Searching journal content for articles similar to Bono et al. 13 (6b): 1318.

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Method: Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq
- Robert A. Policastro,
- R. Taylor Raborn,
- Volker P. Brendel,
- and Gabriel E. Zentner
Genome Res. June 2020 30: 910-923; Published in Advance July 6, 2020, doi:10.1101/gr.261545.120
...). Notably, MAPCap works well with as little as 100 ng total RNA input.A number of other TSS profiling methods use an oligo capping approach, which involves enzymatic removal of the m7G cap and replacement with a synthetic oligo, allowing selection of 5′-complete cDNAs (Suzuki and Sugano 2003; Wakaguri et al...
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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
...transcriptase adds nontemplated nucleotides to cDNAs during 59-RACE and primer extension. Biotechniques 30: 574–580, 582. Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, et al. 2008. Stem cell transcriptome profiling via massive-scale mRNA sequencing...
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ARTICLE: Identification of Putative Noncoding RNAs Among the RIKEN Mouse Full-Length cDNA Collection
- Koji Numata,
- Akio Kanai,
- Rintaro Saito,
- Shinji Kondo,
- Jun Adachi,
- Laurens G. Wilming,
- David A. Hume,
- RIKEN GER Group,
- GSL Members,
- Yoshihide Hayashizaki,
- and Masaru Tomita
Genome Res. June 2003 13: 1301-1306; doi:10.1101/gr.1011603
...-950. ↵ Bono, H., Yagi, K., Kasukawa, T., Nikaido, I., Tominaga, N., Miki, R., Mizuno, Y., Tomaru, Y., Goto, H., Nitanda, H., et al. 2003 . Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays. Genome Res. (this issue). ↵ Bortolin, M.L. and Kiss. T. 1998 . Human U19...
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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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PERSPECTIVE: Promoting transcriptome diversity
- Robert L. Strausberg and
- Samuel Levy
Genome Res. July 2007 17: 965-968; doi:10.1101/gr.6499807
...transcript repertoire is much more diverse than anticipated. In part, transcript diversity is generated through the use of alternative promoters and alternate splicing. In addition, based on discoveries using technologies such as full-length cDNA libraries and whole genome tiling microarrays, it is now...
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Research: CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors
- Kosuke Hashimoto,
- Ana Maria Suzuki,
- Alexandre Dos Santos,
- Christophe Desterke,
- Agnese Collino,
- Serena Ghisletti,
- Emilie Braun,
- Alessandro Bonetti,
- Alexandre Fort,
- Xian-Yang Qin,
- Enrico Radaelli,
- Bogumil Kaczkowski,
- Alistair R.R. Forrest,
- Soichi Kojima,
- Didier Samuel,
- Gioacchino Natoli,
- Marie Annick Buendia,
- Jamila Faivre,
- and Piero Carninci
Genome Res. December 2015 25: 1812-1824; Published in Advance October 28, 2015, doi:10.1101/gr.191031.115
..., Didier Samuel 2 , 3 , Gioacchino Natoli 4 , Marie Annick Buendia 2 , 3 , Jamila Faivre 2 , 3 , 7 and Piero Carninci 1 1 RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, 230-0045 Japan...
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LETTER: Discovery of Imprinted Transcripts in the Mouse Transcriptome Using Large-Scale Expression Profiling
- Itoshi Nikaido,
- Chika Saito,
- Yosuke Mizuno,
- Makiko Meguro,
- Hidemasa Bono,
- Moritoshi Kadomura,
- Tomohiro Kono,
- Gerard A. Morris,
- Paul A. Lyons,
- Mitsuo Oshimura,
- RIKEN GER Group,
- GSL Members,
- Yoshihide Hayashizaki,
- and Yasushi Okazaki
Genome Res. June 2003 13: 1402-1409; doi:10.1101/gr.1055303
...) ( Kamiya et al. 2000 ). To facilitate positional candidate cloning, it is also useful to know the tissue-expression profile of each gene. With this in mind, we have attempted to draw a picture of tissue expression profiles in 49 tissues using the RIKEN 19K cDNA microarray ( Miki et al. 2001 ). Further...
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RESOURCE: Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System
- Takeya Kasukawa,
- Masaaki Furuno,
- Itoshi Nikaido,
- Hidemasa Bono,
- David A. Hume,
- Carol Bult,
- David P. Hill,
- Richard Baldarelli,
- Julian Gough,
- Alexander Kanapin,
- Hideo Matsuda,
- Lynn M. Schriml,
- Yoshihide Hayashizaki,
- Yasushi Okazaki,
- and John Quackenbush
Genome Res. June 2003 13: 1542-1551; doi:10.1101/gr.992803
...of the mouse transcriptome using RIKEN cDNA microarrays. Genome Res . (this issue). ↵ Carninci, P., Waki, K., Shiraki, T., Konno, H., Shibata, K., Itoh, M., Aizawa, K., Arakawa, T., Ishii, Y., Sasaki, D., et al. 2003 . Targeting a complex transcriptome: The construction of the mouse full-length cDNA...
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RESOURCE: Inferring Alternative Splicing Patterns in Mouse from a Full-Length cDNA Library and Microarray Data
- Hiromi Kochiwa,
- Ryosuke Suzuki,
- Takanori Washio,
- Rintaro Saito,
- The RIKEN Genome Exploration Research Group Phase, II Team,
- Hidemasa Bono,
- Piero Carninci,
- Yasushi Okazaki,
- Rika Miki,
- Yoshihide Hayashizaki,
- and Masaru Tomita
Genome Res. August 1, 2002 12: 1286-1293; Published in Advance July 19, 2002, doi:10.1101/gr.220302
...Inferring Alternative Splicing Patterns in Mouse from a Full-Length cDNA Library and Microarray Data Hiromi Kochiwa 1 , 3 , Ryosuke Suzuki 1 , 3 , Takanori Washio 3 , Rintaro Saito 4 , The RIKEN Genome Exploration Research Group Phase, II Team...
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LETTER: Comprehensive Analysis of the Mouse Metabolome Based on the Transcriptome
- Hidemasa Bono,
- Itoshi Nikaido,
- Takeya Kasukawa,
- RIKEN GER Group,
- GSL Members,
- Yoshihide Hayashizaki,
- and Yasushi Okazaki
Genome Res. June 2003 13: 1345-1349; doi:10.1101/gr.974603
...in mouse, or that there is a separate enzyme yet to be identified. A line of evidence that supports the former hypothesis was obtained from the microarray data. We examined the expression profile of the genes on this pathway using the data of the RIKEN 20k mouse cDNA microarray (Nos. 1–3, a total of ∼ 60K...

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