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Sample GSM88811 Query DataSets for GSM88811
Status Public on Dec 22, 2005
Title FeAddBack-2-120 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=20
Organism Helicobacter pylori
Characteristics 1 ug of RNA from experiment 2 T=20
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Environmental conditions, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41623.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
1 961 472 104 84 857 388 630 320 106 87 526 236 0 0 768 343 21 28 100 97 100 93 1245 762 2.209 .453 .449 .433 .442 1.514 80 552 .442 .97 100 1540 38070 94 104 53 63 0 833 148 685 .799 565 416 1.252 .792 -.324 -.337
2 278 146 107 86 171 60 237 144 107 93 130 58 0 0 135 52 23 39 93 56 84 37 231 188 2.85 .351 .446 .384 .346 1.952 32 176 .333 .72 60 1790 38050 94 100 80 86 0 258 152 106 .619 254 102 1.615 .787 -.692 -.345
3 463 283 107 84 356 199 480 263 107 87 373 179 0 0 162 138 20 22 100 91 100 83 555 552 1.789 .559 .48 .396 .491 3.282 12 93 .588 .82 50 2030 38030 92 97 104 109 0 499 148 351 .986 464 316 1.014 .847 -.02 -.24
4 127 98 108 85 19 13 120 92 110 89 12 7 0 0 40 39 23 30 26 22 15 10 32 19 1.462 .684 .583 1.021 1.043 3.514 80 656 2.241 .25 110 2250 38040 90 101 123 134 -50 173 150 23 1.207 162 12 .828 1.029 .272 .042
5 126 95 112 87 14 8 123 95 113 89 11 8 0 0 41 28 21 27 31 20 12 5 22 19 1.75 .571 .727 .873 .872 4.305 80 648 -1 -1 110 2490 38030 89 100 147 158 -50 168 154 14 1.008 168 14 .992 1.283 .012 .36
6 151 105 115 89 36 16 130 99 116 93 15 10 0 0 71 39 21 30 43 22 25 8 52 25 2.25 .444 .667 .765 .616 2.963 80 656 .484 .32 110 2730 38030 89 100 171 182 -50 185 157 28 .784 175 18 1.275 1.176 -.35 .234
7 221 121 108 89 113 32 208 122 111 89 100 33 0 0 46 36 21 27 100 58 100 16 145 133 3.531 .283 .33 .347 .426 2.008 12 68 .606 .29 40 2970 38040 94 98 199 203 0 214 157 56 .5 215 58 2.001 .582 -1.001 -.78
8 187 117 101 83 86 34 191 109 103 84 90 26 0 0 57 31 21 23 83 50 75 33 120 116 2.529 .395 .289 .614 .654 5.334 12 68 .555 .26 40 3220 38030 93 97 224 228 0 206 146 60 .698 192 46 1.433 .51 -.519 -.972
9 282 209 106 88 176 121 245 212 105 92 139 124 0 0 105 90 21 27 100 83 91 75 297 263 1.455 .688 .892 .567 .463 2.163 12 104 .89 .74 50 3460 38030 92 97 247 252 0 369 155 214 1.213 374 219 .824 1.574 .279 .655
10 123 118 104 90 19 28 108 97 105 93 4 7 0 0 49 78 22 26 32 30 20 15 47 11 .679 1.474 1.75 .943 .923 3.335 80 648 2.663 .3 110 3680 38010 87 98 266 277 -50 208 159 49 2.601 171 12 .385 3.088 1.379 1.627
11 279 119 110 91 169 28 281 112 112 95 171 21 0 0 92 43 22 30 96 43 90 15 197 192 6.036 .166 .123 .167 .163 3.114 32 236 .182 .35 70 3940 38020 90 97 294 301 0 210 161 49 .292 198 37 3.42 .217 -1.774 -2.206
12 233 168 104 82 129 86 218 151 106 91 114 69 0 0 92 64 24 35 91 100 75 41 215 183 1.5 .667 .605 .797 .631 2.887 12 68 .526 .3 40 4180 38020 92 96 320 324 0 296 145 152 1.176 266 122 .85 1.068 .234 .095
13 253 157 104 86 149 71 224 141 106 87 120 55 0 0 115 58 21 24 94 86 88 61 220 175 2.099 .477 .458 .539 .492 2.772 52 420 .432 .71 90 4410 38010 88 97 340 349 0 277 152 125 .841 249 97 1.189 .809 -.25 -.306
14 564 326 103 86 461 240 354 232 106 95 251 146 0 0 488 233 32 83 98 71 94 50 701 397 1.921 .521 .582 .501 .511 1.914 52 332 .511 .8 80 4630 38000 88 96 363 371 0 575 152 424 .919 409 258 1.088 1.026 -.122 .038
15 114 105 101 85 13 20 102 95 104 88 1 10 0 0 44 60 26 24 16 27 12 12 33 11 .65 1.538 10 1.137 1.111 3.919 80 648 2.298 .24 110 4880 37990 85 96 386 397 -50 185 150 35 2.715 168 18 .368 17.647 1.441 4.141
16 133 122 104 86 29 36 108 101 105 88 4 15 0 0 76 74 23 25 35 40 17 22 65 19 .806 1.241 3.75 1.189 1.148 3.477 80 651 1.062 .59 110 5110 37990 85 96 409 420 -50 215 152 64 2.191 178 26 .456 6.618 1.131 2.726
17 3375 1694 113 89 3262 1605 223 172 114 92 110 83 0 0 8794 4065 28 28 76 71 69 61 4867 193 2.032 .492 .755 .632 .646 3.432 52 340 .448 .94 80 5320 38010 89 97 432 440 0 2989 157 2832 .868 304 146 1.152 1.332 -.204 .413
18 503 174 104 82 399 92 536 170 106 87 432 88 0 0 150 47 20 25 100 91 100 83 491 520 4.337 .231 .204 .218 .217 1.949 12 104 .43 .65 50 1550 38300 119 124 56 61 0 307 145 162 .407 300 155 2.458 .359 -1.297 -1.476
19 251 167 113 87 138 80 183 127 114 91 70 40 0 0 201 134 22 28 84 56 65 43 218 110 1.725 .58 .571 .554 .575 3.951 32 176 .5 .57 60 1780 38290 118 124 79 85 0 295 154 141 1.023 224 71 .977 1.008 .033 .012
20 131 102 109 88 22 14 122 98 112 92 13 10 0 0 45 34 23 29 36 25 13 6 36 23 1.571 .636 .769 .807 .859 4.954 80 656 .719 .21 110 2020 38280 114 125 100 111 -50 180 155 25 1.123 173 18 .89 1.357 .167 .441

Total number of rows: 4608

Table truncated, full table size 969 Kbytes.




Supplementary data files not provided
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