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Sample GSM110520 Query DataSets for GSM110520
Status Public on May 20, 2007
Title Sugarcane transcriptome - ch1: Drought_72h_Exp_2; ch2: control_72h_2 (L)
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 18.259 0.391 1.459 2.189 795 59595 25600 14.582 3.676 5.967 0 0 0 0 0 6.364 0 1.215 1.657 795 59595 25600 2.479 3.885 13.3 0 0 0 0 0 0.946 -0.08009
1 : 1 - 2 19.393 9.375 0.866 2.012 1055 59585 25600 14.936 4.457 6.397 0 0 0 0 0 4.968 4.297 0.507 0.993 1055 59585 25600 2.501 2.467 11.079 0 0 0 0 0 1.807 0.8536
1 : 1 - 3 22.297 6.25 1.362 2.559 1325 59585 25600 15.291 7.006 5.001 0 0 0 0 0 11.065 0 2.061 2.602 1325 59585 25600 2.501 8.564 37.035 0 0 0 0 0 0.818 -0.28983
1 : 1 - 4 27.284 3.516 1.454 2.436 1595 59585 25600 15.409 11.875 8.897 0 0 0 0 0 6.008 0 0.706 0.973 1595 59585 25600 2.533 3.476 14.139 0 0 0 0 0 3.417 1.77273
1 : 1 - 5 25.322 4.688 2.035 3.207 1845 59575 25600 14.978 10.344 17.317 0 0 0 0 0 13.915 0 5.03 5.252 1845 59575 25600 2.567 11.348 47.898 0 0 0 0 0 0.912 -0.13289
1 : 1 - 6 29.749 3.906 1.936 3.409 2115 59585 25600 14.677 15.072 24.445 0 0 0 0 0 19.369 3.516 2.036 3.39 2115 59585 25600 2.584 16.785 67.278 0 0 0 0 0 0.898 -0.15521
1 : 1 - 7 14.973 10.156 0.605 1.627 2425 59565 25600 14.488 0.485 0.755 0 0 0 0 0 2.789 1.172 0.239 0.345 2425 59565 25600 2.572 0.217 0.896 0 0 0 0 0 2.24 1.1635
1 : 1 - 8 18.702 14.063 0.883 2.66 2675 59585 25600 14.197 4.506 8.047 0 0 0 0 0 2.919 1.563 0.273 0.409 2675 59585 25600 2.462 0.457 2.129 0 0 0 0 0 9.864 3.30217
1 : 1 - 9 17.781 12.5 0.694 1.814 2965 59575 25600 14.088 3.693 7.127 0 0 0 0 0 4.75 8.594 0.461 0.998 2965 59575 25600 2.348 2.401 10.619 0 0 0 0 0 1.538 0.62106
1 : 1 - 10 15.06 5.469 0.871 1.55 3295 59565 25600 13.888 1.172 1.887 0 0 0 0 0 2.28 0.391 0.183 0.249 3295 59565 25600 2.247 0.033 0.136 0 0 0 0 0 35.46 5.14812
1 : 1 - 11 50.752 12.5 2.949 9.433 3555 59575 25600 13.692 37.06 61.594 0 0 0 0 0 53.801 15.234 3.699 12.154 3555 59575 25600 2.177 51.624 191.203 0 0 0 0 0 0.718 -0.47794
1 : 1 - 12 15.998 6.641 0.694 1.393 3855 59575 25600 13.517 2.481 4.271 0 0 0 0 0 3.269 0.781 0.267 0.42 3855 59575 25600 2.014 1.255 4.683 0 0 0 0 0 1.976 0.98258
1 : 1 - 13 13.658 8.203 0.449 1.253 4165 59565 25600 13.318 0.34 0.612 0 0 0 0 0 1.996 1.172 0.146 0.229 4165 59565 25600 1.909 0.087 0.459 0 0 0 0 0 3.881 1.95643
1 : 1 - 14 75.437 19.922 4.128 11.433 4465 59575 25600 13.271 62.166 116.157 0 0 0 0 0 63.056 14.453 5.268 12.621 4465 59575 25600 1.903 61.153 318.972 0 0 0 0 0 1.017 0.02432
1 : 1 - 15 40.808 0 6.775 8.759 4765 59575 25600 13.391 27.417 49.528 0 0 0 0 0 30.113 0 5.602 7.298 4765 59575 25600 1.932 28.182 137.158 0 0 0 0 0 0.973 -0.03949
1 : 1 - 16 14.231 6.641 0.641 1.281 5055 59565 25600 13.419 0.812 1.309 0 0 0 0 0 1.919 0.391 0.143 0.215 5055 59565 25600 1.964 0 0 0 0 0 0 0 1e+100 null
1 : 1 - 17 25.919 5.078 1.221 2.222 5355 59575 25600 12.977 12.942 17.315 0 0 0 0 0 9.798 0 1.108 1.426 5355 59575 25600 1.936 7.862 39.589 0 0 0 0 0 1.646 0.71896
1 : 1 - 18 30.559 3.906 2.705 4.26 5645 59555 25600 12.56 17.999 24.978 0 0 0 0 0 27.142 0 6.18 7.279 5645 59555 25600 1.864 25.278 108.229 0 0 0 0 0 0.712 -0.49005
1 : 1 - 19 13.721 4.688 0.752 1.271 5935 59555 25600 12.349 1.372 2.215 0 0 0 0 0 3.542 0 0.494 0.645 5935 59555 25600 1.815 1.727 8.496 0 0 0 0 0 0.794 -0.33279
1 : 1 - 20 31.808 17.188 1.825 4.769 6205 59565 25600 12.299 19.51 30.255 0 0 0 0 0 28.536 6.641 2.679 5.461 6205 59565 25600 1.83 26.706 143.665 0 0 0 0 0 0.731 -0.45206

Total number of rows: 4608

Table truncated, full table size 739 Kbytes.




Supplementary data files not provided
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