ArticleGenome research2000
RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer.
Article in Genome research, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 60 citations in OpenAlex.
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- Androgen-dependent sertoli cell tight junction remodeling is mediated by multiple tight junction components.Molecular endocrinology (Baltimore, Md.) · 2014Article
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- The regulated retrotransposon transcriptome of mammalian cells.Nature genetics · 2009Article
- A resource for transcriptomic analysis in the mouse brain.PloS one · 2008Article
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- Genetic analysis of the cytoplasmic dynein subunit families.PLoS genetics · 2006Article
- Cytoskeletal rearrangements in synovial fibroblasts as a novel pathophysiological determinant of modeled rheumatoid arthritis.PLoS genetics · 2005Article
- Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
- The gene expression of hepatic proteins responsible for DNA repair and cell proliferation in tamoxifen-induced hepatocarcinogenesis.Cancer science · 2003Article
- Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia.Genome research · 2003Article
- DNA book.Genome research · 2003Article
- Identification and analysis of chromodomain-containing proteins encoded in the mouse transcriptome.Genome research · 2003Article
- The use of capillary electrophoresis for DNA polymorphism analysis.Molecular biotechnology · 2003Review
Corrections and comments
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Authors and funding
26 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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