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Sample GSM137242 Query DataSets for GSM137242
Status Public on Sep 01, 2007
Title Low Iron 0vs015_L
Sample type RNA
 
Channel 1
Source name 28oC
Organism Xylella fastidiosa
Characteristics 28oC
Treatment protocol No treatment. Same as "Growth Protocol".
Growth protocol Xylella fastidiosa strain 9a5c isolated form CVC symptomatic Citrus (L.) Osbeck trees were grown in Periwinkle wilt (PW) broth media at 28oC with 80 rpm rotatory agitation. A culture started from a single colony was weekly passaged through serial transfers at a 1/10 dilution in PW medium.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with TRIzol (Invitrogen) and residual DNA was removed by treatment with of RQ1 RNAse-free DNAse I (Promega) and RNAse inhibitor RNAseOUT (Invitrogen). The integrity of the RNA was checked by agarose gel electrophoresis, quantization performed with a NanoDrop spectrophotometer and the lack of residual DNA was checked by PCR.
Label Alexa Fluor 555
Label protocol 20ug of total RNA was reverse transcribed and labeled using SuperScript Indirect cDNA labeling kit (Invitrogen). Unincorporated dye was removed by purification in Millipore filters MAFB000 in guanidine buffer pH 4.8 followed by 4 washes with ethanol 80%. Labeled cDNA was eluted with 90 ul of Tris 10mM, pH8.0 and dried in speed vac.
 
Channel 2
Source name low iron concentrarion, 15'
Organism Xylella fastidiosa
Characteristics low iron concentrarion, 15'
Treatment protocol Treated with 200 uM of 2,2-dipyridyl for 15 minutes.
Growth protocol Xylella fastidiosa strain 9a5c isolated form CVC symptomatic Citrus (L.) Osbeck trees were grown in Periwinkle wilt (PW) broth media at 28oC with 80 rpm rotatory agitation. A culture started from a single colony was weekly passaged through serial transfers at a 1/10 dilution in PW medium.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with TRIzol (Invitrogen) and residual DNA was removed by treatment with of RQ1 RNAse-free DNAse I (Promega) and RNAse inhibitor RNAseOUT (Invitrogen). The integrity of the RNA was checked by agarose gel electrophoresis, quantization performed with a NanoDrop spectrophotometer and the lack of residual DNA was checked by PCR.
Label Alexa Fluor 647
Label protocol 20ug of total RNA was reverse transcribed and labeled using SuperScript Indirect cDNA labeling kit (Invitrogen). Unincorporated dye was removed by purification in Millipore filters MAFB000 in guanidine buffer pH 4.8 followed by 4 washes with ethanol 80%. Labeled cDNA was eluted with 90 ul of Tris 10mM, pH8.0 and dried in speed vac.
 
 
Hybridization protocol AF555 and AF647 fluorescent labeled cDNAs were ressuspended in 13ul of water and mixed in a solution containing 25% of Hybridization Buffer (Amersham Biosciences) and 50% formamide, in a final volume of 56ul. Samples were denatured by heating at 95oC for 2 min and immediately chilled on ice. The targets were applied on the microarray slides, covered with a 24 x 60 mm coverslip (Corning) and hybridized at 42oC for 16h. Washing was performed once in 1xSSC, 0.1% SDS for 10 min, twice in 0.1xSSC, 0.01% SDS for 10 min and in 0.1xSSC for 1 min. The slides were soaked in water for 10s and dried with nitrogen gas.
Scan protocol Microarray slides were scanned with a Generation III DNA Scanner (Amersham Biosciences).
Description Fluorescence mean intensity and surrounding median background from each spot were obtained with ArrayVision v6.0 (Imaging Research, Inc). Unreliable spots, having intensities too similar to local background or saturated were filtered out. Spots presenting mean intensity below 2 times the standard deviation of its background in AF555 and AF647 simultaneously were eliminated from the subsequent analysis since their expression ratio is meaningless. Saturated signals [intensity greater than >990 fluorescence units] were also discarded. Normalization was carried out by LOWESS fitting on a M versus S plot, where M is the fluorescence log-ratio of the iron stress time-point relative to the control condition [M=log2(ratio)] and S is the log-mean fluorescence intensity [S = log2((cy3+cy5)/2)].
Data processing filtering low intensity spots, LOWESS normalization
 
Submission date Sep 21, 2006
Last update date Sep 22, 2006
Contact name Ricardo Z.N. Vêncio
Organization name Universidade de São Paulo
Department Computing and Mathematics Department
Lab http://labpib.fmrp.usp.br
Street address Av. Bandeirantes, 3900
City Ribeirao Preto
State/province SP
ZIP/Postal code 14049-900
Country Brazil
 
Platform ID GPL2708
Series (1)
GSE5888 Global gene expression analysis of the phytopathogen Xylella fastidiosa at low iron availability

Data table header descriptions
ID_REF
VALUE log2(normalized ratio)
C1.MTM Dens - RFU / ?m2 C1. Median-based Trimmed Mean density value for each 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.
C1.% Removed (MTM - RFU/A) C1. Percentage of pixels excluded in the calculation of ARM Density and MTM Density.
C1.MAD - RFU / ?m2 C1. Median Absolute Deviation of foreground density.
C1.SD - RFU / ?m2 C1. Standard deviation of the pixel density values.
C1.Pos X - ?m x
C1.Pos Y - ?m y
C1.Area - ?m2 area
C1.Bkgd C1. Median of a region outside of the spot
C1.sMTMDens C1. Subtracted MTM Density value. MTM Density value of the spot, minus the background Density value.
C1.S/N C1. Signal-to-Noise Ratio. Spot density minus Background density, divided by the SD of the Background density.
C1.Flag Flag = 0 = O.K. ; other = bad spot
C1.% At Floor C1. Proportion of pixels at the lower limit of the density scale. Actual signal intensity may be below the imaging device's threshold of detection.
C1.% At Ceiling C1. Proportion of pixels at the upper limit of the density scale (i.e., saturated). Actual signal intensity may be higher than the recorded value.
C1.% At Floor - Bkgd C1. Backgr. Proportion of pixels at the lower limit of the density scale. Actual signal intensity may be below the imaging device's threshold of detection.
C1.% At Ceiling - Bkgd C1. Backgr. Proportion of pixels at the upper limit of the density scale (i.e., saturated). Actual signal intensity may be higher than the recorded value.
C2.MTM Dens - RFU / ?m2 C2. Median-based Trimmed Mean density value for each 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.
C2.% Removed (MTM - RFU/A) C2. Percentage of pixels excluded in the calculation of ARM Density and MTM Density.
C2.MAD - RFU / ?m2 C2. Median Absolute Deviation of foreground density.
C2.SD - RFU / ?m2 C2. Standard deviation of the pixel density values.
C2.Pos X - ?m x
C2.Pos Y - ?m y
C2.Area - ?m2 area
C2.% At Floor C2. Proportion of pixels at the lower limit of the density scale. Actual signal intensity may be below the imaging device's threshold of detection.
C2.% At Ceiling C2. Proportion of pixels at the upper limit of the density scale (i.e., saturated). Actual signal intensity may be higher than the recorded value.
C2.Bkgd C2. Median of a region outside of the spot
C2.sMTMDens C2. Subtracted MTM Density value. MTM Density value of the spot, minus the background Density value.
C2.S/N C2. Signal-to-Noise Ratio. Spot density minus Background density, divided by the SD of the Background density.
C2.Flag Flag = 0 = O.K. ; other = bad spot
C2.% At Floor - Bkgd C2. Backgr. Proportion of pixels at the lower limit of the density scale. Actual signal intensity may be below the imaging device's threshold of detection.
C2.% At Ceiling - Bkgd C2. Backgr. Proportion of pixels at the upper limit of the density scale (i.e., saturated). Actual signal intensity may be higher than the recorded value.

Data table
ID_REF VALUE C1.MTM Dens - RFU / ?m2 C1.% Removed (MTM - RFU/A) C1.MAD - RFU / ?m2 C1.SD - RFU / ?m2 C1.Pos X - ?m C1.Pos Y - ?m C1.Area - ?m2 C1.Bkgd C1.sMTMDens C1.S/N C1.Flag C1.% At Floor C1.% At Ceiling C1.% At Floor - Bkgd C1.% At Ceiling - Bkgd C2.MTM Dens - RFU / ?m2 C2.% Removed (MTM - RFU/A) C2.MAD - RFU / ?m2 C2.SD - RFU / ?m2 C2.Pos X - ?m C2.Pos Y - ?m C2.Area - ?m2 C2.% At Floor C2.% At Ceiling C2.Bkgd C2.sMTMDens C2.S/N C2.Flag C2.% At Floor - Bkgd C2.% At Ceiling - Bkgd
1 2.82 82.804 7.813 3.929 7.373 705 58945 25600 82.043 0.76 0.137 0 0 0 0 0 14.631 5.859 1.407 2.113 705 58935 25600 0 0 13.051 1.579 1.068 0 0 0
2 0.53 104.228 0.391 10.663 14.163 955 58965 25600 81.46 22.769 3.888 0 0 0 0 0 25.354 0 4.963 6.458 955 58955 25600 0 0 13.213 12.141 9.513 0 0 0
3 1 100.023 0 8.118 10.211 1245 58995 25600 79.887 20.136 4.172 0 0 0 0 0 28.574 0 6.734 7.442 1245 58985 25600 0 0 13.654 14.92 10.198 0 0 0
4 0.47 83.462 5.078 3.876 5.889 1535 58945 25600 81.695 1.766 0.344 0 0 0 0 0 14.686 1.953 1.343 1.814 1535 58935 25600 0 0 13.962 0.723 0.423 0 0 0
5 0 76.694 5.078 4.423 6.839 1805 58945 25600 82.754 0 0 0 0 0 0 0 11.671 2.734 1.163 1.697 1805 58935 25600 0 0 14.039 0 0 0 0 0
6 0.04 85.56 4.688 3.478 5.253 2085 58945 25600 82.885 2.675 0.308 0 0 0 0 0 15.187 4.688 1.31 1.9 2085 58935 25600 0 0 14.306 0.881 0.631 0 0 0
7 0 75.814 1.953 4.845 6.385 2365 58945 25600 81.014 0 0 0 0 0 0 0 12.497 3.125 1.218 1.724 2365 58935 25600 0 0 14.313 0 0 0 0 0
8 0 78.907 1.953 3.566 4.678 2655 58945 25600 79.844 0 0 0 0 0 0 0 14.885 9.766 1.061 1.798 2655 58935 25600 0 0 14.024 0.861 0.653 0 0 0
9 0 75.228 1.563 4.41 5.75 2945 58945 25600 79.672 0 0 0 0 0 0 0 12.914 1.953 1.067 1.471 2945 58935 25600 0 0 14.034 0 0 0 0 0
10 0 79.288 5.078 3.147 4.984 3235 58945 25600 78.853 0.435 0.086 0 0 0 0 0 14.24 5.859 0.928 1.462 3235 58935 25600 0 0 14.293 0 0 0 0 0
11 0 73.877 5.859 3.843 5.831 3515 58945 25600 78.336 0 0 0 0 0 0 0 12.896 5.469 1.039 1.616 3515 58935 25600 0 0 14.627 0 0 0 0 0
12 0.08 110.752 2.344 9.451 13.63 3805 58965 25600 77.856 32.895 5.196 0 0 0 0 0 27.031 0.391 3.108 4.129 3805 58955 25600 0 0 14.298 12.733 9.038 0 0 0
13 0.28 237.695 0 62.746 80.359 4085 58975 25600 76.445 161.25 36.509 0 0 0 0 0 83.091 0 26.338 30.427 4085 58965 25600 0 0 14.168 68.923 53.62 0 0 0
14 0.19 99.111 7.422 9.192 14.306 4385 58965 25600 75.893 23.218 4.754 0 0 0 0 0 23.894 3.906 3.11 4.451 4385 58955 25600 0 0 14.223 9.672 6.693 0 0 0
15 0.86 86.064 2.344 3.511 4.864 4665 58975 25600 75.666 10.398 2.176 0 0 0 0 0 21.482 2.344 1.965 2.819 4665 58965 25600 0 0 14.622 6.86 4.11 0 0 0
16 0.04 79.216 1.953 6.43 8.123 4955 58945 25600 75.511 3.705 0.782 0 0 0 0 0 16.138 3.125 2.057 2.938 4955 58935 25600 0 0 14.856 1.281 0.792 0 0 0
17 0.2 78.743 6.25 4.242 6.052 5245 58945 25600 76.325 2.418 0.494 0 0 0 0 0 15.494 7.813 1.453 2.592 5245 58935 25600 0 0 14.632 0.862 0.61 0 0 0
18 -1.65 145.409 0 26.56 32.749 5565 58975 25600 85.704 59.705 2.701 0 0 0 0 0 21.855 0.391 2.539 3.446 5565 58965 25600 0 0 14.997 6.858 4.348 0 0 0
19 0.49 155.556 1.953 22.509 31.755 5835 58955 25600 106.069 49.487 2.875 0 0 0 0 0 40.8 1.953 5.092 7.147 5835 58945 25600 0 0 15.366 25.434 17.219 0 0 0
20 0.16 169.459 2.344 15.517 20.628 6115 58955 25600 127.826 41.634 2.812 0 0 0 0 0 33.218 3.516 4.546 6.584 6115 58945 25600 0 0 16.705 16.513 8.366 0 0 0

Total number of rows: 4608

Table truncated, full table size 660 Kbytes.




Supplementary data files not provided
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