|
| Status |
Public on Apr 11, 2010 |
| Title |
tra1-1 strain and wild-type fission yeast third repeat |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Fission yeast cells from tra1-1 mutant
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
cDNA from Schizosaccharomyces pombe tra1-1 strain
|
| Growth protocol |
Yeast cells were cultured at 30 degree centigrade
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cDNA of the tra1-1 strain generated from total RNA as describled in materials and metholds
|
| 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
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
Reference total RNA of the WT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA of the WT cells were extracted as describled in materials and metholds
|
| 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 centigrade under MAUI system (BioMicro). Hybridized slides were washed consecutively in 2¡Á SSC/0.1% SDS for 1 min, 1¡Á SSC for 4 min, 0.2¡Á SSC for 4 min, and 0.05¡Á 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 tra1-1 strain and wild-type fission yeast third repeats
|
| 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 |
Sep 04, 2008 |
| Last update date |
Apr 11, 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) |
| GSE12674 |
TRRAP-mediated regulation of Wee1 |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
Median of log2 ratio defined by CH1/CH2 but with flagged values removed |
| 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. |
| UNF_VALUE |
Median of log2 ratio defined by CH1/ CH2 |
