|
| Status |
Public on May 24, 2005 |
| Title |
Filling panicle AP2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Panicle(or root or panicle etc)
|
| Organism |
Oryza sativa Indica Group |
| Extracted molecule |
total RNA |
| |
|
| Channel 2 |
| Source name |
cultured cell (for all samples)
|
| Organism |
Oryza sativa Indica Group |
| Extracted molecule |
total RNA |
| |
|
| |
| Description |
Panicle vs cultured cell
Sample_extract_protocol_ch[1]: Trizol/RNeasy
Sample_extract_protocol_ch[2]: Trizol/RNeasy
Sample_hyb_protocol: 42C 50% formamide
Sample_label_ch[1]: cy5
Sample_label_ch[2]: cy3
Sample_label_protocol_ch[1]: amino-allyl and monofunctional dye
Sample_label_protocol_ch[2]: amino-allyl and monofunctional dye
Sample_molecule_ch[1]: total RNA
Sample_molecule_ch[2]: total RNA
Sample_organism_ch[1]: Oryza sativa (indica cultivar-group)
Sample_organism_ch[2]: Oryza sativa (indica cultivar-group)
Sample_scan_protocol: Axon GenePix 4000B
Sample_specimen_provider_ch[1]: Deng
Sample_specimen_provider_ch[2]: Deng
Sample_transformation: raw data
|
| |
|
| Submission date |
May 19, 2005 |
| Last update date |
May 29, 2005 |
| Contact name |
Ligeng Ma |
| E-mail(s) |
ligeng.ma@yale.edu
|
| Phone |
203-432-8909
|
| Organization name |
Yale University
|
| Department |
Molecular, Cellular & Developmental Biology
|
| Lab |
Deng Lab
|
| Street address |
165 Prospect
|
| City |
NEW HAVEN |
| State/province |
CT |
| ZIP/Postal code |
06520 |
| Country |
USA |
| |
|
| Platform ID |
GPL1773 |
| Series (1) |
| GSE2691 |
Rice Transcriptome - Slide A; Slide B |
|
| Data table header descriptions |
| ID_REF |
ID in YMD – Yale Microarray Database |
| CH1_median |
Channel 1 (635 nm, Cy5, Experiment) median pixel intensity |
| CH2_median |
Channel 2 (532 nm, Cy3, Reference) median pixel intensity |
| CH1_back |
Channel 1 Background |
| CH2_back |
Channel 2 Background |
| CH1_MEAN |
Channel 1 Mean |
| CH2_MEAN |
|
| CH1_SD |
Channel 1 Standard Deviation |
| CH2_SD |
Channel 2 Standard Deviation |
| pixels |
Number of pixels used to determine signal. |
| bpixels |
Number of pixels used to determine background. |
| x |
X-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image |
| y |
Y-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image |
| diameter |
diameter in µm of the feature-indicator |
| %>CH1_back+1SD |
percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, for Channel 1 |
| %>CH1_back+2SD |
percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, for Channel 1 |
| %>CH2_back+1SD |
percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, for Channel 2 |
| %>CH2_back+2SD |
percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, for Channel 2 |
| CH1_%Sat |
percentage of pixel saturation within feature for Channel 1 |
| CH2_%Sat |
percentage of pixel saturation within feature for Channel 2 |
| QUALITY |
Compute median for the "B635 median" and "B532 median" respectively. Store them in median_B635 and median_B532 respectively. For each row, set quality to 0 if any of following is true: a: "F635 Median - B635"/max(median_B635 ,"B635 Median")<1 and "F532 Median - B532"/max(median_B532,"B532 Median")<1; b: flag <0; c: "% > B532+1SD" <75 and "% > B635+1SD" <75. else, set the quality to 1 |
| flag |
An extension of GenePix 3.0 flags described at http://twiki.med.yale.edu/twiki/bin/view/YMD/YMDFlagFields |
| ratio_calc |
(CH1_median-CH1_back)/(CH2_median-CH2_back) |
| VALUE |
log ratio (log2 of PRE_VALUE) |
| norm_factor |
Normalization factor calculated as described at http://twiki.med.yale.edu/twiki/bin/view/YMD/NormalizationAndFilterMethods |
| PRE_VALUE |
[(Experiment channel median intensity - background)/(Reference channel median intensity - background)]*(norm_factor) |
