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Sample GSM110518 Query DataSets for GSM110518
Status Public on May 20, 2007
Title Sugarcane transcriptome - ch2: Drought_72h_Exp_1; ch1: control_72h_1 (L)
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 74.34 0 11.322 16.448 865 59705 25600 34.463 39.877 28.018 0 0 0 0 0 74.934 0 14.749 18.46 885 59705 25600 24.765 50.17 52.953 0 0 0 0 0 0.795 -0.33097
1 : 1 - 2 54.876 6.25 2.756 5.256 1145 59705 25600 34.697 20.179 14.172 0 0 0 0 0 41.248 1.172 3.003 4.494 1165 59705 25600 25.329 15.919 15.419 0 0 0 0 0 1.268 0.34255
1 : 1 - 3 72.903 4.297 7.177 11.199 1415 59705 25600 34.977 37.926 26.994 0 0 0 0 0 67.043 0 7.552 11.555 1435 59705 25600 26.091 40.952 10.443 0 0 0 0 0 0.926 -0.11092
1 : 1 - 4 59.486 5.078 2.205 4.145 1705 59695 25600 35.05 24.436 17.031 0 0 0 0 0 34.56 0 2.546 3.412 1725 59695 25600 25.797 8.762 2.172 0 0 0 0 0 2.789 1.47975
1 : 1 - 5 62.723 0 9.565 12.183 1955 59685 25600 34.887 27.835 15.933 0 0 0 0 0 55.377 0 12.088 14.941 1975 59685 25600 25.453 29.924 30.405 0 0 0 0 0 0.93 -0.1047
1 : 1 - 6 116.824 9.375 13.238 26.744 2225 59705 25600 34.346 82.478 51.602 0 0 0 0 0 111.96 3.906 13.283 22.002 2245 59705 25600 25.609 86.351 92.202 0 0 0 0 0 0.955 -0.06643
1 : 1 - 7 35.905 10.547 1.41 3.551 2545 59685 25600 34.197 1.707 1.106 0 0 0 0 0 26.062 6.641 1.221 2.367 2565 59685 25600 25.606 0.456 0.409 0 0 0 0 0 3.745 1.90497
1 : 1 - 8 47.93 9.766 4.154 9.317 2815 59685 25600 34.624 13.306 8.013 0 0 0 0 0 28.363 9.375 5.545 11.189 2835 59685 25600 26.056 2.307 1.936 0 0 0 0 0 5.767 2.52782
1 : 1 - 9 60.908 12.109 3.135 9.474 3095 59695 25600 34.673 26.235 10.163 0 0 0 0 0 31.617 0 3.935 4.823 3115 59695 25600 25.762 5.854 4.931 0 0 0 0 0 4.481 2.16382
1 : 1 - 10 46.981 0 6.255 7.132 3435 59685 25600 35.038 11.944 4.221 0 0 0 0 0 22.515 0 1.949 2.439 3455 59685 25600 25.425 0 0 0 0 0 0 0 1e+100 null
1 : 1 - 11 209.681 12.891 25.1 68.01 3675 59695 25600 35.531 174.149 75.827 0 0 0 0 0 384.308 19.922 30.077 118.787 3695 59695 25600 24.724 359.584 199.62 0 0 0 0 0 0.484 -1.04692
1 : 1 - 12 44.133 3.516 1.512 2.977 3975 59685 25600 33.977 10.156 4.109 0 0 0 0 0 36.033 13.281 1.849 4.748 3995 59685 25600 23.757 12.276 11.845 0 0 0 0 0 0.827 -0.27404
1 : 1 - 13 33.95 6.641 1.344 2.737 4295 59685 25600 33.118 0.832 0.433 0 0 0 0 0 23.662 7.031 0.996 1.915 4315 59685 25600 23.42 0.242 0.168 0 0 0 0 0 3.443 1.78367
1 : 1 - 14 231.714 10.547 8.417 24.072 4575 59685 25600 32.524 199.19 120.017 0 0 0 0 0 322.009 3.516 19.151 32.474 4595 59685 25600 23.102 298.907 199.235 0 0 0 0 0 0.666 -0.58641
1 : 1 - 15 134.064 0 29.688 37.577 4875 59695 25600 31.776 102.288 77.662 0 0 0 0 0 174.036 0 47.209 58.298 4895 59695 25600 23.178 150.858 129.092 0 0 0 0 0 0.678 -0.56064
1 : 1 - 16 31.84 5.859 1.206 2.319 5175 59685 25600 31.606 0.234 0.176 0 0 0 0 0 18.389 0 2.837 3.47 5195 59685 25600 23.115 0 0 0 0 0 0 0 1e+100 null
1 : 1 - 17 62.172 6.641 2.325 5.382 5465 59685 25600 32.055 30.117 19.875 0 0 0 0 0 50.78 0.391 3.19 4.498 5485 59685 25600 23.337 27.443 15.577 0 0 0 0 0 1.097 0.13356
1 : 1 - 18 113.606 1.172 14.993 23.297 5755 59675 25600 31.962 81.643 29.48 0 0 0 0 0 109.193 0 18.254 28.132 5775 59675 25600 22.8 86.394 45.186 0 0 0 0 0 0.945 -0.08161
1 : 1 - 19 36.24 0 2.157 3.202 6025 59685 25600 30.999 5.241 1.933 0 0 0 0 0 31.351 0 3.087 3.775 6045 59685 25600 22.865 8.485 6.488 0 0 0 0 0 0.618 -0.69432
1 : 1 - 20 180.117 26.953 9.18 41.883 6305 59685 25600 31.375 148.742 80.462 0 0 0 0 0 143.975 16.797 11.436 30.51 6325 59685 25600 23.827 120.147 98.832 0 0 0 0 0 1.238 0.30801

Total number of rows: 4608

Table truncated, full table size 753 Kbytes.




Supplementary data files not provided
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