|
Status |
Public on Sep 20, 2006 |
Title |
Rice suspension cells under suc starvation for 12 hours, replicate 2 |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
Oryza sativa suspension cells under suc starvation for 12 hours
|
Organism |
Oryza sativa |
Characteristics |
Oryza sativa cv Tainung67 suspension cells culture in suc free medium for 12 hours.
|
Growth protocol |
Oryza sativa suspension cells cultured in Murashige and Skoog medium without sucrose for 12 hours.
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Total RNA was extracted by use of the TripureTM Kit according to the manufacturer's manual (Genesis Biotech, Taipei, Taiwan). mRNA from control and Suc-starved cells were purified from the respective 200 ug total RNA by use of Oligotex mRNA Mini Kit (Qiagen, Valencia, CA, USA).
|
Label |
Cy5
|
Label protocol |
Total RNA extraction and mRNA purified from Suc-starved cells and the labeling of fluorescent cDNA probes were performed by the methods described in http://www.botany.sinica.edu.tw/microarray/protocols.htm
|
|
|
Channel 2 |
Source name |
Oryza sativa suspension cells control treatment for 12 hours
|
Organism |
Oryza sativa |
Characteristics |
As a control RNA, Oryza sativa cv Tainung67 suspension cells culture in medium within 3% sucrose for 12 hours.
|
Growth protocol |
Oryza sativa suspension cells cultured in Murashige and Skoog medium within 3% sucrose for 12 hours.
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Total RNA was extracted by use of the TripureTM Kit according to the manufacturer's manual (Genesis Biotech, Taipei, Taiwan). mRNA from control and Suc-starved cells were purified from the respective 200 ug total RNA by use of Oligotex mRNA Mini Kit (Qiagen, Valencia, CA, USA).
|
Label |
Cy3
|
Label protocol |
Total RNA extraction and mRNA purified from control cells and the labeling of fluorescent cDNA probes were performed by the methods described in http://www.botany.sinica.edu.tw/microarray/protocols.htm
|
|
|
|
Scan protocol |
The hybridization signals for each DNA element were detected with the use of Axon GenePix 4000B and analyzed with use of GenePix 4.0 (Axon Instruments, Inc., Union City, CA, USA).
|
Description |
Rice suspension cells under suc starvation for 12 hours, replecate 2
|
Data processing |
After background correction and removal of flagged values, log base 2 expression ratios were mean centered and linear transformed to obtain the log and linear values given in the data table.
|
|
|
Submission date |
Aug 30, 2006 |
Last update date |
Sep 19, 2006 |
Contact name |
Huei-Jing Wang |
E-mail(s) |
nkk388@gate.sinica.edu.tw
|
Organization name |
Academia sinica
|
Department |
Inst of plant and microbial biology
|
Lab |
126
|
Street address |
Academia Road, 128, Sec.2, Nankang
|
City |
Taipei |
State/province |
Taipei |
ZIP/Postal code |
11529 |
Country |
Taiwan |
|
|
Platform ID |
GPL892 |
Series (1) |
GSE5853 |
Transcriptomic adaptations in rice suspension cells under sucrose starvation |
|
Data table header descriptions |
ID_REF |
|
VALUE |
same as UNF_VALUE but with flagged values removed |
CH1_Median |
Channel 1 median intensity |
CH1_MEAN |
Channel 1 mean intensity |
CH1_SD |
Channel 1 mean standard deviation |
CH1_BKD_Median |
|
CH1_BKD_MEAN |
|
CH1_BKD_SD |
|
% > CH1_BKD_+1SD |
Percent of feature pixels that were greater than one standard deviations of the background over the background signal |
% > CH1_BKD_+2SD |
Percent of feature pixels that were greater than two standard deviations of the background over the background signal |
CH2_Median |
Channel 2 median intensity |
CH2_MEAN |
Channel 2 mean intensity |
CH2_SD |
Channel 2 mean standard deviation |
CH2_BKD_Median |
|
CH2_BKD_MEAN |
|
CH2_BKD_SD |
|
% > CH2_BKD_+1SD |
Percent of feature pixels that were greater than one standard deviations of the background over the background signal |
% > CH2_BKD_+2SD |
Percent of feature pixels that were greater than two standard deviations of the background over the background signal |
Ratio_of_Medians |
Unnormalized, untransformed ratio of medians |
Ratio_of_Means |
Unnormalized, untransformed ratio of means |
Log_Ratio |
unnormalized log2 ratio of means defined as CH1 divided by CH2 |
CH1_Median - CH1_BKD_ |
Channel 1 median signal |
CH2_Median - CH2_BKD_ |
Channel 2 median signal |
CH1_Mean - CH1_BKD_ |
Channel 1 mean signal |
CH2_Mean - CH2_BKD_ |
Channel 2 mean signal |
Flags |
0 denotes satisfactory features, while <0 denotes features that did not meet |
UNF_VALUE |
lowess Normalized log2 ratio of means defined as CH1 divided by CH2 |