RT Journal
A1 Shibata, Kazuhiro
A1 Itoh, Masayoshi
A1 Aizawa, Katsunori
A1 Nagaoka, Sumiharu
A1 Sasaki, Nobuya
A1 Carninci, Piero
A1 Konno, Hideaki
A1 Akiyama, Junichi
A1 Nishi, Katsuo
A1 Kitsunai, Tokuji
A1 Tashiro, Hideo
A1 Itoh, Mari
A1 Sumi, Noriko
A1 Ishii, Yoshiyuki
A1 Nakamura, Shin
A1 Hazama, Makoto
A1 Nishine, Tsutomu
A1 Harada, Akira
A1 Yamamoto, Rintaro
A1 Matsumoto, Hiroyuki
A1 Sakaguchi, Sumito
A1 Ikegami, Takashi
A1 Kashiwagi, Katsuya
A1 Fujiwake, Syuji
A1 Inoue, Kouji
A1 Togawa, Yoshiyuki
A1 Izawa, Masaki
A1 Ohara, Eiji
A1 Watahiki, Masanori
A1 Yoneda, Yuko
A1 Ishikawa, Tomokazu
A1 Ozawa, Kaori
A1 Tanaka, Takumi
A1 Matsuura, Shuji
A1 Kawai, Jun
A1 Okazaki, Yasushi
A1 Muramatsu, Masami
A1 Inoue, Yorinao
A1 Kira, Akira
A1 Hayashizaki, Yoshihide
T1 RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer
JF Genome Research 
JO Genome Research 
YR 2000 
FD November 01 
VO 10 
IS 11 
SP 1757 
OP 1771 
DO 10.1101/gr.152600 
UL http://genome.cshlp.org/content/10/11/1757.abstract 
AB 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.