligation detection) sequencing, the method used here, is a DNA ligase-based synchronous ensemble detection method...
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