This work was performed as a part of the R&D Project of Industrial Science and Technology Frontier Program supported by NEDO(New Energy and Industrial Technology Development Organization).
Under Construction
cDNA sequence was deduced from our EST clustering database for each of the clone supplied from Kazusa DNA Research Institute. Then we attempted to design the probe sequence of the microarray, with about 300 bases long, for each of the clone using our original program which can search minimum homology region of genes. More than 8,000 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 8,000 genes by AGI code spotted, was produced.
We collected 228,716 transcript sequences of Arabidopsis thaliana including ESTs (Expression Sequence Tags) and full-length cDNA sequenses from Genbank, RIKEN and Kazusa DNA Research Institute. Next, we performed clustering and assembling these sequences with Paracel Clustering Package, using 26,620 deduced ORF sequences of MIPS genome database as seed sequence. By clustering and assembling, they were classified into 30,767 non-redundant transcripts including seed singlet (MIPS ORF sequence) and no singlet transcript sequence.
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2003/10/01 | version 1.0 | Open site |
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2003/11/14 | version 1.1 | Add advanced search |
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2003/11/20 | version 1.2 | Update spot specificity data |
Last Update : 2003/11/20