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Sample GSM110519 Query DataSets for GSM110519
Status Public on May 20, 2007
Title Sugarcane transcriptome - ch2: Drought_72h_Exp_1; ch1: control_72h_1 (R)
Sample type RNA
 
Channel 1
Source name Drought_72h_control_1
Organism Saccharum hybrid cultivar SP90-1638
Characteristics Leaves of sugarcane, variety SP90-1638 (pool of 6 control plants) collected after 72h, experiment 1
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Drought_72h_Exp_1
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 1
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 1
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 49.37 0 6.96 10.104 555 59745 25600 29.224 20.145 8.394 0 0 0 0 0 46.089 0 8.257 10.242 555 59745 25600 20.938 25.151 25.192 0 0 0 0 0 0.801 -0.32013
1 : 1 - 2 36.77 7.422 1.566 3.293 805 59745 25600 29.15 7.619 6.139 0 0 0 0 0 19.228 0.391 1.002 1.504 805 59745 25600 21.612 0 0 0 0 0 0 0 1e+100 null
1 : 1 - 3 43.846 8.594 2.145 4.21 1055 59745 25600 29.556 14.29 11.241 0 0 0 0 0 32.038 0.781 3.19 4.698 1055 59745 25600 21.721 10.317 10.924 0 0 0 0 0 1.385 0.46989
1 : 1 - 4 42.86 9.766 1.747 3.929 1355 59725 25600 29.187 13.673 10.28 0 0 0 0 0 15.155 9.375 0.957 2.036 1355 59725 25600 21.199 0 0 0 0 0 0 0 1e+100 null
1 : 1 - 5 47.475 0 5.326 6.505 1615 59725 25600 28.858 18.617 16.487 0 0 0 0 0 31.129 0 6.365 8.323 1615 59725 25600 20.759 10.37 3.005 0 0 0 0 0 1.795 0.84398
1 : 1 - 6 58.391 10.547 3.647 8.294 1885 59735 25600 29.124 29.267 22.651 0 0 0 0 0 41.482 5.859 3.013 5.575 1885 59735 25600 20.481 21.001 5.984 0 0 0 0 0 1.394 0.47923
1 : 1 - 7 30.015 9.375 1.058 2.703 2185 59725 25600 29.28 0.734 0.571 0 0 0 0 0 20.884 0.781 1.202 1.846 2185 59725 25600 20.113 0.771 0.807 0 0 0 0 0 0.952 -0.07097
1 : 1 - 8 31.039 1.172 2.144 2.794 2495 59725 25600 28.615 2.423 1.739 0 0 0 0 0 17.333 0 1.497 1.777 2495 59725 25600 19.63 0 0 0 0 0 0 0 1e+100 null
1 : 1 - 9 32.952 2.734 2.638 4.291 2765 59725 25600 27.661 5.291 4.682 0 0 0 0 0 16.846 0 1.526 1.988 2765 59725 25600 19.917 0 0 0 0 0 0 0 1e+100 null
1 : 1 - 10 27.941 6.641 1.1 2.301 3065 59725 25600 27.351 0.59 0.522 0 0 0 0 0 16.976 0 2.311 2.779 3065 59725 25600 20.104 0 0 0 0 0 0 0 1e+100 null
1 : 1 - 11 79.356 16.797 4.202 15.239 3305 59735 25600 27.265 52.091 36.807 0 0 0 0 0 103.783 12.891 9.293 25.163 3305 59735 25600 19.32 84.463 93.193 0 0 0 0 0 0.617 -0.69666
1 : 1 - 12 30.182 6.641 0.95 1.934 3605 59725 25600 26.89 3.292 2.094 0 0 0 0 0 22.053 9.766 1.34 2.654 3605 59725 25600 19.423 2.63 1.692 0 0 0 0 0 1.252 0.32423
1 : 1 - 13 26.959 5.859 1.013 1.922 3915 59725 25600 26.79 0.169 0.103 0 0 0 0 0 19.563 2.344 0.794 1.27 3915 59725 25600 19.843 0 0 0 0 0 0 0 1e+100 null
1 : 1 - 14 206.6 0.391 25.415 36.096 4195 59715 25600 26.549 180.051 109.792 0 0 0 0 0 283.286 0 31.482 48.368 4195 59715 25600 19.834 263.452 173.858 0 0 0 0 0 0.683 -0.55004
1 : 1 - 15 90.399 0.781 18.95 29.213 4495 59735 25600 25.762 64.636 50.602 0 0 0 0 0 108.274 0 27.325 39.17 4495 59735 25600 19.706 88.568 77.205 0 0 0 0 0 0.73 -0.45403
1 : 1 - 16 26.473 4.297 0.8 1.668 4795 59725 25600 25.502 0.972 0.673 0 0 0 0 0 15.727 0 2.466 2.64 4795 59725 25600 19.23 0 0 0 0 0 0 0 1e+100 null
1 : 1 - 17 57.248 1.172 3.357 4.614 5085 59715 25600 25.509 31.739 21.245 0 0 0 0 0 54.671 0 8.911 9.886 5085 59715 25600 19.164 35.507 31.07 0 0 0 0 0 0.894 -0.16165
1 : 1 - 18 59.003 0 6.404 8.799 5375 59715 25600 25.634 33.369 22.74 0 0 0 0 0 58.185 0 9.133 11.476 5375 59715 25600 19.206 38.98 36.53 0 0 0 0 0 0.856 -0.22432
1 : 1 - 19 28.633 1.953 1.137 1.919 5665 59715 25600 26.182 2.45 0.72 0 0 0 0 0 23.508 0 1.577 2.318 5665 59715 25600 19.08 4.428 4.934 0 0 0 0 0 0.553 -0.85465
1 : 1 - 20 85.089 11.328 7.089 15.231 5945 59715 25600 29.117 55.972 15.334 0 0 0 0 0 48.657 1.953 3.937 6.866 5945 59715 25600 19.116 29.542 32.863 0 0 0 0 0 1.895 0.9222

Total number of rows: 4608

Table truncated, full table size 744 Kbytes.




Supplementary data files not provided
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