Searching journal content for articles similar to Carninci et al. 13 (6b): 1273.

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Method: Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ
- Yongkang Long,
- Bin Zhang,
- Shuye Tian,
- Jia Jia Chan,
- Juexiao Zhou,
- Zhongxiao Li,
- Yisheng Li,
- Zheng An,
- Xingyu Liao,
- Yu Wang,
- Shiwei Sun,
- Ying Xu,
- Yvonne Tay,
- Wei Chen,
- and Xin Gao
Genome Res. April 2023 33: 644-657; Published in Advance April 28, 2023, doi:10.1101/gr.277177.122
...). These results suggested that tumor cells with IPA of ERCC1 would have dysregulated DNA repair functions, which might contribute to HCC development.Finally, we validated these two candidates by performing a 3′ rapid amplification of cDNA ends (3′ RACE) experiment in the liver cancer cell line HepG2. As shown...
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Resource: The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution
- Adam D. Warner,
- Louis Gevirtzman,
- LaDeana W. Hillier,
- Brent Ewing,
- and Robert H. Waterston
Genome Res. June 2019 29: 1036-1045; Published in Advance May 23, 2019, doi:10.1101/gr.243394.118
...-cell RNA-seq methods also rely on the end sequencing of cDNA molecules and thus largely fail to capture alternative splicing events.To address the need for a more comprehensive mRNA data set that captures the transcripts in specific tissues during embryonic development, we have used fluorescence...
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LETTER: Systematic Expression Profiling of the Mouse Transcriptome Using RIKEN cDNA Microarrays
- Hidemasa Bono,
- Ken Yagi,
- Takeya Kasukawa,
- Itoshi Nikaido,
- Naoko Tominaga,
- Rika Miki,
- Yosuke Mizuno,
- Yasuhiro Tomaru,
- Hitoshi Goto,
- Hiroyuki Nitanda,
- Daisuke Shimizu,
- Hirochika Makino,
- Tomoyuki Morita,
- Junshin Fujiyama,
- Takehito Sakai,
- Takashi Shimoji,
- David A. Hume,
- RIKEN GER Group,
- GSL Members,
- Yoshihide Hayashizaki,
- and Yasushi Okazaki
Genome Res. June 2003 13: 1318-1323; doi:10.1101/gr.1075103
..., because the mammalian transcriptome has been incomplete. The RIKEN Mouse Encyclopedia project aims to make a library of all transcribed sequences as cDNA clones ( The RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium 2001 ). Analysis of the expression pattern for these cDNAs...
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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
...; ‘t Hoen et al. 2008; Suzuki et al. 2009; Valen et al. 2009; Levin et al. 2010; Plessy et al. 2010; Wu et al. 2010; Sam et al. 2011). The majority of transcriptome protocols running on second-generation sequencing platforms have relied on two PCR amplification steps: one for preamplication of cDNA...
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Research: Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome
- Tim R. Mercer,
- Marcel E. Dinger,
- Cameron P. Bracken,
- Gabriel Kolle,
- Jan M. Szubert,
- Darren J. Korbie,
- Marjan E. Askarian-Amiri,
- Brooke B. Gardiner,
- Gregory J. Goodall,
- Sean M. Grimmond,
- and John S. Mattick
Genome Res. December 2010 20: 1639-1650; Published in Advance November 2, 2010, doi:10.1101/gr.112128.110
...various combinations of alternative splicing, transcription initiation, and polyadenylation. The enormous complexity of the mammalian transcriptome was first exposed by large-scale sequencing of full-length cDNA transcripts frommouse (Okazaki et al. 2002;Maeda et al. 2006) and chromosome tiling array...
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Method: Transcript amplification from single bacterium for transcriptome analysis
- Yun Kang,
- Michael H. Norris,
- Jan Zarzycki-Siek,
- William C. Nierman,
- Stuart P. Donachie,
- and Tung T. Hoang
Genome Res. June 2011 21: 925-935; Published in Advance May 2, 2011, doi:10.1101/gr.116103.110
...). Accordingly, the average efficiencies of each target arewithin 4.1%differences (<5%) andpermit accurate analysis. The expression level of mRNA BTH_I2028 was taken as 1 for each amplified sample tested, and the amounts of tRNA and rRNAs were normalized relative to this value. cDNA library construction...
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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
...encyclopedia. Genome Res . (this issue). ↵ The FANTOM Consortium and the RIKEN Genome Exploration Research Group Phase I and II Team. 2002 . Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420 : 563 -573. ↵ The Gene Ontology Consortium. 2001 . Creating...
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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
...disease loci. These data provide a major resource for understanding the role of imprinting in mammalian inherited traits. The FANTOM2 set of mouse full-length cDNAs has provided the first global view of a mammalian transcriptome and is an essential resource for annotation ( The FANTOM Consortium...
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LETTER: Analysis of the Mouse Transcriptome for Genes Involved in the Function of the Nervous System
- Stefano Gustincich,
- Serge Batalov,
- Kirk W. Beisel,
- Hidemasa Bono,
- Piero Carninci,
- Colin F. Fletcher,
- Sean Grimmond,
- Nobutaka Hirokawa,
- Erich D. Jarvis,
- Tim Jegla,
- Yuka Kawasawa,
- Julianna LeMieux,
- Harukata Miki,
- Elio Raviola,
- Rohan D. Teasdale,
- Naoko Tominaga,
- Ken Yagi,
- Andreas Zimmer,
- RIKEN GER Group,
- GSL Members,
- Yoshihide Hayashizaki,
- and Yasushi Okazaki
Genome Res. June 2003 13: 1395-1401; doi:10.1101/gr.1135303
...Enzymol. 303 : 19 -44. ↵ 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 encyclopedia. Genome Res. (this issue). ↵ Catterall, W.A. 2000...
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LETTER: Systematic Characterization of the Zinc-Finger-Containing Proteins in the Mouse Transcriptome
- Timothy Ravasi,
- Thomas Huber,
- Mihaela Zavolan,
- Alistair Forrest,
- Terry Gaasterland,
- Sean Grimmond,
- RIKEN GER Group,
- GSL Members,
- and David A. Hume
Genome Res. June 2003 13: 1430-1442; doi:10.1101/gr.949803
...an incomplete and imperfect prediction and description of the full-length transcripts and splice variants that can be transcribed from the . The RIKEN Mouse Gene Encyclopedia Project has provided the most comprehensive collection of full-length mammalian complementary DNAs (cDNAs; Okazaki et al. 2002...

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