Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia

Carninci, P., Waki, K., Shiraki, T., Konno, H., Shibata, K., Itoh, M., Aizawa, K., Arakawa, T., Ishii, Y., Sasaki, D. S., Bono, H., Kondo, S., Sugahara, Y., Saito, R. and Osato, N. (2003) Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia. Genome Research, 13 6B: 1273-1289. doi:10.1101/gr.1119703

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Author Carninci, P.
Waki, K.
Shiraki, T.
Konno, H.
Shibata, K.
Itoh, M.
Aizawa, K.
Arakawa, T.
Ishii, Y.
Sasaki, D. S.
Bono, H.
Kondo, S.
Sugahara, Y.
Saito, R.
Osato, N.
Title Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia
Journal name Genome Research   Check publisher's open access policy
ISSN 1088-9051
1549-5469
Publication date 2003-01-01
Sub-type Article (original research)
DOI 10.1101/gr.1119703
Open Access Status File (Publisher version)
Volume 13
Issue 6B
Start page 1273
End page 1289
Total pages 17
Place of publication Cold Spring Harbor, NY, United States
Publisher Cold Spring Harbor Laboratory Press
Collection year 2003
Language eng
Abstract We report the construction of the mouse full-length cDNA encyclopedia, the most extensive view of a complex transcriptome, on the basis of preparing and sequencing 246 libraries. Before cloning, cDNAs were enriched in full-length by Cap-Trapper, and in most cases, aggressively subtracted/normalized. We have produced 1,442,236 successful 3'-end sequences clustered into 171,144 groups, from which 60,770 clones were fully sequenced cDNAs annotated in the FANTOM-2 annotation. We have also produced 547,149 5' end reads, which clustered into 124,258 groups. Altogether, these cDNAs were further grouped in 70,000 transcriptional units (TU), which represent the best coverage of a transcriptome so far. By monitoring the extent of normalization/subtraction, we define the tentative equivalent coverage (TEC), which was estimated to be equivalent to >12,000,000 ESTs derived from standard libraries. High coverage explains discrepancies between the very large. numbers of clusters (and TUs) of this project, which also include non-protein-coding RNAs, and the lower gene number estimation of genome annotations. Altogether, S'-end clusters identify regions that are potential promoters for 8637 known genes and S'-end clusters suggest the presence of almost 63,000 transcriptional starting points. An estimate of the frequency of polyadenylation signals suggests that at least half of the singletons in the EST set represent real mRNAs. Clones accounting for about half of the predicted TUs await further sequencing. The continued high-discovery rate suggests that the task of transcriptome discovery is not yet complete.
Keyword Biochemistry & Molecular Biology
Biotechnology & Applied Microbiology
Genetics & Heredity
Expressed Sequence Tags
Trapper-selected Cdnas
Human Messenger-rnas
Gene-expression
Cap-trapper
Dna-sequence
Reverse Transcription
Functional Annotation
Libraries
Cloning
Q-Index Code C1
Institutional Status UQ
Additional Notes Authors of this document: Carninci, P; Waki, K; Shiraki, T; Konno, H; Shibata, K; Itoh, M; Aizawa, K; Arakawa, T; Ishii, Y; Sasaki, D; Bono, H; Kondo, S; Sugahara, Y; Saito, R; Osato, N; Fukuda, S; Sato, K; Watahiki, A; Hirozane-Kishikawa, T; Nakamura, M; Shibata, Y; Yasunishi, A; Kikuchi, N; Yoshiki, A; Kusakabe, M; Gustincich, S; Beisel, K; Pavan, W; Aidinis, V; Nakagawara, A; Held, WA; Iwata, H; Kono, T; Nakauchi, H; Lyons, P; Wells, C; Hume, DA; Fagiolini, M; Hensch, TK; Brinkmeier, M; Camper, S; Hirota, J; Mombaerts, P; Muramatsu, M; Okazaki, Y; Kawai, J; Hayashizaki, Y.

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2004 Higher Education Research Data Collection
Institute for Molecular Bioscience - Publications
 
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Citation counts: TR Web of Science Citation Count  Cited 123 times in Thomson Reuters Web of Science Article | Citations
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Created: Wed, 15 Aug 2007, 12:50:49 EST