title: Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia.
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,5'-end clusters identify regions that are potential promoters for 8637 known genes and 5'-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.
authors.affiliation: Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Piero
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authors.lastname: Carninci
authors.forename: Kazunori
authors.initials: K
authors.lastname: Waki
authors.forename: Toshiyuki
authors.initials: T
authors.lastname: Shiraki
authors.forename: Hideaki
authors.initials: H
authors.lastname: Konno
authors.forename: Kazuhiro
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authors.lastname: Shibata
authors.forename: Masayoshi
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authors.lastname: Itoh
authors.forename: Katsunori
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authors.lastname: Aizawa
authors.forename: Takahiro
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authors.lastname: Arakawa
authors.forename: Yoshiyuki
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authors.lastname: Ishii
authors.forename: Daisuke
authors.initials: D
authors.lastname: Sasaki
authors.forename: Hidemasa
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authors.lastname: Bono
authors.forename: Shinji
authors.initials: S
authors.lastname: Kondo
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Sugahara
authors.forename: Rintaro
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authors.lastname: Saito
authors.forename: Naoki
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authors.lastname: Osato
authors.forename: Shiro
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authors.lastname: Fukuda
authors.forename: Kenjiro
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authors.lastname: Sato
authors.forename: Akira
authors.initials: A
authors.lastname: Watahiki
authors.forename: Tomoko
authors.initials: T
authors.lastname: Hirozane-Kishikawa
authors.forename: Mari
authors.initials: M
authors.lastname: Nakamura
authors.forename: Yuko
authors.initials: Y
authors.lastname: Shibata
authors.forename: Ayako
authors.initials: A
authors.lastname: Yasunishi
authors.forename: Noriko
authors.initials: N
authors.lastname: Kikuchi
authors.forename: Atsushi
authors.initials: A
authors.lastname: Yoshiki
authors.forename: Moriaki
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authors.lastname: Kusakabe
authors.forename: Stefano
authors.initials: S
authors.lastname: Gustincich
authors.forename: Kirk
authors.initials: K
authors.lastname: Beisel
authors.forename: William
authors.initials: W
authors.lastname: Pavan
authors.forename: Vassilis
authors.initials: V
authors.lastname: Aidinis
authors.forename: Akira
authors.initials: A
authors.lastname: Nakagawara
authors.forename: William A
authors.initials: WA
authors.lastname: Held
authors.forename: Hiroo
authors.initials: H
authors.lastname: Iwata
authors.forename: Tomohiro
authors.initials: T
authors.lastname: Kono
authors.forename: Hiromitsu
authors.initials: H
authors.lastname: Nakauchi
authors.forename: Paul
authors.initials: P
authors.lastname: Lyons
authors.forename: Christine
authors.initials: C
authors.lastname: Wells
authors.forename: David A
authors.initials: DA
authors.lastname: Hume
authors.forename: Michela
authors.initials: M
authors.lastname: Fagiolini
authors.forename: Takao K
authors.initials: TK
authors.lastname: Hensch
authors.forename: Michelle
authors.initials: M
authors.lastname: Brinkmeier
authors.forename: Sally
authors.initials: S
authors.lastname: Camper
authors.forename: Junji
authors.initials: J
authors.lastname: Hirota
authors.forename: Peter
authors.initials: P
authors.lastname: Mombaerts
authors.forename: Masami
authors.initials: M
authors.lastname: Muramatsu
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Okazaki
authors.forename: Jun
authors.initials: J
authors.lastname: Kawai
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
mesh_terms: D000818:Animals; D003001:Cloning, Molecular / Q000379:methods; D016000:Cluster Analysis; D018076:DNA, Complementary / Q000235:genetics*; D030541:Databases, Genetic / Q000706:statistics & numerical data; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods / Q000706:statistics & numerical data; D015723:Gene Library; D005796:Genes / Q000235:genetics / Q000502:physiology; D016678:Genome; D051379:Mice; D008810:Mice, Inbred C57BL; D009928:Organ Specificity / Q000235:genetics; D026723:Polyadenylation / Q000235:genetics; D012315:RNA Caps / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods / Q000706:statistics & numerical data; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D012315:RNA Caps