About ARTRA™ DB
About a new gene-specific DNA Microarray
About our Arabidopsis Transcriptome Database
Reference
What's newA part of this work was performed as one of the technology development projects of the "Green Biotechnology Program" supported by NEDO (New Energy and Industrial Technology Development Organization).
Under Construction
Arabidopsis thaliana transcript sequence was deduced from our EST clustering database. Then we attempted to design the probe sequence of the microarray, with about 300 bases long, using our original program which can search minimum homology region of genes. More than 25,000 probe sequences thus designed (approximately 300 bases long) were amplified by using the cDNA from Kazusa DNA Research Institute or genomic DNA of A. thaliana as a template. An isothermal gene amplification method, which we call Isothermal and Chimeric primer-initiated Amplification of Nucleic acids (abbreviated as ICAN below), was used for preparation of DNA fragments in large amount. ICAN allows amplification of DNA in large volume. Only one of two primers was 5'-amino-modified in ICAN reaction and this gave amplified DNA fragments having 5' end of the sense strand amino-modified. Each DNA fragment which passed quality control was spotted on a slide glass, Takara-Hubble Slide. This slide glass is coated with active esters on its surface and this enabled preparation of DNA microarray on which only the sense DNA strand is immobilized by covalent bond. Finally A. thaliana DNA microarray, which has about 25,000 genes by AGI code spotted, was produced.
We collected 262,196 transcript sequences of Arabidopsis thaliana from ESTs (Expression Sequence Tags) and full-length cDNA sequences in GenBank and RIKEN and Kazusa DNA Research Institute to get much more transcript sequences. And these collected sequences are redundant, we performed clustering and assembling these sequences by Paracel Clustering Package to generate non-redundant transcript sequences. We made use of 26,637 deduced ORF sequences on MIPS genome database as seed sequence in clustering to classify above collected sequences into seed sequences. The seed using clustering results in 19,380 non-redundant transcript sequences containing seed sequences and 4,875 non-redundant transcript sequences without seed sequences. We annotated these non-redundant transcipt sequences by BLAST homology search to TAIR(The Arabidopsis Information Resource) database. Then there are some sequences whose search hit E-value are low(E-value >=1e-100) and we executed one more BLAST search to NCBI nr(non redundant) database to give more precious annotation to each transcript sequences.
Under Construction
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2005/07/04 | version 3.0 | ARI3 LOT3 data release. |
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2004/07/20 | version 2.0 | ARI3 data release. Clustering data update |
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2003/11/20 | version 1.2 | Update spot specificity data |
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2003/11/14 | version 1.1 | Add advanced search |
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2003/10/01 | version 1.0 | Open site |
Last Update : 2004/07/17