|
| Status |
Public on May 31, 2014 |
| Title |
JYH_dsk1_-N2_060m.gpr_1104 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
fission yeast culture of //kinase deletion strain// (OD600 was around 0.3) in Minimal Mediium without nitrogen supplement for 60min or // 60m //
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: kinase deletion
|
| Growth protocol |
Yeast cells were cultivated at 30 degree centigrade.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of cell samples were extracted using a hot phenol protocol describled in materials and metholds.
|
| Label |
Cy5
|
| Label protocol |
For fluorescence labeling of cDNAs, ~30 micro gramme 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 gramme 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
|
| |
|
| Channel 2 |
| Source name |
Fission yeast cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: pool of wild type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of cell samples were extracted using a hot phenol protocol describled in materials and metholds.
|
| Label |
Cy3
|
| Label protocol |
For fluorescence labeling of cDNAs, ~30 micro gramme 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 gramme 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
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.
|
| 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 3.0 or 4.0 analysis software.
|
| Description |
fission yeast log-phase growing kinase mutant cells in minimal medium with nitrogen supplement (0min).
|
| 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 |
May 31, 2013 |
| Last update date |
May 31, 2014 |
| 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) |
| GSE47544 |
Transcriptional profiling analysis of S. pombe kinase deletin strains treated (60min) or untreated (0min) with nitrogen starvation in comparison with a common reference. |
|
