|
| Status |
Public on Jan 08, 2010 |
| Title |
CZQ_C delta94_8HU_010min_R2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Fission yeast cells, CZQ_C delta94_8HU_010min_R2
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
CZQ_C delta94, 8 mM HU treated, 010min
|
| Growth protocol |
Schizosaccharomyces pombe rep2 truncations and a site mutation cells indicated growing in YES medium to mid log phase treated with 8 mM HU for various time points with two repeat. Yeast cells were cultured at 30 degree centigrade.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of tissue samples were extracted using hot phenol methold described in materials and methods.
|
| Label |
Cy5
|
| Label protocol |
For fluorescence labeling of cDNAs, ~30 micro gram total RNA was used to synthesize cDNA coupled with amino allyl-dUTP (aa-dUTP) by reverse transcriptase (Superscript-II, Invitrogen, Carlsbad, CA). cDNA was subsequently washed with Milli-Q water using microcon-YM30 (Millipore, Billerica,MA). ~1.5 micro gram cDNA was used to couple with Cy5-fluorescence dye for 1 h in dark and purified through a spin column (Qiagen, Hilden, Germany) followed by washing on a micorcon YM-30.
|
| |
|
| Channel 2 |
| Source name |
Fission yeast wildtype cells, reference
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
Reference RNA was obtained by pooling equal amount of total RNA extracted from Schizosaccharomyces pombe mid-log phase cells (OD600 was around 0.3) growing at 30 degree centigrade.
|
| Growth protocol |
Reference RNA was obtained by pooling equal amount of total RNA extracted from Schizosaccharomyces pombe mid-log phase cells (OD600 was around 0.3) growing at 30 degree centigrade.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of tissue samples were extracted using hot phenol methold described in materials and methods.
|
| Label |
Cy3
|
| Label protocol |
For fluorescence labeling of cDNAs, ~30 micro gram total RNA was used to synthesize cDNA coupled with amino allyl-dUTP (aa-dUTP) by reverse transcriptase (Superscript-II, Invitrogen, Carlsbad, CA) according to manufacturer's instruction. cDNA was subsequently washed with Milli-Q water using microcon-YM30 (Millipore, Billerica,MA). ~1.5 micro gram cDNA was used to couple with Cy3-fluorescence dye for 1 h in dark and purified through a spin column (Qiagen, Hilden, Germany) followed by washing on a micorcon YM-30.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed using EasyHyb solution (Roche) in a MUAI mixer (BioMicro systems). Hybridized slides were washed in a series of buffers containing various concentration of SSC (2x - 0.2x) with or without 1% SDS.
|
| 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 |
Schizosaccharomyces pombe ployg mutant cells growing in YES medium at 30 degree centigrade vs Schizosaccharomyces pombe asynchronized mid log phase WT cells (OD600 was around 0.3).
|
| 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. Medians of log base 2 expression ratios were given in the data table.
|
| |
|
| Submission date |
Mar 20, 2008 |
| Last update date |
Jan 29, 2009 |
| Contact name |
Zhaoqing Chu |
| E-mail(s) |
chuz@gis.a-star.edu.sg
|
| Phone |
65-64788128
|
| Organization name |
Genome Institute of Singapore
|
| Street address |
60, Biopolis Streat
|
| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL1932 |
| Series (1) |
| GSE10901 |
Altered genes expression profile of Rep2 mutants in Fission Yeast upon HU treatment. |
|
| Data table header descriptions |
| ID_REF |
Unique ID |
| VALUE |
Median of log2 ratio defined by CH1/CH2 but with flagged values (-50, -75) 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. |
| 2Fold_F/B |
Denotes which features met our filtering criterion. Zero value means that the feature whose intensity did not pass either F635/B635>=2 or F532/B532>=2, that is, low-intensity features. |
| UNF_VALUE |
Median of log2 ratio defined by CH1/CH2 |
