NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM110477 Query DataSets for GSM110477
Status Public on May 20, 2007
Title Sugarcane transcriptome - ch2: Herbivory_24h_exp_2; ch1: Herbivory_control_24h_2 (R)
Sample type RNA
 
Channel 1
Source name Herbivory_24h_control_2
Organism Saccharum hybrid cultivar SP80-3280
Characteristics Leaves of sugarcane, variety SP80-3280 (pool of 2 control plants) collected after 24h, experiment 2
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Herbivory_24h_exp_2
Organism Saccharum hybrid cultivar SP80-3280
Characteristics Leaves of sugarcane, variety SP80-3280 (pool of 2 individuals) collected after 24h of exposure to Diatraea saccharalis, 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 Herbivory by Diatraea saccharalis: 24h_experimental x 24h_control (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 (1)
GSE4967 Sugarcane transcriptome - Response to herbivory by Diatraea saccharalis

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 36.856 0.781 2.776 4.621 295 59615 25600 26.154 10.701 7.586 0 0 0 0 0 56.549 0 10.994 15.787 305 59605 25600 15.417 41.132 40.062 0 0 0 0 0 0.26 -1.94342
1 : 1 - 2 31.224 0.781 1.394 2.059 535 59595 25600 26.549 4.675 3.396 0 0 0 0 0 19.113 0.391 1.03 1.364 545 59585 25600 15.762 3.351 3.453 0 0 0 0 0 1.395 0.48027
1 : 1 - 3 30.657 3.125 1.075 1.824 785 59605 25600 26.769 3.888 2.695 0 0 0 0 0 20.261 0 1.03 1.614 795 59595 25600 15.748 4.513 5.176 0 0 0 0 0 0.862 -0.21424
1 : 1 - 4 30.457 3.906 1.175 2.236 1045 59605 25600 26.925 3.532 2.272 0 0 0 0 0 18.241 3.125 0.747 1.231 1055 59595 25600 15.773 2.469 2.357 0 0 0 0 0 1.431 0.51702
1 : 1 - 5 33.251 1.172 1.354 1.967 1325 59605 25600 26.836 6.415 3.888 0 0 0 0 0 23.018 1.563 1.251 2.04 1335 59595 25600 16.276 6.742 5.214 0 0 0 0 0 0.951 -0.07248
1 : 1 - 6 34.185 0.391 1.681 2.562 1595 59605 25600 26.613 7.572 5.07 0 0 0 0 0 31.204 0 3.056 4.226 1605 59595 25600 16.504 14.7 11.647 0 0 0 0 0 0.515 -0.95736
1 : 1 - 7 27.959 8.984 1.203 4.417 1895 59595 25600 26.567 1.392 1.071 0 0 0 0 0 17.524 4.297 0.706 1.206 1905 59585 25600 16.342 1.182 1.185 0 0 0 0 0 1.178 0.23634
1 : 1 - 8 30.073 3.516 1.22 2.145 2135 59595 25600 26.081 3.993 3.337 0 0 0 0 0 18.276 5.469 0.813 1.473 2145 59585 25600 16.041 2.235 2.57 0 0 0 0 0 1.786 0.83673
1 : 1 - 9 35.386 0.781 1.513 2.28 2415 59605 25600 25.398 9.989 8.42 0 0 0 0 0 27.43 0 1.927 2.654 2425 59595 25600 15.623 11.808 13.446 0 0 0 0 0 0.846 -0.24127
1 : 1 - 10 26.83 4.297 0.863 1.522 2695 59595 25600 25.108 1.722 1.515 0 0 0 0 0 16.937 0 0.609 0.898 2705 59585 25600 15.24 1.697 1.96 0 0 0 0 0 1.014 0.02006
1 : 1 - 11 75.498 8.594 5.475 11.847 2995 59605 25600 24.734 50.763 42.118 0 0 0 0 0 92.839 0 14.526 20.436 3005 59595 25600 15.184 77.655 74.808 0 0 0 0 0 0.654 -0.61264
1 : 1 - 12 27.074 1.172 0.936 1.387 3275 59605 25600 24.326 2.748 2.44 0 0 0 0 0 16.737 1.172 0.626 0.952 3285 59595 25600 15.345 1.392 0.613 0 0 0 0 0 1.974 0.98112
1 : 1 - 13 25.459 7.813 0.759 1.84 3545 59595 25600 24.214 1.245 1.122 0 0 0 0 0 15.976 0.781 0.706 1.02 3555 59585 25600 15.307 0.669 0.293 0 0 0 0 0 1.861 0.89608
1 : 1 - 14 113.753 2.734 15.234 23.595 3845 59595 25600 24.167 89.586 80.822 0 0 0 0 0 185.953 0 27.666 41.524 3855 59585 25600 14.811 171.141 151.909 0 0 0 0 0 0.523 -0.93512
1 : 1 - 15 35.603 6.25 1.96 3.811 4125 59605 25600 24.144 11.46 8.999 0 0 0 0 0 34.979 0 3.696 5.362 4135 59595 25600 14.277 20.702 21.911 0 0 0 0 0 0.554 -0.85204
1 : 1 - 16 24.963 5.859 0.841 1.647 4435 59595 25600 23.851 1.112 0.755 0 0 0 0 0 14.692 0.391 0.642 0.939 4445 59585 25600 13.993 0.699 0.808 0 0 0 0 0 1.591 0.66993
1 : 1 - 17 49.52 1.563 3.536 5.516 4705 59595 25600 23.39 26.13 19.515 0 0 0 0 0 61.35 1.172 7.092 11.154 4715 59585 25600 13.996 47.354 55.486 0 0 0 0 0 0.552 -0.85726
1 : 1 - 18 54.195 0 8.512 12.427 4985 59605 25600 23.135 31.06 27.556 0 0 0 0 0 83.731 0 20.047 24.69 4995 59595 25600 13.809 69.922 79.138 0 0 0 0 0 0.444 -1.17137
1 : 1 - 19 24.371 6.641 0.816 1.66 5275 59605 25600 22.842 1.529 1.345 0 0 0 0 0 18.799 0 1.302 1.773 5285 59595 25600 13.517 5.282 6.873 0 0 0 0 0 0.289 -1.79086
1 : 1 - 20 42.285 6.25 3.252 5.845 5575 59595 25600 22.505 19.779 16.362 0 0 0 0 0 39.005 0 6.804 8.018 5585 59585 25600 13.709 25.295 30.671 0 0 0 0 0 0.782 -0.35476

Total number of rows: 4608

Table truncated, full table size 743 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap