|
| Status |
Public on Jul 19, 2010 |
| Title |
WT strain treated with 0.5mM H2O2 at 60min time point and WT strain with no treatment (2nd repeat) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Fission yeast cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
cDNA from WT strain treated with 0.5mM H2O2 at 60min time point (2nd repeat)
|
| Growth protocol |
Yeast cells were cultured at 30 degree Celsius
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cDNA of the WT strain treated with 0.5mM H2O2 at 60min time point generated from total RNA as described in materials and methods
|
| Label |
Cy5
|
| Label protocol |
Approximately 30 ug of total RNA was used to synthesize cDNA coupled with aa-dUTP by reverse transcriptase. Approximately 1.5 ug of cDNA was coupled with Cy5 fluorescence dye and purified through a Microcon YM-30. Cy5- and Cy3-labeled cDNA were pooled and hybridized to the spotted S. pombe oligonucleotide (oligo)-based DNA microarrays
|
| |
|
| Channel 2 |
| Source name |
cDNA from WT strain with no treatment
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
Reference total RNA of the WT strain with no treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA of the WT cells were extracted as described in materials and methods
|
| Label |
Cy3
|
| Label protocol |
Approximately 30 ug of total RNA was used to synthesize cDNA coupled with aa-dUTP by reverse transcriptase. Approximately 1.5 ug of cDNA was coupled with Cy3 fluorescence dye and purified through a Microcon YM-30. Cy5- and Cy3-labeled cDNA were pooled and hybridized to the spotted S. pombe oligonucleotide (oligo)-based DNA microarrays
|
| |
|
| |
| Hybridization protocol |
Samples were mixed with DIG Easy Hyb buffer (Roche) and Herring Sperm DNA (Invitrogen) before applying to MAUI mixer-slide assembly. The slides were hybridized overnight for 16 hours at 42 degree Celsius under MAUI system (BioMicro). Hybridized slides were washed consecutively in 2x SSC/0.1% SDS for 1 min, 1x SSC for 4 min, 0.2x SSC for 4 min, and 0.05x SSC for 1 min, and then spin-dried before scanning.
|
| Scan protocol |
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.
|
| Description |
hybridization of WT strain treated with 0.5mM H2O2 at 60min time point and WT strain with no treatment (2nd repeat)
|
| Data processing |
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software. After background correction and removal of flagged values, features with low intensity (F/B<2 at either 635 or 532 channel) were removed. Meidans of log base 2 expression ratios were given in the data table.
|
| |
|
| Submission date |
Oct 03, 2008 |
| Last update date |
Jul 19, 2010 |
| Contact name |
Majid Eshaghi |
| E-mail(s) |
meshaghi@hotmail.com
|
| Organization name |
Genome Institute of Singapore
|
| Department |
Bilogical Investigation
|
| Lab |
System Biology
|
| Street address |
Biopolis
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL1932 |
| Series (1) |
| GSE13053 |
Atf1-mediated active gene response to H2O2 challenge. |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
Median of log2 ratio defined by CH1/ CH2 |
| CH1_Median |
CH1 (F635) median fluorescence intensity |
| CH1_BKD |
CH1 (B635) background median fluorescence intensity |
| CH2_Median |
CH2 (F532) median fluorescence intensity |
| CH2_BKD |
CH2 (B532) background median fluorescence intensity |
| CH1_Median - CH1_BKD |
Channel 1 median signal - absolute intensity |
| CH2_Median - CH2_BKD |
Channel 2 median signal - absolute intensity |
| Flags |
Denotes which features met our filtering criterion. A negative value means that the feature did not have at least 60% of its pixels greater than two standard deviations over the background intensity. |
