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Sample GSM88796 Query DataSets for GSM88796
Status Public on Dec 22, 2005
Title Log Chelate T=90m
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=90min
Organism Helicobacter pylori
Characteristics 1ug Log chelate T=90min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Environmental conditions, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31380.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 4012 3438 154 157 3858 3281 3919 3330 155 162 3765 3173 0 0 738 709 27 45 100 100 100 100 7139 6938 1.176 .85 .843 .844 .837 1.106 52 338 .864 .98 90 1230 12740 45 54 42 51 0 2914 133 2781 .721 2822 2689 1.388 .714 -.473 -.486
2 1217 1040 153 137 1064 903 1246 1077 154 142 1093 940 0 0 468 396 26 41 100 100 100 100 1967 2033 1.178 .849 .86 .855 .864 1.342 52 340 .842 .96 80 1480 12760 48 56 68 76 0 881 116 765 .719 913 797 1.39 .729 -.475 -.456
3 1713 1622 146 148 1567 1474 1502 1498 149 154 1356 1350 0 0 958 952 26 62 100 100 100 100 3041 2706 1.063 .941 .996 .906 .872 1.27 52 412 .958 .97 90 1740 12740 45 54 93 102 0 1375 125 1249 .797 1269 1144 1.254 .844 -.327 -.245
4 512 390 139 140 373 250 518 396 144 152 379 256 0 0 194 140 34 46 100 91 100 83 623 635 1.492 .67 .675 .589 .712 2.058 12 104 .762 .82 50 1970 12750 48 53 118 123 0 331 119 212 .568 336 217 1.761 .572 -.816 -.805
5 647 447 151 154 496 293 678 427 153 154 527 273 0 0 145 119 24 44 100 100 100 100 789 800 1.693 .591 .518 .58 .608 1.498 12 68 .622 .88 40 2220 12750 49 53 144 148 0 379 131 248 .501 362 231 1.998 .439 -.998 -1.188
6 618 485 155 163 463 322 514 457 160 170 359 294 0 0 304 234 36 54 100 93 93 68 785 653 1.438 .695 .819 .619 .719 1.962 32 236 .724 .92 70 2460 12750 47 54 166 173 0 411 138 273 .589 387 249 1.697 .694 -.763 -.527
7 1002 1108 147 152 855 956 841 871 158 157 694 719 0 0 536 788 65 47 100 100 100 100 1811 1413 .894 1.118 1.036 .967 1.006 1.425 52 412 1.261 .95 90 2710 12740 45 54 190 199 0 939 129 810 .948 738 609 1.055 .878 -.078 -.188
8 1117 1504 146 155 971 1349 1112 1496 148 162 966 1341 0 0 509 733 31 77 100 100 100 100 2320 2307 .72 1.389 1.388 1.359 1.348 1.324 52 412 1.414 .97 90 2950 12740 45 54 214 223 0 1275 131 1143 1.177 1268 1136 .849 1.176 .236 .234
9 2813 3119 151 158 2662 2961 2842 2865 155 169 2691 2707 0 0 1327 1617 37 81 100 100 100 100 5623 5398 .899 1.112 1.006 1.077 1.074 1.201 52 405 1.148 .99 90 3190 12730 44 53 238 247 0 2643 134 2509 .943 2428 2294 1.061 .852 -.085 -.23
10 553 618 151 161 402 457 464 544 160 186 313 383 0 0 277 302 63 190 100 82 92 50 859 696 .88 1.137 1.224 1.154 1.141 1.364 52 332 1.561 .77 80 3440 12740 46 54 264 272 0 524 136 387 .963 461 325 1.038 1.037 -.054 .052
11 658 595 162 163 496 432 589 529 166 177 427 366 0 0 347 250 35 55 96 93 93 93 928 793 1.148 .871 .857 .928 .912 1.663 32 176 .804 .94 60 3680 12750 48 54 289 295 0 504 138 366 .738 448 310 1.355 .726 -.438 -.461
12 1386 1395 171 190 1215 1205 1437 1399 171 197 1266 1209 0 0 244 279 29 120 100 100 100 100 2420 2475 1.008 .992 .955 .983 .954 1.186 52 412 1.01 .97 90 3910 12730 44 53 310 319 0 1182 161 1021 .84 1186 1025 1.19 .809 -.251 -.305
13 616 826 168 179 448 647 447 588 172 195 279 409 0 0 520 734 39 119 80 67 65 55 1095 688 .692 1.444 1.466 1.463 1.492 1.897 120 758 1.437 .96 120 4160 12730 43 55 334 346 0 700 152 548 1.224 498 347 .817 1.242 .291 .313
14 948 1219 161 163 787 1056 386 440 166 172 225 277 0 0 990 1341 36 59 85 80 77 75 1843 502 .745 1.342 1.231 1.237 1.345 2.345 120 772 1.362 .98 120 4380 12740 44 56 356 368 0 1033 138 895 1.137 373 235 .879 1.043 .185 .061
15 871 903 164 155 707 748 771 617 166 162 607 462 0 0 516 1322 28 42 100 86 100 78 1455 1069 .945 1.058 .761 .673 .731 2.156 52 332 2.74 .55 80 4640 12740 46 54 384 392 0 765 131 634 .897 523 392 1.115 .645 -.157 -.633
16 1302 2445 158 160 1144 2285 1010 1848 159 163 852 1688 0 0 747 1598 30 44 100 100 100 100 3429 2540 .501 1.997 1.981 1.919 1.936 1.248 32 230 2.186 .96 70 4870 12730 45 52 407 414 0 2072 136 1936 1.693 1566 1431 .591 1.679 .759 .748
17 1989 1260 156 152 1833 1108 1464 915 157 160 1308 763 0 0 1573 1006 29 77 100 100 100 96 2941 2071 1.654 .604 .583 .583 .589 1.332 52 412 .615 .97 90 5120 12730 44 53 431 440 0 1068 129 939 .512 775 647 1.952 .494 -.965 -1.016
18 1215 1285 154 151 1061 1134 1064 1039 155 157 910 888 0 0 722 929 28 43 100 96 100 92 2195 1798 .936 1.069 .976 .809 .84 2.093 52 322 1.18 .92 80 1280 12990 71 79 48 56 0 1089 128 961 .906 881 753 1.104 .827 -.143 -.274
19 1121 1106 150 150 971 956 890 867 151 153 740 717 0 0 703 640 25 41 100 100 100 100 1927 1457 1.016 .985 .969 1.017 1.001 1.416 32 176 .956 .94 60 1510 12990 72 78 72 78 0 937 127 810 .834 735 608 1.199 .821 -.261 -.284
20 655 611 153 146 502 465 754 622 152 150 601 476 0 0 272 251 28 35 100 100 100 91 967 1077 1.08 .926 .792 .91 .888 1.956 12 104 .979 .82 50 1760 12980 71 76 97 102 0 518 124 394 .785 527 403 1.274 .671 -.349 -.575

Total number of rows: 4608

Table truncated, full table size 1060 Kbytes.




Supplementary data files not provided
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