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

¹Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan ²Genome Science Laboratory, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan ³Institute of Basic Medical Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan ⁴Japan Division of Genomic Information Resources, Science of Biological Supramolecular Systems, Graduate School of Integrated Science, Yokohama City University, Tsurumi-Ku, Yokohama 230-0045, Japan ⁵Experimental Animal Research Division, Biogenic Resources Center, RIKEN Tsukuba Institute, Tsukuba, Ibaraki 305-0074, Japan ⁶Dnaform International, Inc., Ami Town, Inashiki District, Ibaraki 300-0332, Japan ⁷Aloka Co., LTD, Kasumigaura-cho, Niihari-gun, Ibaraki 300-0134 Japan ⁸Department of Neurobiology, Harvard Medical School, Boston, Massachusetts 02115, USA ⁹Boys Town National Research Hospital, Omaha, Nebraska 68131, USA ¹⁰National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA ¹¹Institute of Immunology, Biomedical Sciences Research Center A1. Fleming, 16672 Vari, Greece ¹²Chiba Cancer Center Research Institute, Division of Biochemistry, Chuo-ku, Chiba 260-8717, Japan ¹³Roswell Park Cancer Institute, Buffalo, New York 14263, USA ¹⁴Department of Reparative Materials Field of Tissue Engineering, Institute for Frontier Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan ¹⁵Faculty of Applied Bioscience, Department of BioScience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan ¹⁶Laboratory of Stem Cell Therapy Center for Experimental Medicine, Institute of Medical Science, University of Tokyo Minato-ku, Tokyo 108-8639, Japan ¹⁷DRF/WT Diabetes and Inflammation Laboratory Cambridge Institute for Medical Research, Cambridge CB2 2XYUK ¹⁸The Institute for Molecular Biosciences, The University of QLD, St. Lucia Brisbane, QLD 4072 Australia ¹⁹Neuronal Function Research, Lab for Neuronal Circuit Development, RIKEN Brain Science Institute (BSI), Wako-shi, Saitama 300-0198, Japan ²⁰University of Michigan Medical, Ann Arbor, Michigan 48109, USA ²¹Developmental Biology and Neurogenetics, The Rockefeller University, New York, New York 10021, USA

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.

²² Corresponding author.
E-MAIL: rgscerg{at}gsc.riken.go.jp; FAX 8145 503 9216.

[Supplemental material available online at www.genome.org.]

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