NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM110474 Query DataSets for GSM110474
Status Public on May 20, 2007
Title Sugarcane transcriptome - ch1: Herbivory_24h_exp_1; ch2: Herbivory_control_24h_1 (L)
Sample type RNA
 
Channel 1
Source name Herbivory_24h_exp_1
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 1
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Herbivory_24h_control_1
Organism Saccharum hybrid cultivar SP80-3280
Characteristics Leaves of sugarcane, variety SP80-3280 (pool of 2 control plants) collected after 24h, 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 Herbivory by Diatraea saccharalis: 24h_experimental x 24h_control (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 (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 57.582 7.422 1.594 4.402 725 58725 25600 54.189 3.393 1.203 0 0 0 0 0 164.385 3.516 2.87 5.014 725 58715 25600 158.736 5.649 1.675 0 0 0 0 0 0.601 -0.73456
1 : 1 - 2 56.185 6.641 1.566 3.686 985 58725 25600 53.534 2.651 1.153 0 0 0 0 0 159.151 0 3.397 4.94 985 58715 25600 158.338 0.813 0.219 0 0 0 0 0 3.261 1.70531
1 : 1 - 3 55.131 3.906 1.638 2.998 1275 58725 25600 52.908 2.223 1.133 0 0 0 0 0 163.142 0 3.374 4.733 1275 58715 25600 157.932 5.21 1.146 0 0 0 0 0 0.427 -1.22769
1 : 1 - 4 56.747 5.859 1.947 3.776 1525 58745 25600 52.28 4.466 2.284 0 0 0 0 0 170.062 4.297 2.918 5.174 1525 58735 25600 155.277 14.785 3.539 0 0 0 0 0 0.302 -1.72738
1 : 1 - 5 56.136 4.297 1.605 2.917 1795 58725 25600 52.111 4.025 1.824 0 0 0 0 0 166.064 0.391 5.36 7.324 1795 58715 25600 155.234 10.83 3.518 0 0 0 0 0 0.372 -1.42663
1 : 1 - 6 67.099 2.344 3.007 4.819 2075 58735 25600 51.79 15.309 7.563 0 0 0 0 0 175.729 2.734 3.284 5.484 2075 58725 25600 155.722 20.007 7.226 0 0 0 0 0 0.765 -0.38647
1 : 1 - 7 51.499 5.078 1.361 2.62 2395 58725 25600 51.321 0.178 0.094 0 0 0 0 0 159.883 6.25 3.898 7.347 2395 58715 25600 154.935 4.949 1.545 0 0 0 0 0 0.036 -4.79586
1 : 1 - 8 55.07 8.594 1.473 3.721 2635 58725 25600 50.581 4.489 2.257 0 0 0 0 0 164.497 7.813 2.855 6.188 2635 58715 25600 154.371 10.125 3.073 0 0 0 0 0 0.443 -1.17462
1 : 1 - 9 56.956 5.469 1.59 3.505 2925 58735 25600 49.711 7.245 3.842 0 0 0 0 0 166.275 2.734 4.209 7.119 2925 58725 25600 152.542 13.733 3.584 0 0 0 0 0 0.528 -0.92139
1 : 1 - 10 50.301 7.813 1.449 3.682 3245 58725 25600 49.098 1.204 0.571 0 0 0 0 0 153.239 7.813 2.229 4.658 3245 58715 25600 149.387 3.852 1.293 0 0 0 0 0 0.312 -1.68038
1 : 1 - 11 98.404 12.5 5.279 11.772 3495 58735 25600 48.637 49.767 24.672 0 0 0 0 0 199.339 0 9.572 14.06 3495 58725 25600 147.913 51.425 17 0 0 0 0 0 0.968 -0.04692
1 : 1 - 12 50.455 5.859 1.36 2.863 3795 58725 25600 48.398 2.058 1.233 0 0 0 0 0 152.061 3.906 2.845 4.713 3795 58715 25600 147.396 4.666 1.41 0 0 0 0 0 0.441 -1.18115
1 : 1 - 13 49.839 7.031 1.501 3.801 4085 58725 25600 48.541 1.298 0.65 0 0 0 0 0 147.782 9.375 2.708 6.958 4085 58715 25600 145.75 2.033 0.556 0 0 0 0 0 0.638 -0.64837
1 : 1 - 14 238.61 8.984 24.421 49.072 4345 58735 25600 47.684 190.926 90.922 0 0 0 0 0 336.989 2.734 30.422 48.086 4345 58725 25600 142.469 194.52 49.252 0 0 0 0 0 0.982 -0.02621
1 : 1 - 15 76.486 5.859 3.815 7.074 4635 58735 25600 46.891 29.595 16.375 0 0 0 0 0 177.294 3.906 3.815 6.645 4635 58725 25600 138.885 38.408 11.333 0 0 0 0 0 0.771 -0.3752
1 : 1 - 16 48.506 8.984 1.334 2.759 4945 58725 25600 46.9 1.606 0.897 0 0 0 0 0 140.963 4.688 3.547 6.197 4945 58715 25600 138.457 2.506 0.812 0 0 0 0 0 0.641 -0.6416
1 : 1 - 17 96.812 7.031 4.098 9.945 5225 58735 25600 46.707 50.105 24.73 0 0 0 0 0 192.832 5.859 5.623 9.808 5225 58725 25600 138.303 54.529 17.068 0 0 0 0 0 0.919 -0.12186
1 : 1 - 18 86.917 0 9.533 13.478 5515 58735 25600 46.506 40.411 21.75 0 0 0 0 0 171.023 0.391 6.969 10.716 5515 58725 25600 138.069 32.954 10.684 0 0 0 0 0 1.226 0.29396
1 : 1 - 19 46.984 5.078 1.159 2.401 5805 58725 25600 47.178 0 0 0 0 0 0 0 138.499 0.781 2.46 3.592 5805 58715 25600 137.449 1.051 0.308 0 0 0 0 0 0 null
1 : 1 - 20 53.395 2.344 1.815 2.996 6105 58715 25600 47.112 6.283 3.193 0 0 0 0 0 153.456 0.781 4.99 7.674 6105 58705 25600 136.894 16.563 4.513 0 0 0 0 0 0.379 -1.39973

Total number of rows: 4608

Table truncated, full table size 721 Kbytes.




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