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Sample GSM110516 Query DataSets for GSM110516
Status Public on May 20, 2007
Title Sugarcane transcriptome - ch1: Drought_24h_Exp_2; ch2: control_24h_2 (L)
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 56.723 0 9.674 11.406 835 58825 25600 32.952 23.771 10.479 0 0 0 0 0 9.626 0 1.367 1.719 845 58825 25600 6.219 3.407 4.944 0 0 0 0 0 6.977 2.80261
1 : 1 - 2 40.04 0 2.519 3.581 1095 58815 25600 33.578 6.462 2.958 0 0 0 0 0 13.296 0 1.732 2.243 1105 58815 25600 6.195 7.101 10.175 0 0 0 0 0 0.91 -0.13606
1 : 1 - 3 47.574 0.781 3.238 4.898 1375 58815 25600 34.378 13.195 5.4 0 0 0 0 0 20.569 0 3.7 4.681 1385 58815 25600 6.255 14.315 19.83 0 0 0 0 0 0.922 -0.11716
1 : 1 - 4 40.817 0.391 2.135 2.909 1645 58805 25600 34.977 5.841 2.597 0 0 0 0 0 9.213 0.391 0.704 0.985 1655 58805 25600 6.428 2.786 3.76 0 0 0 0 0 2.097 1.06833
1 : 1 - 5 43.998 0.391 3.434 4.875 1905 58805 25600 34.169 9.829 4.611 0 0 0 0 0 18.924 0 5.753 6.501 1915 58805 25600 6.562 12.362 15.93 0 0 0 0 0 0.795 -0.33097
1 : 1 - 6 63.685 4.688 4.755 8.623 2175 58815 25600 33.554 30.132 14.548 0 0 0 0 0 28.72 3.125 2.636 4.084 2185 58815 25600 6.711 22.009 20.715 0 0 0 0 0 1.369 0.45312
1 : 1 - 7 30.446 0.781 1.384 1.935 2505 58795 25600 31.869 0 0 0 0 0 0 0 6.558 0.391 0.55 0.831 2515 58795 25600 6.652 0 0 0 0 0 0 0 0 null
1 : 1 - 8 36.831 3.125 1.995 3.449 2745 58815 25600 29.866 6.964 3.528 0 0 0 0 0 8.633 0 1.349 1.915 2755 58815 25600 6.459 2.174 2.554 0 0 0 0 0 3.203 1.67942
1 : 1 - 9 37.471 0.391 2.272 3.301 3045 58805 25600 28.969 8.503 4.418 0 0 0 0 0 17.039 0 2.408 3.188 3055 58805 25600 6.222 10.817 12.896 0 0 0 0 0 0.786 -0.3474
1 : 1 - 10 27.831 2.734 1.221 1.999 3405 58795 25600 28.707 0 0 0 0 0 0 0 6.45 0.391 0.63 0.876 3415 58795 25600 6.147 0.303 0.335 0 0 0 0 0 0 null
1 : 1 - 11 131.307 2.734 14.715 22.877 3635 58795 25600 28.417 102.889 52.709 0 0 0 0 0 169.91 0 25.489 31.613 3645 58795 25600 6.225 163.685 192.726 0 0 0 0 0 0.629 -0.66887
1 : 1 - 12 31.151 1.563 1.255 1.891 3935 58805 25600 28.121 3.03 1.623 0 0 0 0 0 8.852 0.391 0.915 1.318 3945 58805 25600 6.081 2.771 3.712 0 0 0 0 0 1.093 0.12829
1 : 1 - 13 28.549 0.391 1.383 1.828 4255 58795 25600 29.47 0 0 0 0 0 0 0 5.942 0.781 0.455 0.71 4265 58795 25600 6.074 0 0 0 0 0 0 0 0 null
1 : 1 - 14 99.764 3.516 8.001 12.651 4545 58795 25600 29.926 69.838 32.388 0 0 0 0 0 106.729 0 9.609 11.922 4555 58795 25600 6.14 100.589 119.387 0 0 0 0 0 0.694 -0.52699
1 : 1 - 15 58.474 2.734 5.2 8.039 4845 58795 25600 27.701 30.774 13.329 0 0 0 0 0 48.235 0 9.624 12.181 4855 58795 25600 5.979 42.255 47.613 0 0 0 0 0 0.728 -0.45799
1 : 1 - 16 25.025 0.391 1.328 1.854 5135 58795 25600 27.373 0 0 0 0 0 0 0 5.346 0 0.632 0.88 5145 58795 25600 5.715 0 0 0 0 0 0 0 0 null
1 : 1 - 17 36.967 1.953 1.713 2.888 5435 58795 25600 28.49 8.477 4.846 0 0 0 0 0 16.191 0 2.509 3.026 5445 58795 25600 5.536 10.654 13.544 0 0 0 0 0 0.796 -0.32916
1 : 1 - 18 58.77 1.172 6.187 8.236 5725 58785 25600 27.711 31.058 15.612 0 0 0 0 0 46.152 0 9.218 10.881 5735 58785 25600 5.259 40.893 55.345 0 0 0 0 0 0.759 -0.39783
1 : 1 - 19 29.132 1.953 1.294 2.249 5995 58795 25600 27.668 1.464 0.696 0 0 0 0 0 7.061 0.391 0.693 0.995 6005 58795 25600 5.421 1.64 2.093 0 0 0 0 0 0.892 -0.16488
1 : 1 - 20 56.962 3.516 4.273 10.942 6285 58795 25600 28.381 28.582 14.981 0 0 0 0 0 34.613 3.516 3.651 6.762 6295 58795 25600 5.593 29.02 38.046 0 0 0 0 0 0.985 -0.0218

Total number of rows: 4608

Table truncated, full table size 733 Kbytes.




Supplementary data files not provided
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