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METHODS: A Computer-Based Method of Selecting Clones for a Full-Length cDNA Project: Simultaneous Collection of Negligibly Redundant and Variant cDNAs
- Naoki Osato,
- Masayoshi Itoh,
- Hideaki Konno,
- Shinji Kondo,
- Kazuhiro Shibata,
- Piero Carninci,
- Toshiyuki Shiraki,
- Akira Shinagawa,
- Takahiro Arakawa,
- Shoshi Kikuchi,
- Kouji Sato,
- Jun Kawai,
- and Yoshihide Hayashizaki
Genome Res. July 1, 2002 12: 1127-1134; Published in Advance June 18, 2002, doi:10.1101/gr.75202
.... Acad. Sci. 95 : 520 – 524 . ↵ Carninci P. , Shibata Y. , Hayatsu N. , Sugahara Y. , Shibata K. , Itoh M. , Konno H. , Okazaki Y. , Muramatsu M. , Hayashizaki Y. ( 2000 ) Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes...
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ARTICLE: Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia
- Piero Carninci,
- Kazunori Waki,
- Toshiyuki Shiraki,
- Hideaki Konno,
- Kazuhiro Shibata,
- Masayoshi Itoh,
- Katsunori Aizawa,
- Takahiro Arakawa,
- Yoshiyuki Ishii,
- Daisuke Sasaki,
- Hidemasa Bono,
- Shinji Kondo,
- Yuichi Sugahara,
- Rintaro Saito,
- Naoki Osato,
- Shiro Fukuda,
- Kenjiro Sato,
- Akira Watahiki,
- Tomoko Hirozane-Kishikawa,
- Mari Nakamura,
- Yuko Shibata,
- Ayako Yasunishi,
- Noriko Kikuchi,
- Atsushi Yoshiki,
- Moriaki Kusakabe,
- Stefano Gustincich,
- Kirk Beisel,
- William Pavan,
- Vassilis Aidinis,
- Akira Nakagawara,
- William A. Held,
- Hiroo Iwata,
- Tomohiro Kono,
- Hiromitsu Nakauchi,
- Paul Lyons,
- Christine Wells,
- David A. Hume,
- Michela Fagiolini,
- Takao K. Hensch,
- Michelle Brinkmeier,
- Sally Camper,
- Junji Hirota,
- Peter Mombaerts,
- Masami Muramatsu,
- Yasushi Okazaki,
- Jun Kawai,
- and Yoshihide Hayashizaki
Genome Res. June 2003 13: 1273-1289; doi:10.1101/gr.1119703
...available ( Waterston et al. 2002 ). RESULTS Gene Discovery by Sequencing We based the gene discovery on large-scale sequencing of libraries enriched for full-length subtracted/normalized cDNA. We clustered cDNA sequences from 3′-end reads ( Konno et al. 2001 ), because 3′ cDNA priming is relatively...
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RESOURCE: The Drosophila Gene Collection: Identification of Putative Full-Length cDNAs for 70% of D. melanogaster Genes
- Mark Stapleton,
- Guochun Liao,
- Peter Brokstein,
- Ling Hong,
- Piero Carninci,
- Toshiyuki Shiraki,
- Yoshihide Hayashizaki,
- Mark Champe,
- Joanne Pacleb,
- Ken Wan,
- Charles Yu,
- Joe Carlson,
- Reed George,
- Susan Celniker,
- and Gerald M. Rubin
Genome Res. August 1, 2002 12: 1294-1300; doi:10.1101/gr.269102
.... , Konno H. , Okazaki Y. , Muramatsu M. , Hayashizaki Y. ( 2000 ) Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome Res. 10 : 1617 – 1630 . ↵ Carninci P. , Shibata Y. , Hayatsu N. , Itoh M. , Shiraki T. , Hirozane T...
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METHODS: Computer-Based Methods for the Mouse Full-Length cDNA Encyclopedia: Real-Time Sequence Clustering for Construction of a Nonredundant cDNA Library
- Hideaki Konno,
- Yoshifumi Fukunishi,
- Kazuhiro Shibata,
- Masayoshi Itoh,
- Piero Carninci,
- Yuichi Sugahara,
- and Yoshihide Hayashizaki
Genome Res. February 1, 2001 11: 281-289; Published in Advance January 18, 2001, doi:10.1101/gr.145701
...and subtraction of cap-trapper selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome Res. 10 : 1617 – 1730 . ↵ Edwalds-Gilbert G. , Veraldi K.L. , Milcarek C. ( 1997 ) Alternative poly(A) site selection in complex transcription units: Means to an end? Nucleic Acids Res. 25...
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METHODS: Construction of Long-Transcript Enriched cDNA Libraries from Submicrogram Amounts of Total RNAs by a Universal PCR Amplification Method
- Yulan Piao,
- Naomi T. Ko,
- Meng K. Lim,
- and Minoru S.H. Ko
Genome Res. September 1, 2001 11: 1553-1558; doi:10.1101/gr.185501
...by biotinylated CAP trapper. Genomics 37 : 327 – 336 . ↵ Carninci P. , Shibata Y. , Hayatsu N. , Sugahara Y. , Shibata K. , Itoh M. , Konno H. , Okazaki Y. , Muramatsu M. , Hayashizaki Y. ( 2000 ) Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery...
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RESOURCE: An Oligonucleotide Fingerprint Normalized and Expressed Sequence Tag Characterized Zebrafish cDNA Library
- Matthew D. Clark,
- Steffen Hennig,
- Ralf Herwig,
- Sandy W. Clifton,
- Marco A. Marra,
- Hans Lehrach,
- Stephen L. Johnson,
- and the WU-GSC EST Group
Genome Res. September 1, 2001 11: 1594-1602; Published in Advance August 16, 2001, doi:10.1101/gr.186901
.... , Sugahara Y. , Shibata K. , Itoh M. , Konno H. , Okazaki Y. , Muramatsu M. , Hayashizaki Y. ( 2000 ) Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome Res. 10 : 1617 – 30 . ↵ Clark M.D. , Panopoulou G.D. , Cahill D...
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LETTER: Annotated Expressed Sequence Tags and cDNA Microarrays for Studies of Brain and Behavior in the Honey Bee
- Charles W. Whitfield,
- Mark R. Band,
- Maria F. Bonaldo,
- Charu G. Kumar,
- Lei Liu,
- Jose R. Pardinas,
- Hugh M. Robertson,
- M. Bento Soares,
- and Gene E. Robinson
Genome Res. April 1, 2002 12: 555-566; doi:10.1101/gr.5302
.... Nature 403 : 537 – 540 . ↵ Carninci P. , Shibata Y. , Hayatsu N. , Sugahara Y. , Shibata K. , Itoh M. , Konno H. , Okazaki Y. , Muramatsu M. , Hayashizaki Y. ( 2000 ) Normalization and subtraction of cap-trapper–selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome...
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LETTER: Continued Discovery of Transcriptional Units Expressed in Cells of the Mouse Mononuclear Phagocyte Lineage
- Christine A. Wells,
- Timothy Ravasi,
- Razvan Sultana,
- Ken Yagi,
- Piero Carninci,
- Hidemasa Bono,
- Geoffrey Faulkner,
- Yasushi Okazaki,
- John Quackenbush,
- David A. Hume,
- RIKEN GER Group,
- GSL Members,
- and Paul A. Lyons
Genome Res. June 2003 13: 1360-1365; doi:10.1101/gr.1056103
...., Muramatsu, M. and Hayashizaki, Y. 2000 . Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome Res. 10 : 1617 -1630. ↵ Ehrt, S., Schnappinger, D., Bekiranov, S., Drenkow, J., Shi, S., Gingeras, T.R., Gaasterland, T...
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LETTER: 1274 Full-Open Reading Frames of Transcripts Expressed in the Developing Mouse Nervous System
- Maria F. Bonaldo,
- Thomas B. Bair,
- Todd E. Scheetz,
- Einat Snir,
- Ike Akabogu,
- Jennifer L. Bair,
- Brian Berger,
- Keith Crouch,
- Aja Davis,
- Mari E. Eyestone,
- Catherine Keppel,
- Tamara A. Kucaba,
- Mark Lebeck,
- Jenny L. Lin,
- Anna I.R. de Melo,
- Joshua Rehmann,
- Rebecca S. Reiter,
- Kelly Schaefer,
- Christina Smith,
- Dylan Tack,
- Kurtis Trout,
- Val C. Sheffield,
- Jim J-C. Lin,
- Thomas L. Casavant,
- and Marcelo B. Soares
Genome Res. October 15, 2004 14: 2053-2063; doi:10.1101/gr.2601304
...., Shibata, Y., Hayatsu, N., Sugahara, Y., Shibata, K., Itoh, M., Konno, H., Okazaki, Y., Muramatsu, M., and Hayashizaki, Y. 2000 . Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome Res. 10 : 1617 -1630. ↵ Carninci, P...
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Methods: A Transcript Finishing Initiative for Closing Gaps in the Human Transcriptome
- The Ludwig–FAPESP Transcript Finishing Initiative,
- Mari Cleide Sogayar,
- and Anamaria A. Camargo
Genome Res. July 2004 14: 1413-1423; Published in Advance June 14, 2004, doi:10.1101/gr.2111304
...here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21% of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2% of these TFUs was not correctly...

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