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Sample GSM137241 Query DataSets for GSM137241
Status Public on Sep 01, 2007
Title Low Iron 060vs0_R
Sample type RNA
 
Channel 1
Source name low iron concentrarion, 60'
Organism Xylella fastidiosa
Characteristics low iron concentrarion, 60'
Treatment protocol Treated with 200 uM of 2,2-dipyridyl for 60 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 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 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 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 0 83.941 5.078 2.964 4.555 615 58935 25600 89.657 0 0 0 0 0 0 0 14.584 13.281 2.52 11.26 625 58925 25600 0 0 12.006 2.577 2.028 0 0 0
2 0 90.717 7.422 3.563 9.406 885 58935 25600 123.439 0 0 0 0 0 0 0 15.235 22.266 3.132 6.298 895 58925 25600 0 0 12.434 2.801 2.058 0 0 0
3 0 96.13 14.063 10.214 21.143 1155 58935 25600 110.679 0 0 0 0 0 0 0 11.534 1.953 1.136 1.477 1165 58925 25600 0 0 12.381 0 0 0 0 0
4 0.51 97.281 28.906 13.667 44.051 1435 58935 25600 96.184 1.097 0.064 0 0 0 0 0 12.858 8.594 0.701 1.15 1445 58925 25600 0 0 12.446 0.412 0.303 0 0 0
5 0 141.233 16.016 9.136 20.488 1715 58935 25600 108.294 32.939 1.857 0 0 0 0 0 10.583 3.125 1.394 1.966 1725 58925 25600 0 0 12.741 0 0 0 0 0
6 4.25 160.41 8.203 16.588 34.521 1905 58935 25600 109.397 51.013 3.69 0 0 0 0 0 18.18 8.594 2.299 6.118 1915 58925 25600 0 0 13.441 4.739 2.941 0 0 0
7 0 111.525 3.906 6.451 9.331 2265 58935 25600 104.49 7.035 0.725 0 0 0 0 0 12.854 3.906 1.074 1.568 2275 58925 25600 0 0 14.803 0 0 0 0 0
8 0 103.341 14.844 2.442 5.16 2555 58935 25600 103.643 0 0 0 0 0 0 0 14.647 3.906 1.026 1.472 2565 58925 25600 0 0 15.079 0 0 0 0 0
9 0 104.116 5.469 3.38 5.354 2845 58935 25600 105.843 0 0 0 0 0 0 0 13.449 4.297 1.124 1.803 2855 58925 25600 0 0 14.957 0 0 0 0 0
10 -0.05 109.236 9.375 5.678 10.103 3115 58935 25600 105.504 3.732 0.399 0 0 0 0 0 17.461 4.297 1.17 1.803 3125 58925 25600 0 0 15.55 1.911 1.12 0 0 0
11 0 91.591 13.281 4.885 10.954 3415 58935 25600 105.208 0 0 0 0 0 0 0 13.992 8.984 2.75 4.919 3425 58925 25600 0 0 16.193 0 0 0 0 0
12 -1.39 108.583 2.734 10.17 14.521 3665 58955 25600 98.821 9.763 0.716 0 0 0 0 0 58.539 1.172 12.993 18.094 3675 58945 25600 0 0 14.321 44.218 13.617 0 0 0
13 -0.28 116.389 0.391 9.542 11.679 3935 58955 25600 92.323 24.066 2.652 0 0 0 0 0 64.988 0 19.641 21.427 3945 58945 25600 0 0 12.871 52.117 35.504 0 0 0
14 -1.58 93.023 7.031 3.522 6.897 4225 58955 25600 90.309 2.714 0.445 0 0 0 0 0 20.283 1.563 2.642 3.445 4235 58945 25600 0 0 12.08 8.202 5.843 0 0 0
15 0 92.857 7.031 2.702 4.843 4555 58925 25600 87.917 4.94 0.763 0 0 0 0 0 7.993 12.891 1.028 1.969 4565 58915 25600 0 0 11.98 0 0 0 0 0
16 0 72.997 5.078 3.617 6.118 4835 58925 25600 78.451 0 0 0 0 0 0 0 11.193 5.859 0.733 1.176 4845 58915 25600 0 0 12.397 0 0 0 0 0
17 0 75.48 6.25 4.666 7.413 5125 58925 25600 77.541 0 0 0 0 0 0 0 14.676 10.156 1.505 2.831 5135 58915 25600 0 0 12.439 2.237 1.88 0 0 0
18 -2.37 86.25 12.109 5.06 10.045 5435 58935 25600 82.51 3.739 0.482 0 0 0 0 0 38.021 0 9.569 11.005 5445 58925 25600 0 0 12.426 25.595 22.622 0 0 0
19 0.52 116.632 0.391 7.067 9.01 5715 58935 25600 89.157 27.474 4.365 0 0 0 0 0 46.574 2.734 7.828 11.093 5725 58925 25600 0 0 12.332 34.242 29.209 0 0 0
20 0.62 137.547 1.172 11.038 15.273 6005 58925 25600 94.64 42.907 6.135 0 0 0 0 0 59.866 0 12.73 16.811 6015 58915 25600 0 0 12.037 47.828 37.304 0 0 0

Total number of rows: 4608

Table truncated, full table size 669 Kbytes.




Supplementary data files not provided
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