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Sample GSM86043 Query DataSets for GSM86043
Status Public on Dec 15, 2005
Title M9 iron starvation 10 min
Sample type mixed
 
Channel 1
Source name SL1344 genomic DNA
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics SL1344 genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name M9 500 uM dipyridyl 10 min
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics M9 500 uM dipyridyl 10 min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Chemical effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24752.gif
Measurement: concentration(absolute) 500 uM
name: 24752_Starvation
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Dec 02, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3048
Series (1)
GSE3734 Dipyridyl Treatment

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE same as UNF_VALUE but with flagged values removed
UNF_VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE UNF_VALUE
1 638 186 44 112 594 74 640 159 44 114 596 47 0 0 363 94 6 25 100 65 100 46 668 643 8.027 .125 .079 .094 .088 2.95 32 236 .09 .45 70 1320 18560 92 99 96 103 0 715 431 285 .479 612 181 2.087 .303 -1.061 -1.721 -1.721
2 736 167 41 108 695 59 704 156 41 109 663 48 0 0 372 47 6 25 100 71 100 50 754 711 11.78 .085 .072 .077 .086 1.991 32 236 .085 .75 70 1540 18560 92 99 118 125 0 642 415 227 .327 600 185 3.063 .278 -1.615 -1.844 -1.844
3 354 134 42 106 312 28 322 121 43 109 280 15 0 0 133 67 6 27 100 25 100 8 340 295 11.143 .09 .054 .104 .075 3.274 12 68 .085 .16 40 1770 18560 94 98 143 147 0 515 408 108 .345 465 58 2.897 .206 -1.535 -2.279 -2.279
4 917 157 42 109 875 48 869 136 42 111 827 27 0 0 507 78 4 25 100 51 100 26 923 854 18.229 .055 .033 .051 .049 2.263 52 420 .057 .51 90 1990 18570 92 101 162 171 0 604 419 185 .211 523 104 4.74 .126 -2.245 -2.993 -2.993
5 844 165 43 109 801 56 915 158 44 110 872 49 0 0 336 70 6 25 100 65 100 48 857 921 14.304 .07 .056 .064 .064 2.22 52 420 .074 .58 90 2230 18570 92 101 186 195 0 635 419 215 .269 608 188 3.719 .216 -1.895 -2.21 -2.21
6 750 166 44 104 706 62 720 145 45 106 676 41 0 0 295 82 6 23 100 71 100 46 768 717 11.387 .088 .061 .079 .076 2.497 32 230 .07 .43 70 2450 18550 91 98 209 216 0 638 400 238 .338 558 158 2.961 .233 -1.566 -2.1 -2.1
7 572 149 45 108 527 41 412 149 57 120 367 41 0 0 391 50 142 104 84 6 62 0 568 408 12.854 .078 .112 .102 .111 2.004 32 236 .076 .62 70 2690 18560 92 99 233 240 0 573 415 158 .299 573 158 3.342 .43 -1.741 -1.219 -1.219
8 844 158 46 115 798 43 730 141 48 122 684 26 0 0 453 77 25 80 100 15 100 6 841 710 18.558 .054 .038 .056 .045 2.664 32 230 .035 .12 70 2900 18550 91 98 254 261 0 608 442 165 .207 542 100 4.825 .146 -2.271 -2.774 -2.774
9 889 158 46 112 843 46 676 134 48 115 630 22 0 0 531 75 8 25 100 46 100 32 889 652 18.326 .055 .035 .059 .063 1.908 52 332 .07 .66 80 3130 18550 91 99 277 285 0 608 431 177 .21 515 85 4.765 .134 -2.252 -2.896 -2.896
10 616 162 45 112 571 50 492 147 46 114 447 35 0 0 333 85 6 24 100 59 100 42 621 482 11.42 .088 .078 .08 .074 2.18 52 332 .113 .61 80 3360 18550 91 99 300 308 0 623 431 192 .337 565 135 2.969 .301 -1.57 -1.731 -1.731
11 253 212 44 115 209 97 240 138 44 116 196 23 0 0 116 231 4 27 100 50 100 16 306 219 2.155 .464 .117 .243 .154 3.225 12 62 1.401 .7 40 3580 18550 93 97 324 328 0 815 442 373 1.785 531 88 .56 .451 .836 -1.148 -1.148
12 954 185 48 110 906 75 994 149 48 111 946 39 0 0 243 128 6 22 100 71 100 40 981 985 12.08 .083 .041 .061 .062 2.635 32 230 .071 .4 70 3810 18540 90 97 345 352 0 712 423 288 .318 573 150 3.141 .159 -1.651 -2.657 -2.657
13 181 267 50 118 131 149 134 228 51 119 84 110 0 0 109 117 6 20 100 91 100 91 280 194 .879 1.137 1.31 1.004 1.147 2.264 12 62 1.22 .76 40 4040 18550 93 97 370 374 0 1027 454 573 4.375 877 423 .229 5.037 2.129 2.332 2.332
14 66 147 47 109 19 38 49 112 48 111 2 3 0 0 60 148 5 24 31 25 13 16 57 5 .5 2 1.5 3.673 4.506 3.894 80 648 3.26 .72 110 4250 18540 88 99 387 398 -50 565 419 146 7.692 431 12 .13 5.769 2.943 2.528
15 130 272 46 111 84 161 57 179 46 113 11 68 0 0 150 280 4 25 68 71 62 56 245 79 .522 1.917 6.182 2.387 3.167 2.686 32 170 2.42 .67 60 4480 18550 92 98 413 419 0 1046 427 619 7.372 688 262 .136 23.776 2.882 4.571 4.571
16 62 151 46 113 16 38 49 115 47 116 3 2 0 0 43 170 5 28 33 20 20 11 54 5 .421 2.375 .667 2.924 3.296 4.605 80 648 10.861 .62 110 4700 18540 88 99 432 443 -50 581 435 146 9.135 442 8 .109 2.564 3.191 1.358
17 144 350 42 111 102 239 91 244 43 115 49 133 0 0 119 244 6 28 100 93 90 81 341 182 .427 2.343 2.714 2.621 2.54 1.789 32 236 2.32 .9 70 1330 18790 115 122 97 104 0 1346 427 919 9.012 938 512 .111 10.44 3.172 3.384 3.384
18 133 516 41 113 92 403 106 360 41 113 65 247 0 0 100 362 4 26 100 100 100 91 495 312 .228 4.38 3.8 4.597 3.976 1.596 12 104 3.517 .91 50 1540 18800 117 122 119 124 0 1985 435 1550 16.848 1385 950 .059 14.615 4.074 3.869 3.869
19 54 124 44 110 10 14 47 109 44 113 3 -1 0 0 23 72 6 24 28 21 18 6 24 2 .714 1.4 null 4.351 5 3.406 80 650 5.124 .44 110 1770 18780 112 123 139 150 -50 477 423 54 5.385 419 null .186 null 2.429 null
20 59 120 44 110 15 10 49 112 45 113 5 2 0 0 27 50 5 25 47 20 38 7 25 7 1.5 .667 .4 1.611 1.984 5.365 80 644 5.503 .36 110 1990 18780 112 123 161 172 -50 462 423 38 2.564 431 8 .39 1.538 1.358 .621

Total number of rows: 7680

Table truncated, full table size 1673 Kbytes.




Supplementary data files not provided
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