@article{Shibata01112000,
author = {Shibata, Kazuhiro and Itoh, Masayoshi and Aizawa, Katsunori and Nagaoka, Sumiharu and Sasaki, Nobuya and Carninci, Piero and Konno, Hideaki and Akiyama, Junichi and Nishi, Katsuo and Kitsunai, Tokuji and Tashiro, Hideo and Itoh, Mari and Sumi, Noriko and Ishii, Yoshiyuki and Nakamura, Shin and Hazama, Makoto and Nishine, Tsutomu and Harada, Akira and Yamamoto, Rintaro and Matsumoto, Hiroyuki and Sakaguchi, Sumito and Ikegami, Takashi and Kashiwagi, Katsuya and Fujiwake, Syuji and Inoue, Kouji and Togawa, Yoshiyuki and Izawa, Masaki and Ohara, Eiji and Watahiki, Masanori and Yoneda, Yuko and Ishikawa, Tomokazu and Ozawa, Kaori and Tanaka, Takumi and Matsuura, Shuji and Kawai, Jun and Okazaki, Yasushi and Muramatsu, Masami and Inoue, Yorinao and Kira, Akira and Hayashizaki, Yoshihide}, 
title = {RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer},
volume = {10}, 
number = {11}, 
pages = {1757-1771}, 
year = {2000}, 
doi = {10.1101/gr.152600}, 
abstract ={The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary 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 a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. 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 >99% accuracy in 2.7 h (90 kb/h). 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 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can be revealed by seven RISA systems within one month.}, 
URL = {http://genome.cshlp.org/content/10/11/1757.abstract}, 
eprint = {http://genome.cshlp.org/content/10/11/1757.full.pdf+html}, 
journal = {Genome Research} 
}