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Sample GSM110517 Query DataSets for GSM110517
Status Public on May 20, 2007
Title Sugarcane transcriptome - ch1: Drought_24h_Exp_2; ch2: control_24h_2 (R)
Sample type RNA
 
Channel 1
Source name Drought_24h_Exp_2
Organism Saccharum hybrid cultivar SP90-1638
Characteristics Leaves of sugarcane, variety SP90-1638 (pool of 6 individuals) collected after 24h of exposure to drought conditions, experiment 2
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Drought_24h_control_2
Organism Saccharum hybrid cultivar SP90-1638
Characteristics Leaves of sugarcane, variety SP90-1638 (pool of 6 control plants) collected after 24h, 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 (24h) 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 27.525 0 3.207 4.303 505 58855 25600 20.665 6.86 4.404 0 0 0 0 0 5.604 1.172 0.581 0.87 525 58855 25600 4.533 1.071 1.651 0 0 0 0 0 6.406 2.67942
1 : 1 - 2 21.824 1.172 1.186 1.809 765 58835 25600 21.016 0.807 0.501 0 0 0 0 0 5.408 0.391 0.518 0.714 785 58835 25600 4.543 0.865 1.352 0 0 0 0 0 0.934 -0.09851
1 : 1 - 3 24.98 2.734 1.316 2.248 1005 58855 25600 22.499 2.481 1.239 0 0 0 0 0 7.483 0 1.06 1.277 1025 58855 25600 4.664 2.819 4.157 0 0 0 0 0 0.88 -0.18442
1 : 1 - 4 26.068 0 1.594 2.263 1305 58835 25600 23.39 2.678 1.469 0 0 0 0 0 4.87 1.172 0.458 0.773 1325 58835 25600 4.801 0.069 0.101 0 0 0 0 0 38.827 5.27899
1 : 1 - 5 24.9 0 1.383 2.016 1545 58845 25600 23.099 1.801 0.982 0 0 0 0 0 9.513 0 2.183 2.4 1565 58845 25600 4.851 4.662 6.856 0 0 0 0 0 0.386 -1.37333
1 : 1 - 6 30.009 0.391 1.66 2.446 1825 58855 25600 22.829 7.18 4.061 0 0 0 0 0 9.896 1.953 0.899 1.417 1845 58855 25600 4.664 5.232 7.299 0 0 0 0 0 1.372 0.45628
1 : 1 - 7 20.403 0.781 1.073 1.462 2125 58835 25600 21.708 0 0 0 0 0 0 0 4.388 0.391 0.404 0.583 2145 58835 25600 4.323 0.065 0.105 0 0 0 0 0 0 null
1 : 1 - 8 23.755 0 1.392 2.047 2375 58855 25600 20.249 3.506 1.859 0 0 0 0 0 4.81 1.172 0.474 0.702 2395 58855 25600 4.228 0.581 0.89 0 0 0 0 0 6.031 2.5924
1 : 1 - 9 21.304 2.734 1.362 2.187 2655 58835 25600 19.575 1.729 1.129 0 0 0 0 0 6.047 1.172 0.641 1.01 2675 58835 25600 4.165 1.882 2.909 0 0 0 0 0 0.919 -0.12186
1 : 1 - 10 18.72 2.344 1.015 1.648 2945 58835 25600 19.314 0 0 0 0 0 0 0 4.249 0.781 0.393 0.588 2965 58835 25600 4.155 0.093 0.154 0 0 0 0 0 0 null
1 : 1 - 11 41.091 6.25 3.018 5.292 3245 58845 25600 19.411 21.68 14.775 0 0 0 0 0 40.63 2.734 3.691 6.257 3265 58845 25600 4.183 36.447 55.793 0 0 0 0 0 0.595 -0.74904
1 : 1 - 12 20.206 0.781 1.212 1.767 3565 58835 25600 19.532 0.674 0.425 0 0 0 0 0 4.6 7.031 0.588 1.304 3585 58835 25600 4.115 0.486 0.75 0 0 0 0 0 1.387 0.47197
1 : 1 - 13 20.225 0 1.271 1.742 3865 58835 25600 20.027 0.198 0.102 0 0 0 0 0 4.054 0.391 0.419 0.622 3885 58835 25600 4.074 0 0 0 0 0 0 0 1e+100 null
1 : 1 - 14 91.656 4.297 11.4 20.262 4145 58835 25600 20.172 71.484 35.384 0 0 0 0 0 151.735 0 36.237 45.571 4165 58835 25600 4.084 147.651 238.798 0 0 0 0 0 0.484 -1.04692
1 : 1 - 15 29.094 1.563 1.952 2.936 4435 58845 25600 18.793 10.301 5.106 0 0 0 0 0 21.662 1.563 2.282 3.555 4455 58845 25600 3.945 17.717 28.698 0 0 0 0 0 0.581 -0.78339
1 : 1 - 16 17.578 1.172 0.912 1.446 4735 58835 25600 19.287 0 0 0 0 0 0 0 3.764 1.953 0.375 0.587 4755 58835 25600 4.025 0 0 0 0 0 0 0 0 null
1 : 1 - 17 26.249 0.391 1.487 2.11 5045 58835 25600 20.631 5.618 0.385 0 0 0 0 0 14.1 0.391 1.531 2.124 5065 58835 25600 4.129 9.971 4.026 0 0 0 0 0 0.563 -0.82879
1 : 1 - 18 28.792 0 1.709 2.543 5335 58835 25600 19.88 8.912 4.521 0 0 0 0 0 18.257 0 2.363 3.317 5355 58835 25600 3.994 14.262 24.697 0 0 0 0 0 0.625 -0.67807
1 : 1 - 19 20.164 0.781 1.211 1.899 5615 58835 25600 19.874 0.291 0.126 0 0 0 0 0 4.457 0 0.452 0.665 5635 58835 25600 3.945 0.511 0.813 0 0 0 0 0 0.568 -0.81604
1 : 1 - 20 27.287 3.516 1.452 2.448 5905 58835 25600 20.956 6.33 2.494 0 0 0 0 0 11.189 2.344 1.067 1.74 5925 58835 25600 3.934 7.255 11.187 0 0 0 0 0 0.873 -0.19595

Total number of rows: 4608

Table truncated, full table size 725 Kbytes.




Supplementary data files not provided
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