|
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 |