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Sample GSM110521 Query DataSets for GSM110521
Status Public on May 20, 2007
Title Sugarcane transcriptome - ch1: Drought_72h_Exp_2; ch2: control_72h_2 (R)
Sample type RNA
 
Channel 1
Source name Drought_72h_Exp_2
Organism Saccharum hybrid cultivar SP90-1638
Characteristics Leaves of sugarcane, variety SP90-1638 (pool of 6 individuals) collected after 72h of exposure to drought conditions, experiment 2
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Drought_72h_control_2
Organism Saccharum hybrid cultivar SP90-1638
Characteristics Leaves of sugarcane, variety SP90-1638 (pool of 6 control plants) collected after 72h, experiment 2
Extracted molecule total RNA
Label Cy5
 
 
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with a Generation III Scanner and image intensity data were extracted with ArrayVision software.
Description Plants under drought conditions (72h) x control plants, experiment 2
Data processing Raw and background corrected data
 
Submission date May 24, 2006
Last update date Apr 09, 2010
Contact name Milton Yutaka Nishiyama Jr
E-mail(s) yutakajr@gmail.com
URL http://sucest-fun.org
Organization name Universidade de São Paulo - USP
Department Biochemistry
Lab Signal Transduction Laboratory
Street address Av. Professor Lineu Prestes, 748
City São Paulo
State/province São Paulo
ZIP/Postal code 05508-000
Country Brazil
 
Platform ID GPL3799
Series (2)
GSE4971 Sugarcane transcriptome - Drought response
GSE14732 Sugarcane genes associated with sucrose content relate to drought and cell wall metabolism

Data table header descriptions
ID_REF Spot labels
ch1_MTM Dens - RFU / µm2 Median-based Trimmed Mean density value for the spot. The reported value represents the mean of all the pixels remaining in a target, after first removing pixels with density values that exceed four median absolute deviations (MADs) above or below the median. This measure removes the influence of image artifacts (e.g., dust particles) on density estimation.
ch1_% Removed (MTM - RFU/A) Percentage of pixels excluded in the calculation of MTM Density.
ch1_MAD - RFU / µm2 Median of the absolute values of deviations from the median density (i.e., the absolute values of pixel densities - median density). It is a measure of the variation around the median density value of the spot.
ch1_SD - RFU / µm2 Standard deviation of the pixel density values
ch1_Pos X - µm Horizontal coordinate of the spot
ch1_Pos Y - µm Vertical coordinate of the spot
ch1_Area - µm2 Area of the spot
ch1_Bkgd Background density
ch1_sMTMDens Subtracted MTM Density value. MTM Density value of the spot, minus the background Density value.
ch1_S/N Signal-to-Noise Ratio. Spot density minus Background density, divided by the SD of the Background density.
ch1_Flag Valid spots receive value 0, low-quality spots receive value 1.
ch1_% At Floor Proportion of pixels at the lower limit of the density scale. Actual signal intensity may be below the threshold of detection of the imaging device.
ch1_% At Ceiling Proportion of pixels at the upper limit of the density scale (i.e., saturated). Actual signal intensity may be higher than the recorded value.
ch1_% At Floor - Bkgd Proportion of pixels within the background region that are at the lower limit of the density scale
ch1_% At Ceiling - Bkgd Proportion of pixels within the background region that are at the upper limit of the density scale
ch2_MTM Dens - RFU / µm2 Median-based Trimmed Mean density value for the spot. The reported value represents the mean of all the pixels remaining in a target, after first removing pixels with density values that exceed four median absolute deviations (MADs) above or below the median. This measure removes the influence of image artifacts (e.g., dust particles) on density estimation.
ch2_% Removed (MTM - RFU/A) Percentage of pixels excluded in the calculation of MTM Density.
ch2_MAD - RFU / µm2 Median of the absolute values of deviations from the median density (i.e., the absolute values of pixel densities - median density). It is a measure of the variation around the median density value of the spot.
ch2_SD - RFU / µm2 Standard deviation of the pixel density values
ch2_Pos X - µm Horizontal coordinate of the spot
ch2_Pos Y - µm Vertical coordinate of the spot
ch2_Area - µm2 Area of the spot
ch2_Bkgd Background density
ch2_sMTMDens Subtracted MTM Density value. MTM Density value of the spot, minus the background Density value.
ch2_S/N Signal-to-Noise Ratio. Spot density minus Background density, divided by the SD of the Background density.
ch2_Flag Valid spots receive value 0, low-quality spots receive value 1.
ch2_% At Floor Proportion of pixels at the lower limit of the density scale. Actual signal intensity may be below the threshold of detection of the imaging device.
ch2_% At Ceiling Proportion of pixels at the upper limit of the density scale (i.e., saturated). Actual signal intensity may be higher than the recorded value.
ch2_% At Floor - Bkgd Proportion of pixels within the background region that are at the lower limit of the density scale
ch2_% At Ceiling - Bkgd Proportion of pixels within the background region that are at the upper limit of the density scale
Ratio (sMTMDens): ch_1 / ch_2 Expression ratio
VALUE Logratios: base-2 log of ch_1 / ch_2

Data table
ID_REF ch1_MTM Dens - RFU / µm2 ch1_% Removed (MTM - RFU/A) ch1_MAD - RFU / µm2 ch1_SD - RFU / µm2 ch1_Pos X - µm ch1_Pos Y - µm ch1_Area - µm2 ch1_Bkgd ch1_sMTMDens ch1_S/N ch1_Flag ch1_% At Floor ch1_% At Ceiling ch1_% At Floor - Bkgd ch1_% At Ceiling - Bkgd ch2_MTM Dens - RFU / µm2 ch2_% Removed (MTM - RFU/A) ch2_MAD - RFU / µm2 ch2_SD - RFU / µm2 ch2_Pos X - µm ch2_Pos Y - µm ch2_Area - µm2 ch2_Bkgd ch2_sMTMDens ch2_S/N ch2_Flag ch2_% At Floor ch2_% At Ceiling ch2_% At Floor - Bkgd ch2_% At Ceiling - Bkgd Ratio (sMTMDens): ch_1 / ch_2 VALUE
1 : 1 - 1 15.555 0 2.316 2.712 475 59625 25600 10.548 5.007 10.38 0 0 0 0 0 6.267 0 1.822 2.113 475 59625 25600 1.729 4.537 22.371 0 0 0 0 0 1.104 0.14274
1 : 1 - 2 14.847 6.25 1.002 2.323 725 59635 25600 10.702 4.145 8.321 0 0 0 0 0 4.167 6.25 0.514 1.035 725 59635 25600 1.871 2.296 10.072 0 0 0 0 0 1.805 0.852
1 : 1 - 3 21.18 1.563 2.088 3.453 965 59635 25600 10.853 10.327 19.303 0 0 0 0 0 13.261 0 2.983 3.782 965 59635 25600 1.925 11.336 49.467 0 0 0 0 0 0.911 -0.13448
1 : 1 - 4 20.053 0.781 1.244 1.899 1245 59635 25600 10.964 9.089 16.754 0 0 0 0 0 4.394 0 0.681 0.952 1245 59635 25600 2.04 2.354 5.663 0 0 0 0 0 3.861 1.94897
1 : 1 - 5 23.129 2.344 2.575 3.915 1505 59615 25600 10.976 12.154 21.332 0 0 0 0 0 14.533 0 5.362 5.855 1505 59615 25600 2.053 12.48 31.954 0 0 0 0 0 0.974 -0.03801
1 : 1 - 6 29.826 5.078 3.533 6.606 1775 59625 25600 11.005 18.82 31.044 0 0 0 0 0 23.634 10.156 3.031 6.559 1775 59625 25600 1.889 21.745 106.728 0 0 0 0 0 0.865 -0.20923
1 : 1 - 7 11.182 9.766 0.434 1.235 2035 59635 25600 10.98 0.202 0.352 0 0 0 0 0 2.2 0.391 0.167 0.237 2035 59635 25600 1.839 0.361 1.779 0 0 0 0 0 0.559 -0.83908
1 : 1 - 8 15.032 7.813 1.382 2.765 2275 59625 25600 10.83 4.201 8.316 0 0 0 0 0 2.687 0.781 0.361 0.529 2275 59625 25600 1.844 0.843 4.084 0 0 0 0 0 4.984 2.3173
1 : 1 - 9 14.5 5.859 0.743 1.482 2575 59615 25600 10.583 3.917 7.922 0 0 0 0 0 4.406 0 0.48 0.726 2575 59615 25600 1.854 2.552 13.353 0 0 0 0 0 1.535 0.61824
1 : 1 - 10 11.291 5.469 0.793 1.418 2935 59615 25600 10.512 0.779 1.521 0 0 0 0 0 1.994 0.781 0.156 0.236 2935 59615 25600 1.851 0.144 0.65 0 0 0 0 0 5.422 2.43883
1 : 1 - 11 61.796 2.344 6.398 10.195 3175 59625 25600 10.579 51.217 99.515 0 0 0 0 0 60.15 2.344 6.36 10.651 3175 59625 25600 1.819 58.331 256.302 0 0 0 0 0 0.878 -0.18771
1 : 1 - 12 13.805 4.688 0.631 1.19 3465 59615 25600 10.583 3.222 1.723 0 0 0 0 0 4.021 0.781 0.395 0.623 3465 59615 25600 1.806 2.215 5.969 0 0 0 0 0 1.454 0.54003
1 : 1 - 13 10.601 6.25 0.388 1.067 3795 59615 25600 10.603 0 0 0 0 0 0 0 1.767 0.781 0.138 0.191 3795 59615 25600 1.756 0.011 0.028 0 0 0 0 0 0 null
1 : 1 - 14 124.111 0 17.277 26.744 4065 59615 25600 10.632 113.479 207.06 0 0 0 0 0 109.164 0 24.489 29.848 4065 59615 25600 1.809 107.355 442.346 0 0 0 0 0 1.057 0.07998
1 : 1 - 15 37.688 7.031 4.89 8.938 4365 59625 25600 10.736 26.952 50.96 0 0 0 0 0 27.717 0 4.588 7.292 4365 59625 25600 1.796 25.921 115.89 0 0 0 0 0 1.04 0.05658
1 : 1 - 16 11.834 3.125 0.912 1.388 4685 59615 25600 10.882 0.951 1.631 0 0 0 0 0 1.685 6.641 0.145 0.544 4685 59615 25600 1.7 0 0 0 0 0 0 0 1e+100 null
1 : 1 - 17 28.201 7.813 1.049 2.788 4965 59605 25600 11.197 17.004 25.586 0 0 0 0 0 14.576 0 2.094 2.79 4965 59605 25600 1.804 12.772 38.726 0 0 0 0 0 1.331 0.41251
1 : 1 - 18 32.911 0.391 4.128 5.3 5265 59605 25600 11.246 21.666 32.258 0 0 0 0 0 37.304 0 9.135 10.786 5265 59605 25600 1.843 35.461 109.25 0 0 0 0 0 0.611 -0.71076
1 : 1 - 19 13.587 1.953 0.66 1.08 5555 59605 25600 11.577 2.009 2.829 0 0 0 0 0 3.797 0 0.763 0.923 5555 59605 25600 1.799 1.998 9.155 0 0 0 0 0 1.006 0.00863
1 : 1 - 20 39.867 11.719 3.317 7.6 5835 59605 25600 11.803 28.065 40.295 0 0 0 0 0 50.51 1.563 6.325 11.009 5835 59605 25600 1.814 48.696 224.912 0 0 0 0 0 0.576 -0.79586

Total number of rows: 4608

Table truncated, full table size 734 Kbytes.




Supplementary data files not provided
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