Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 10 mM (final concentration) then the yeast cells were exposed for 2 h.
Extracted molecule
polyA RNA
Extraction protocol
Hot-phenol and oligotex dt mRNA purification kit (TaKaRa)
Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking until OD=1, then grown for 2 h without any treatment.
Extracted molecule
polyA RNA
Extraction protocol
Hot-phenol and oligotex dt mRNA purification kit (TaKaRa)
Scan Array 4000 (PerkinElmer Japan Co., Ltd) was used for scanning. Array images were analyzed with Gene Pix Pro 4.0 (Axon Instrument).
Description
In order to rescue data that had a higher intensity than the scanning range, the array were scanned twice with different laser power. This data were result from high power scanning. Data with flag value 0 were used for LOWESS normalization processing, although original raw data were remaining in this table. Merging high and low scanned data were done on the GeneSpring and represented as “AVG_VALUE”. However, the data in “AVG_VALUE” was not used for further analysis.
average log ratio from high and low scanned data (log2)
Cy5F
Cy5 inner intensity (median)
Cy5B
Cy5 intensity surrounding each spot (background), (median)
Cy3F
Cy3 inner intensity (median)
Cy3B
Cy3 intensity surrounding each spot (background), (median)
Cy5FB
Cy5 intensity subtracted from background intensity
Cy3FB
Cy3 intensity subtracted from background intensity
FlagGPR
Flag from GenePix Pro analysis
Flag
Additional flags by LOCUS_NAME1 as following; TE, TE; NG, NGT; QU, _ or -; C3, Cy3; C5, Cy5; EM, empty. Additional flags by Cy5F and Cy3F as following; BL, both data Cy3F and Cy5F is less than reliable limit; 5L, Cy5F is less than reliable limit; 3L, Cy3F is less than reliable limit; BM, both data Cy3F and Cy5F is over than scanning range; 5M, Cy5F is over than scanning range; 3M, Cy3F is over than scanning range.
