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Sample GSM88820 Query DataSets for GSM88820
Status Public on Dec 22, 2005
Title FeAddBack-1-120 repeat
Sample type RNA
 
Channel 1
Source name 1 ug of RNA from experiment 1 T=0
Organism Helicobacter pylori
Characteristics 1 ug of RNA from experiment 1 T=0
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 1 ug of RNA from experiment 1 T=120
Organism Helicobacter pylori
Characteristics 1 ug of RNA from experiment 1 T=120
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Environmental conditions, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41619.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
1 916 544 205 143 711 401 661 413 211 158 456 270 0 0 522 290 75 219 100 61 100 38 1112 726 1.773 .564 .592 .555 .535 1.529 80 642 .558 .92 110 1570 38270 81 92 79 90 0 881 232 649 .913 669 437 1.095 .959 -.131 -.06
2 550 234 210 145 340 89 515 252 216 153 305 107 0 0 104 63 43 48 100 83 100 58 429 412 3.82 .262 .351 .291 .293 1.671 12 104 .24 .4 50 1780 38250 82 87 103 108 0 379 235 144 .424 408 173 2.359 .568 -1.238 -.816
3 783 533 195 151 588 382 724 473 204 149 529 322 0 0 271 278 53 45 100 100 100 91 970 851 1.539 .65 .609 .554 .595 1.566 12 54 .769 .9 40 2030 38240 82 86 129 133 0 863 245 619 1.052 766 522 .95 .986 .073 -.021
4 224 167 197 136 27 31 195 153 201 143 -2 17 0 0 87 74 46 51 23 23 13 8 58 15 .871 1.148 null 1.06 1.099 3.26 80 656 .523 .18 110 2290 38240 78 89 151 162 -50 270 220 50 1.86 248 28 .538 null .895 null
5 227 151 200 145 27 6 212 147 202 159 12 2 0 0 65 42 42 107 31 1 15 0 33 14 4.5 .222 .167 .731 .742 4.078 80 656 13.594 .15 110 2520 38240 78 89 174 185 -50 245 235 10 .36 238 3 2.778 .27 -1.474 -1.889
6 400 201 194 134 206 67 418 182 198 139 224 48 0 0 102 58 41 35 91 58 91 41 273 272 3.075 .325 .214 .29 .327 2.662 12 68 .274 .4 40 2770 38250 83 87 203 207 0 326 217 109 .527 295 78 1.898 .347 -.925 -1.527
7 504 221 212 139 292 82 485 214 207 146 273 75 0 0 127 57 43 43 100 75 100 50 374 348 3.561 .281 .275 .279 .267 2.433 12 68 .17 .4 40 3010 38250 83 87 227 231 0 358 225 133 .455 347 121 2.199 .445 -1.137 -1.168
8 244 151 203 139 41 12 233 147 205 144 30 8 0 0 72 39 44 43 36 23 17 3 53 38 3.417 .293 .267 .773 .716 4.134 80 648 -1 -1 110 3240 38220 76 87 246 257 -50 245 225 19 .474 238 13 2.11 .432 -1.077 -1.211
9 209 164 192 145 17 19 196 161 196 150 4 16 0 0 83 52 51 47 22 21 13 10 36 20 .895 1.118 4 .759 .84 2.787 80 651 .566 .31 110 3480 38220 76 87 270 281 -50 266 235 31 1.81 261 26 .552 6.478 .856 2.696
10 191 160 183 142 8 18 186 157 777 340 3 15 0 0 55 45 5528 2061 0 0 0 0 26 18 .444 2.25 5 1.109 .904 5.105 80 656 .034 .46 110 3720 38220 76 87 294 305 -50 259 230 29 3.644 254 24 .274 8.098 1.866 3.018
11 187 150 178 136 9 14 170 147 181 140 -8 11 0 0 61 47 40 40 26 23 8 10 23 3 .643 1.556 null .836 .86 3.386 80 648 .596 .12 110 3960 38210 75 86 318 329 -50 243 220 23 2.519 238 18 .397 null 1.333 null
12 230 168 182 136 48 32 210 148 185 139 28 12 0 0 96 65 44 39 36 32 17 20 80 40 1.5 .667 .429 .902 .704 3.701 80 654 .566 .42 110 4200 38210 75 86 342 353 -50 272 220 52 1.08 240 19 .926 .694 .111 -.527
13 616 377 176 142 440 235 604 351 181 145 428 209 0 0 206 127 38 39 100 100 100 93 675 637 1.872 .534 .488 .516 .517 1.537 32 170 .545 .86 60 4450 38210 78 84 370 376 0 611 230 381 .865 568 338 1.156 .791 -.209 -.338
14 657 418 196 144 461 274 440 306 200 149 244 162 0 0 524 315 45 44 82 75 72 63 735 406 1.682 .594 .664 .599 .606 1.639 80 648 .606 .92 110 4670 38200 74 85 389 400 0 677 233 444 .963 496 262 1.039 1.075 -.055 .105
15 192 171 184 142 8 29 182 161 187 145 -2 19 0 0 62 85 46 43 20 28 11 12 37 17 .276 3.625 null 1.19 1.167 4.303 80 656 3.011 .09 110 4910 38200 74 85 413 424 -50 277 230 47 5.871 261 31 .17 null 2.554 null
16 211 169 181 141 30 28 194 160 185 146 13 19 0 0 72 63 43 50 30 25 12 10 58 32 1.071 .933 1.462 .971 1.037 3.964 80 648 2.854 .15 110 5150 38190 73 84 437 448 -50 274 228 45 1.512 259 31 .662 2.367 .596 1.243
17 206 173 182 143 24 30 175 153 217 294 -7 10 0 0 112 81 588 2744 0 0 0 0 54 3 .8 1.25 null 1.23 1.033 3.83 80 648 .809 .38 110 5390 38190 73 84 461 472 -50 280 232 49 2.025 248 16 .494 null 1.018 null
18 277 169 199 138 78 31 208 142 204 152 9 4 0 0 198 78 74 218 21 5 15 0 109 13 2.516 .397 .444 .785 .704 5.101 80 642 .335 .59 110 1570 38490 103 114 79 90 -50 274 224 50 .644 230 6 1.554 .72 -.636 -.474
19 472 241 194 146 278 95 453 221 193 146 259 75 0 0 128 87 41 39 100 66 91 50 373 334 2.926 .342 .29 .298 .283 1.842 12 68 .413 .75 40 1810 38500 108 112 107 111 0 390 236 154 .553 358 121 1.807 .469 -.853 -1.092
20 230 172 196 134 34 38 219 157 198 141 23 23 0 0 64 100 41 52 40 28 23 8 72 46 .895 1.118 1 .969 1 3.623 80 656 2.66 .19 110 2050 38480 102 113 127 138 -50 279 217 62 1.81 254 37 .552 1.62 .856 .696

Total number of rows: 4608

Table truncated, full table size 991 Kbytes.




Supplementary data files not provided
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