International Mammalian Genome Society

The 14th International Mouse Genome Conference (2000)


D16. RIKEN Integrated Sequence Analysis System (RISA System) - 384-Format Sequencing Pipeline with 384 Multi-Capillary Sequencer

Kazuhiro Shibata1, Masayoshi Itoh1, Katsunori Aizawa1, Sumiharu Nagaoka1,8, Nobuya Sasaki1,9, Piero Carninci1, Hideaki Konno1, Junichi Akiyama1, Mari Itoh1, Noriko Kikuchi1, Yoshiyuki Ishii1, Shin Nakamura1, Makoto Hazama1, Tsutomu Nishine1, Akira Harada1, Rintaro Yamamoto1, Hiroyuki Matsumoto1, Sumito Sakaguchi1, Takashi Ikegami1, Katsuya Kashiwagi1, Syuji Fujiwake1, Kouji Inoue1, Yoshiyuki Togawa1, Masaki Izawa1,4, Eiji Ohara 4, Masanori Watahiki4, Yuko Yoneda4, Tomokazu Ishikawa1,5, Kaori Ozawa5, Takumi Tanaka5, Shuji Matsuura5, Jun Kawai1, Yasushi Okazaki1, Masami Muramatsu1, Yorinao Inoue6, Akira Kira7, and Yoshihide Hayashizaki1.3.10
1Genome Exploration Research Group, RIKEN, Genomic Sciences Center (GSC) and Genome Science Laboratory, RIKEN, Tsukuba Institute, Core Research of Evolutional Science and Technology (CREST), Japan Science and Technology Corporation (JST), Tsukuba-shi, Ibaraki, 305-0074, Japan;
2Department of Research Fundamentals Technology, RIKEN, Wako-shi, Saitama, 351-0198, Japan;
3Medical School, Tsukuba University, Tsukuba-shi, Ibaraki 305-8575, Japan;
4Research & Development, Nippon Gene Co., Ltd., 1-1-24, Arakawa, Toyama, 930-0834, Japan;
5Osaka Research Laboratories, Wako Pure Chemical Industries, Ltd. 6-1, Takada-cho, Amagasaki, Hyogo 661-0963, Japan;
6RIKEN Harima Institute at SPring-8, Kouto, Mikazuki, Sayou, Hyougo 679-5148, Japan;
7RIKEN, Wako-shi, Saitama, 351-0198, Japan; present address
8
Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Kyoto 606-8585, Japan;
9
Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113, Japan;
10Corresponding author. E-MAIL yosihide@rtc.riken.go.jp FAX +81 298 36 9098

The RIKEN high throughput 384-format sequencing pipeline (RISA system) including a 384 multi-capillary sequencer, the so-called RISA sequencer, was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction and the sequencing process. A novel high throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of (1) a 384 multi-capillary auto sequencer (RISA sequencer), (2) a 384 multi-capillary array assembler (CAS), and (3) a 384 multi-capillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The RISA sequencer can simultaneously analyze 384 independent sequencing products. For long read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with more than 99% accuracy in 2.7 hrs (90 kb/hr). For short read sequencing to cluster the 3 end and 5 end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 hrs. The RISA system consisting of 16 RISA sequencers can process 50,000 DNA samples/day.


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