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Sample GSM88818 Query DataSets for GSM88818
Status Public on Dec 22, 2005
Title Log Chelate T=60m
Sample type RNA
 
Channel 1
Source name 1ug Log Chelate T=0
Organism Helicobacter pylori
Characteristics 1ug Log Chelate T=0
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 1ug Log chelate T=60min
Organism Helicobacter pylori
Characteristics 1ug Log chelate T=60min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Environmental conditions, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31379.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 3383 2178 179 174 3204 2004 3299 2231 181 190 3120 2057 0 0 635 415 33 102 100 100 100 100 5208 5177 1.599 .625 .659 .623 .63 1.136 52 384 .63 .98 90 1360 39960 83 92 55 64 0 2269 181 2088 .652 2324 2143 1.535 .687 -.618 -.542
2 1154 855 176 154 978 701 1121 844 178 159 945 690 0 0 275 195 28 43 100 100 100 100 1679 1635 1.395 .717 .73 .715 .714 1.224 32 236 .707 .96 70 1610 39960 84 91 81 88 0 891 160 730 .747 879 719 1.339 .761 -.422 -.395
3 1446 1037 178 154 1268 883 1016 841 180 155 838 687 0 0 875 603 27 37 100 100 100 100 2151 1525 1.436 .696 .82 .7 .664 1.357 52 400 .688 .98 90 1840 39940 81 90 103 112 0 1080 160 920 .725 876 716 1.379 .854 -.463 -.228
4 596 441 183 169 413 272 542 400 186 171 359 231 0 0 190 156 28 48 100 100 100 100 685 590 1.518 .659 .643 .643 .636 1.496 12 68 .712 .91 40 2090 39970 87 91 131 135 0 459 176 283 .686 417 241 1.458 .67 -.544 -.577
5 744 537 365 282 379 255 834 514 368 279 469 232 0 0 218 139 42 61 100 100 91 83 634 701 1.486 .673 .495 .742 .662 1.764 12 62 .646 .84 40 2320 39960 86 90 154 158 0 559 294 266 .701 535 242 1.427 .515 -.513 -.957
6 587 469 342 269 245 200 471 378 325 270 129 109 0 0 272 213 83 82 65 55 46 42 445 238 1.225 .816 .845 .808 .817 2.964 52 340 .766 .9 80 2560 39980 86 94 176 184 0 489 280 208 .85 394 114 1.176 .88 -.234 -.184
7 1189 1093 219 192 970 901 1239 1062 222 196 1020 870 0 0 250 285 38 51 100 100 100 100 1871 1890 1.077 .929 .853 .924 .949 1.222 32 236 .945 .96 70 2820 39960 84 91 202 209 0 1139 200 939 .968 1106 906 1.034 .888 -.048 -.171
8 1245 1245 324 254 921 991 1286 1188 314 259 962 934 0 0 301 373 77 68 100 100 100 100 1912 1896 .929 1.076 .971 1.059 1.084 1.22 32 176 1.103 .97 60 3040 39960 85 91 225 231 0 1297 265 1032 1.121 1238 973 .892 1.011 .165 .016
9 2114 1597 339 243 1775 1354 2085 1656 321 245 1746 1413 0 0 557 398 93 76 100 100 100 100 3129 3159 1.311 .763 .809 .768 .761 1.13 32 230 .759 .98 70 3290 39940 82 89 249 256 0 1664 253 1410 .795 1725 1472 1.258 .843 -.332 -.246
10 525 442 221 179 304 263 452 358 238 197 231 179 0 0 290 282 69 86 81 68 65 50 567 410 1.156 .865 .775 .799 .839 1.774 32 170 .958 .91 60 3540 39950 84 90 275 281 0 460 186 274 .901 373 186 1.11 .807 -.15 -.309
11 352 281 203 174 149 107 233 186 207 179 30 12 0 0 316 245 41 68 41 31 30 20 256 42 1.393 .718 .4 .993 .852 2.88 80 648 .495 .84 110 3780 39940 80 91 296 307 -50 293 181 111 .748 194 13 1.337 .417 -.419 -1.263
12 1188 1040 200 177 988 863 1170 991 194 180 970 814 0 0 161 185 60 60 100 100 100 100 1851 1784 1.145 .873 .839 .866 .866 1.159 32 236 .859 .98 70 4020 39940 82 89 322 329 0 1083 184 899 .91 1032 848 1.099 .874 -.136 -.194
13 517 528 208 175 309 353 420 411 632 567 212 236 0 0 385 401 4203 4444 0 0 0 0 662 448 .875 1.142 1.113 .927 1.039 2.069 80 522 1.19 .98 100 4290 39920 79 89 348 358 0 550 182 368 1.19 428 246 .84 1.16 .251 .214
14 789 680 215 173 574 507 507 409 222 182 292 236 0 0 916 656 68 88 70 66 61 57 1081 528 1.132 .883 .808 .848 .852 2.053 80 552 .744 .9 100 4510 39940 81 91 370 380 0 708 180 528 .92 426 246 1.087 .842 -.12 -.248
15 1139 766 219 187 920 579 1226 768 222 189 1007 581 0 0 239 170 48 47 100 100 100 100 1499 1588 1.589 .629 .577 .629 .6 1.307 12 104 .619 .95 50 4740 39950 84 89 395 400 0 798 195 603 .656 800 605 1.525 .601 -.609 -.735
16 632 850 212 168 420 682 466 638 212 173 254 470 0 0 447 664 27 42 90 98 88 94 1102 724 .616 1.624 1.85 1.69 1.549 1.614 52 306 1.56 .97 80 5000 39920 80 88 420 428 0 885 175 710 1.691 665 490 .591 1.927 .758 .947
17 1319 632 213 170 1106 462 792 385 213 173 579 215 0 0 1196 591 28 43 96 90 94 73 1568 794 2.394 .418 .371 .324 .371 1.773 52 384 .462 .97 90 5240 39910 78 87 443 452 0 658 177 481 .435 401 224 2.298 .387 -1.2 -1.37
18 1284 1456 176 166 1108 1290 1477 1612 178 173 1301 1446 0 0 504 566 26 42 100 100 100 100 2398 2747 .859 1.164 1.111 1.174 1.133 1.374 32 230 1.127 .97 70 1390 40190 107 114 59 66 0 1517 173 1344 1.213 1679 1506 .825 1.158 .278 .211
19 1129 951 174 170 955 781 1038 870 178 169 864 700 0 0 595 534 27 40 100 100 100 96 1736 1564 1.223 .818 .81 .761 .832 1.367 32 236 .845 .98 70 1640 40200 108 115 84 91 0 991 177 814 .852 906 729 1.174 .844 -.231 -.245
20 544 511 182 171 362 340 568 493 182 175 386 322 0 0 248 226 33 41 91 100 83 91 702 708 1.065 .939 .834 1.056 .992 2.02 12 104 .865 .9 50 1880 40210 110 115 109 114 0 532 178 354 .978 514 335 1.022 .869 -.032 -.203

Total number of rows: 4608

Table truncated, full table size 1046 Kbytes.




Supplementary data files not provided
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