strain: DL1-L genotype: wild-type treatment: control medium: YPD
Extracted molecule
total RNA
Extraction protocol
Isolation of RNA and cDNA synthesis were carried out as described in Oh et al., 2004. Oh, K.S., Kwon, O., Oh, Y.W., Sohn, M.J., Jung, S., Kim, Y.K., Kim, M.-G., Rhee, S.K., Gellissen, G., and Kang, H.A. (2004) Fabrication of a partial genome microarray of the methylotrophic yeast Hansenula polymorpha: Optimization and evaluation of transcript profiling. J. Microbiol. Biotechnol. 14, 1239-1248.
Label
Cy5
Label protocol
The labeling of target cDNAs was performed using the 3DNA™ Submicro® EX Expression Array Detection Kit (Genisphere, Hatfield, PA, USA) as described previously (Oh et al.).
Isolation of RNA and cDNA synthesis were carried out as described in Oh et al., 2004. Oh, K.S., Kwon, O., Oh, Y.W., Sohn, M.J., Jung, S., Kim, Y.K., Kim, M.-G., Rhee, S.K., Gellissen, G., and Kang, H.A. (2004) Fabrication of a partial genome microarray of the methylotrophic yeast Hansenula polymorpha: Optimization and evaluation of transcript profiling. J. Microbiol. Biotechnol. 14, 1239-1248.
Label
Cy3
Label protocol
The labeling of target cDNAs was performed using the 3DNA™ Submicro® EX Expression Array Detection Kit (Genisphere, Hatfield, PA, USA) as described previously (Oh et al.).
Hybridization protocol
Hybridization was performed using the 3DNA™ Submicro® EX Expression Array Detection Kit (Genisphere, Hatfield, PA, USA) according to the manufacturer's instructions as described previously (Oh et al.).
Scan protocol
The hybridized slides were scanned with the ScanArray 5000 scanner (Axon, Foster City, CA, U.S.A.).
Data processing
Using GenePixTM Pro 4.0 (Axon) software, spot intensity was quantified for each channel and transferred to a Microsoft Excel spreadsheet. All arrays were analyzed using Quintet, an R-based unified cDNA microarray data analysis system with GUI (Choe et al., 2005). Choe, J.-K., T.-H. Chung, S. Park, H. G. Cho, and C.-G. Hur. 2005. An open source microarray data analysis system with GUI: Quintet. In Slezak D. et al., (Eds) RSFDGrC 2005, LNAI 3642, pp. 392-401, Springer-Verlag Berling Heidelberg.
