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  • Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia

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    Author(s)
    Carninci, Piero
    Waki, Kazunori
    Shiraki, Toshiyuki
    Konno, Hideaki
    Shibata, Kazuhiro
    Itoh, Masayoshi
    Aizawa, Katsunori
    Arakawa, Takahiro
    Ishii, Yoshiyuki
    Sasaki, Daisuke
    Bono, Hidemasa
    Kondo, Shinji
    Sugahara, Yuichi
    Saito, Rintaro
    Osato, Naoki
    Fukuda, Shiro
    Sato, Kenjiro
    Watahiki, Akira
    Hirozane-Kishikawa, Tomoko
    Nakamura, Mari
    Shibata, Yuko
    Yasunishi, Ayako
    Kikuchi, Noriko
    Yoshiki, Atsushi
    Kusakabe, Moriaki
    Gustincich, Stefano
    Beisel, Kirk
    Pavan, William
    Aidinis, Vassilis
    Nakagawara, Akira
    Held, William A.
    Iwata, Hiroo
    Kono, Tomohiro
    Nakauchi, Hiromitsu
    Lyons, Paul
    Wells, C.
    Hume, David A.
    Fagiolini, Michela
    et al.
    Griffith University Author(s)
    Wells, Christine
    Year published
    2003
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    Abstract
    We report the construction of the mouse full-length cDNA encyclopedia,th e 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 ...
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    We report the construction of the mouse full-length cDNA encyclopedia,th e 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,an d 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.
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    Journal Title
    Genome Research
    Volume
    13
    Issue
    6b
    DOI
    https://doi.org/10.1101/gr.1119703
    Copyright Statement
    © 2003 Cold Spring Harbor Laboratory Press. The attached file is reproduced here in accordance with the copyright policy of the publisher. Please refer to the journal's website for access to the definitive, published version.
    Subject
    Genetics not elsewhere classified
    Biological Sciences
    Medical and Health Sciences
    Publication URI
    http://hdl.handle.net/10072/27150
    Collection
    • Journal articles

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