|
| Status |
Public on Dec 04, 2008 |
| Title |
S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 15 min after A-factor addition 2nd |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
experiment
|
| Organism |
Streptomyces griseus subsp. griseus NBRC 13350 |
| Characteristics |
S. griseus IFO13350 afsA deficient mutant 15 min after A-factor addition
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by RNAqueous mini kit (Ambion) and carried out DNaseI treatment to remove contaminated genomic DNA.
|
| Label |
Cy3
|
| Label protocol |
Cy3 labeled cDNA were prepared by indirect labeling.
|
| |
|
| Channel 2 |
| Source name |
control
|
| Organism |
Streptomyces griseus subsp. griseus NBRC 13350 |
| Characteristics |
S. griseus IFO13350 afsA deficient mutant
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by RNAqueous mini kit (Ambion) and carried out DNaseI treatment to remove contaminated genomic DNA.
|
| Label |
Cy5
|
| Label protocol |
Cy5 labeled cDNA were prepared by indirect labeling.
|
| |
|
| |
| Hybridization protocol |
Microarray hybridization was carried out at 42°C for 18 h with mixing by using 120 μl per slide of SlideHyb#1 hybridization solution (Ambion) in a GeneTac HybStation (Genomic Solution). The posthybridization washing consisted of three cycles of 20-second incubations with each of the following solutions: 2× SSC plus 0.1% SDS (medium stringency) at 42°C, 0.1× SSC plus 0.05% SDS (high stringency) at 25°C, and 0.1× SSC (low stringency) at 25°C. After being washed, the slides were dried by centrifugation for 5 min at 350 × g at room temperature.
|
| Scan protocol |
The slides scanned with with a 428 array scanner (Affymetrix). The spot intensities were quantified using Imagene 6.1 (BioDiscovery, Inc.).
|
| Description |
To correct for non-specific (background) signal for each channel (each dye), the mean signal of 10% of the probes in each sub grid with the lowest intensity was subtracted from that of all probes in the corresponding sub grid.
|
| Data processing |
Expression ratios were normalized using the Limma loess method by ArrayPipe 2.0. Average normalized expression ratios (experiment/control) were calculated for each gene and tested for significance (p < 0.05). Ratio of experiment compared with control were further screened for difference from control, which was defined as having an expression ratio of either >2.0 or <0.5.
|
| |
|
| Submission date |
Dec 03, 2008 |
| Last update date |
Dec 03, 2008 |
| Contact name |
Yasuo Ohnishi |
| E-mail(s) |
ayasuo@mail.ecc.u-tokyo.ac.jp
|
| Organization name |
University of Tokyo
|
| Department |
Biotechnology
|
| Lab |
Hakko
|
| Street address |
1-1-1 Yayoi
|
| City |
Bunkyo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
113-8657 |
| Country |
Japan |
| |
|
| Platform ID |
GPL5473 |
| Series (1) |
| GSE13804 |
Time course effect of A-factor addition |
|
