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Sample GSM88804 Query DataSets for GSM88804
Status Public on Dec 22, 2005
Title FeAddBack-2-60 repeat
Sample type RNA
 
Channel 1
Source name 1 ug of RNA from experiment 2 T=0
Organism Helicobacter pylori
Characteristics 1 ug of RNA from experiment 2 T=0
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 1 ug of RNA from experiment 2 T=60
Organism Helicobacter pylori
Characteristics 1 ug of RNA from experiment 2 T=60
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Environmental conditions, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41622.gif
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 21, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
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 GPL15
Series (1)
GSE3888 Growth phase-dependent response of Helicobacter pylori to iron starvation.

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 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
1 748 746 159 110 589 636 393 324 191 169 234 214 0 0 850 950 143 219 52 50 47 36 1225 448 .926 1.08 .915 1.008 1.068 2.796 256 1914 1.166 .93 190 1140 13100 88 107 48 67 -100 656 97 559 .95 285 188 1.053 .804 -.074 -.314
2 370 233 145 89 225 144 324 205 148 92 179 116 0 0 176 114 35 25 84 81 78 75 369 295 1.563 .64 .648 .593 .627 1.903 32 170 .612 .85 60 1350 13070 92 98 76 82 0 205 78 127 .563 180 102 1.777 .57 -.829 -.811
3 747 722 122 70 625 652 809 725 125 76 687 655 0 0 232 261 26 39 100 100 100 100 1277 1342 .959 1.043 .953 1.035 .999 1.37 12 104 1.035 .9 50 1610 13070 92 97 102 107 0 635 62 573 .918 638 576 1.09 .839 -.124 -.254
4 284 288 128 65 156 223 263 202 127 70 135 137 0 0 143 202 27 19 75 91 66 83 379 272 .7 1.429 1.015 1.127 1.138 2.357 12 68 1.565 .57 40 1830 13070 93 97 125 129 0 253 57 196 1.257 178 120 .795 .893 .33 -.164
5 298 249 131 69 167 180 254 167 135 73 123 98 0 0 142 226 28 19 83 58 83 50 347 221 .928 1.078 .797 .695 1.159 8.144 12 68 1.5 .61 40 2070 13070 93 97 149 153 0 219 61 158 .948 147 86 1.055 .701 -.077 -.513
6 168 103 123 67 45 36 136 78 125 68 13 11 0 0 105 86 26 17 36 37 22 25 81 24 1.25 .8 .846 .904 .705 3.611 80 656 .726 .75 110 2320 13050 87 98 170 181 -50 91 59 32 .704 69 10 1.421 .744 -.507 -.426
7 465 649 126 67 339 582 478 654 128 69 352 587 0 0 192 343 24 18 100 100 100 100 921 939 .582 1.717 1.668 1.734 1.618 2.207 12 68 1.881 .83 40 2560 13060 92 96 198 202 0 571 59 512 1.51 575 516 .662 1.467 .595 .553
8 156 122 125 69 31 53 127 74 126 71 2 5 0 0 96 150 27 18 30 32 13 22 84 7 .585 1.71 2.5 .874 .944 3.833 80 656 1.583 .75 110 2800 13040 86 97 218 229 -50 107 61 47 1.504 65 4 .665 2.199 .589 1.137
9 590 591 138 72 452 519 598 467 139 73 460 395 0 0 251 436 29 17 100 100 100 91 971 855 .871 1.148 .859 .798 .965 2.577 12 104 1.409 .84 50 3050 13050 90 95 246 251 0 520 63 456 1.01 411 347 .99 .755 .014 -.405
10 266 380 135 71 131 309 202 226 133 72 67 155 0 0 183 380 27 19 66 100 58 100 440 222 .424 2.359 2.313 2.608 2.121 2.64 12 104 1.948 .85 50 3270 13040 89 94 268 273 0 334 62 272 2.075 199 136 .482 2.035 1.053 1.025
11 287 284 135 72 152 212 252 133 142 75 117 61 0 0 125 313 29 22 91 83 75 66 364 178 .717 1.395 .521 .708 .54 2.793 12 104 2.066 .83 50 3510 13050 90 95 292 297 0 250 63 186 1.227 117 54 .815 .459 .295 -1.125
12 337 227 140 72 197 155 272 175 140 74 132 103 0 0 156 164 28 20 91 100 91 83 352 235 1.271 .787 .78 .727 .533 2.193 12 98 .77 .79 50 3750 13020 87 92 316 321 0 200 63 136 .692 154 91 1.445 .686 -.531 -.543
13 438 454 142 70 296 384 350 350 143 73 208 280 0 0 224 296 29 21 98 100 96 100 680 488 .771 1.297 1.346 1.357 1.224 1.682 52 420 1.334 .9 90 3990 13030 86 95 338 347 0 399 62 338 1.141 308 246 .876 1.184 .19 .244
14 983 1023 153 73 830 950 817 789 159 81 664 716 0 0 628 740 43 45 100 100 100 100 1780 1380 .874 1.145 1.078 1.153 1.134 1.493 32 236 1.171 .91 70 4210 13030 87 94 361 368 0 900 64 836 1.007 694 630 .993 .948 .01 -.076
15 218 68 182 64 36 4 179 65 185 66 -3 1 0 0 128 16 36 17 21 15 15 5 40 -2 9 .111 null .218 .174 4.311 80 648 .056 .22 110 4470 13010 83 94 385 396 -50 60 56 4 .098 57 1 10.233 null -3.355 null
16 228 105 202 64 26 41 203 74 204 66 1 10 0 0 108 81 35 16 20 45 15 32 67 11 .634 1.577 10 .758 .743 4.15 80 656 .614 .67 110 4710 13010 83 94 409 420 -50 92 56 36 1.387 65 9 .721 8.795 .472 3.137
17 538 256 208 68 330 188 464 267 204 72 256 199 0 0 183 82 34 22 100 100 100 100 518 455 1.755 .57 .777 .595 .553 1.725 12 68 .414 .8 40 4960 13020 88 92 438 442 0 225 60 165 .501 235 175 1.996 .684 -.997 -.549
18 836 404 194 185 642 219 849 401 223 222 655 216 0 0 182 114 89 130 100 75 100 41 861 871 2.932 .341 .33 .297 .312 1.713 12 104 .531 .61 50 1130 13310 116 121 54 59 0 355 163 193 .3 353 190 3.333 .29 -1.737 -1.786
19 196 151 129 76 67 75 145 99 158 114 16 23 0 0 151 155 146 223 13 10 7 6 142 39 .893 1.119 1.438 .811 1 3.564 80 656 1.017 .87 110 1370 13300 112 123 75 86 -50 133 67 66 .985 87 20 1.016 1.264 -.022 .338
20 143 82 119 70 24 12 127 73 120 72 8 3 0 0 63 41 27 19 28 23 15 15 36 11 2 .5 .375 .671 .731 4.045 80 656 .428 .4 110 1610 13300 112 123 99 110 -50 72 62 11 .44 64 3 2.274 .33 -1.185 -1.6

Total number of rows: 4608

Table truncated, full table size 996 Kbytes.




Supplementary data files not provided
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