|
| Status |
Public on Dec 31, 2005 |
| Title |
Independent sample hyb 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Independent sample of early-log phase wild-type cells
|
| Organism |
Schizosaccharomyces pombe |
| Extracted molecule |
total RNA |
| |
|
| Channel 2 |
| Source name |
Independent sample of early-log phase wild-type cells
|
| Organism |
Schizosaccharomyces pombe |
| Extracted molecule |
total RNA |
| |
|
| |
| Description |
wild-type S. pombe strain LJY1014 (h- leu1-32) at early-log growth phase in YES medium
Self-self hybridization of Independent sample of wild-type fission yeast cells at early-log growth phase
Cells were harvested from a series of independent cultures. Total RNA was extracted using a hot-phenol protocol. ~10 ? was annealed with oligo dT12-18, and reverse-transcribed into cDNA in presence of Cy3- or Cy5-coupled dUTP. Free Cy3- or Cy5-coupled dUTP was removed with a Microcon-30 concentrator. 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.
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.
Keywords = Independent S. pombe wild-type cell sample
|
| |
|
| Submission date |
Mar 28, 2005 |
| Last update date |
May 29, 2005 |
| Contact name |
Jianhua Liu |
| E-mail(s) |
liujh@gis.a-star.edu.sg
|
| Organization name |
Genome Institute of Singapore
|
| Street address |
60 Biopolis Street
|
| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL1932 |
| Series (1) |
| GSE2453 |
Independent repeat hybridizations |
|
| 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. |
| 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. |
