title: RIKEN 16K tobacco cDNA microarray (Slide2A)
status: Public on Feb 06 2007
contact.city: Yokohama
contact.first: Ken
contact.last: Matsuoka
contact.email: kenmat@psc.riken.go.jp
contact.state: Kanagawa
contact.address: 1-7-22 Suehirocho, Tsurumi-ku,
contact.department: Plant Science Center
contact.country: Japan
contact.institute: RIKEN
contact.phone: 81-45-503-9575
organism: Nicotiana tabacum
description: Mirror type slides were used.
manufacture_protocol: DNA for microarrays was prepared by amplification of cDNA cloned inserts using conventional PCR and the universal M13 forward (GTAAAACGACGGCCAGT) and reverse (CAGGAAACAGCTATGAC) vector primers (pGEM-Teasy), or M13 forward (GTAAAACGACG GCCAGT) and KS reverse (TCGAGGTCGACGGTATC) vector primers (pBII KS), with cDNA-containing plasmids as PCR templates. The microarray slides contained cDNA/EST clones described previously [1,2]. Control gene fragments cloned into the pBluescript vector (pBII KSt; Stratagene) were processed together with the cDNA/ESTs during microarray preparation. A complete set of 16 224 amplified cDNA inserts + control DNAs (672) was used to print a custom 16K BY-2 microarray (16,896). The complete microarray consisted of four microarray Bar Coded Slides, Type 7 star* or Lucidea (Amersham Biosciences UK Limited, Buckinghamshire, UK), with each PCRamplified cDNA sample spotted in duplicate on the slides. Standard slide arrangement consisted of 24 blocks with 12 rows and 32 columns each. The Array Spotter Generation III (Molecular Dynamics, Sunnyvale, CA, USA) was used for printing of slides.
  [1] Matsuoka, K., Demura, T., Galis, I., Horiguchi, T., Sasaki, M., Tashiro, G. and Fukuda, H. (2004) A comprehensive gene expression analysis toward the understanding of growth and differentiation of tobacco BY-2 cells. Plant Cell Physiol. 45: 1280-1289.
  [2] Galis, I., Simek, P., Narisawa, T., Sasaki, M., Horiguchi, T., Fukuda, H. and Matsuoka, K. (2006) A novel R2R3 MYB transcription factor NtMYBJS1 is a methyl jasmonate-dependent regulator of phenylpropanoid-conjugate biosynthesis in tobacco. Plant J. 46: 573-592.