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Sample GSM88797 Query DataSets for GSM88797
Status Public on Dec 22, 2005
Title Log Chelate T=0/control
Sample type RNA
 
Channel 1
Source name 1ug Motility control T=0
Organism Helicobacter pylori
Characteristics 1ug Motility control T=0
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Log Chelate T=0 1ug RNA
Organism Helicobacter pylori
Characteristics Log Chelate T=0 1ug RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Environmental conditions, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31631.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 5623 3538 126 94 5497 3444 5325 3548 128 96 5199 3454 0 0 1852 911 23 21 100 100 100 100 8941 8653 1.596 .627 .664 .638 .621 1.166 52 400 .606 .98 90 1320 40700 25 34 39 48 0 3647 97 3551 .646 3658 3561 1.548 .685 -.631 -.546
2 995 686 123 92 872 594 1017 677 125 94 894 585 0 0 383 265 19 20 100 100 100 100 1466 1479 1.468 .681 .654 .681 .667 1.156 52 420 .673 .98 90 1560 40700 25 34 63 72 0 707 95 612 .702 698 603 1.424 .675 -.51 -.568
3 1499 1272 115 79 1384 1193 1377 1211 111 80 1262 1132 0 0 887 717 31 22 100 100 100 100 2577 2394 1.16 .862 .897 .896 .867 1.227 52 332 .834 .98 80 1800 40690 25 33 88 96 0 1311 81 1230 .889 1248 1167 1.125 .925 -.17 -.113
4 558 492 122 91 436 401 585 496 127 94 463 405 0 0 151 144 29 27 100 100 100 100 837 868 1.087 .92 .875 .914 .918 1.127 12 104 .971 .94 50 2040 40710 28 33 113 118 0 507 94 413 .948 511 418 1.055 .902 -.077 -.149
5 464 364 129 100 335 264 432 370 130 103 303 270 0 0 196 113 20 18 100 100 100 100 599 573 1.269 .788 .891 .88 .737 1.573 12 68 .75 .9 40 2270 40710 29 33 137 141 0 375 103 272 .812 381 278 1.231 .919 -.3 -.122
6 682 415 130 96 552 319 753 440 131 99 623 344 0 0 240 134 22 25 100 100 100 100 871 967 1.73 .578 .552 .594 .593 1.35 32 230 .567 .93 70 2520 40690 25 32 160 167 0 428 99 329 .596 454 355 1.678 .569 -.747 -.813
7 1153 843 124 89 1029 754 1178 819 239 341 1054 730 0 0 645 486 1384 2971 26 0 0 0 1783 1784 1.365 .733 .693 .749 .759 1.407 52 340 .737 .97 80 2780 40700 26 34 186 194 0 869 92 777 .755 844 753 1.324 .714 -.405 -.486
8 1237 1046 125 98 1112 948 1258 925 183 130 1133 827 0 0 517 415 723 186 67 100 30 98 2060 1960 1.173 .853 .73 .874 .84 1.23 52 412 .841 .98 90 3000 40690 24 33 207 216 0 1078 101 977 .879 954 853 1.138 .752 -.186 -.41
9 3305 2379 120 90 3185 2289 3679 2593 121 92 3559 2503 0 0 1649 1134 19 19 100 100 100 100 5474 6062 1.391 .719 .703 .734 .726 1.181 52 412 .695 .97 90 3250 40690 24 33 232 241 0 2453 93 2360 .741 2673 2580 1.35 .725 -.433 -.464
10 606 615 119 96 487 519 437 431 121 98 318 335 0 0 375 408 19 23 100 100 100 100 1006 653 .938 1.066 1.053 1.085 1.103 1.3 32 230 1.09 .97 70 3500 40690 25 32 258 265 0 634 99 535 1.099 444 345 .91 1.086 .136 .119
11 656 736 129 104 527 632 480 524 131 107 351 420 0 0 495 607 30 31 100 100 98 98 1159 771 .834 1.199 1.197 1.184 1.196 1.312 52 420 1.221 .98 90 3730 40700 25 34 280 289 0 759 107 652 1.236 540 433 .809 1.234 .306 .303
12 1337 1245 138 111 1199 1134 1325 1230 140 116 1187 1119 0 0 294 302 23 57 100 100 100 100 2333 2306 1.057 .946 .943 .946 .945 1.228 52 420 .976 .97 90 3980 40700 25 34 305 314 0 1284 114 1169 .975 1268 1154 1.026 .972 -.036 -.041
13 1289 1209 138 113 1151 1096 1103 1034 139 117 965 921 0 0 651 646 23 32 100 100 100 100 2247 1886 1.05 .952 .954 .935 .981 1.208 52 340 .965 .99 80 4220 40700 26 34 330 338 0 1246 116 1130 .982 1066 949 1.019 .984 -.027 -.023
14 1030 1265 131 109 899 1156 800 1018 136 115 669 909 0 0 799 1018 27 35 97 93 93 93 2055 1578 .778 1.286 1.359 1.219 1.267 1.461 80 560 1.291 .98 100 4460 40700 25 35 353 363 0 1304 112 1192 1.326 1049 937 .754 1.401 .407 .486
15 697 656 139 113 558 543 504 480 376 197 365 367 0 0 440 437 3578 1172 0 9 0 0 1101 732 1.028 .973 1.005 .976 .951 1.571 52 340 .985 .98 80 4710 40700 26 34 379 387 0 676 116 560 1.003 495 378 .997 1.037 .005 .052
16 700 1273 137 117 563 1156 581 1154 138 120 444 1037 0 0 473 938 23 32 92 96 92 94 1719 1481 .487 2.053 2.336 2.066 2.169 1.771 52 340 2.07 .96 80 4940 40710 27 35 402 410 0 1312 121 1192 2.117 1190 1069 .472 2.408 1.082 1.268
17 1417 1871 132 110 1285 1761 1082 1393 134 114 950 1283 0 0 960 1326 20 31 100 100 100 100 3046 2233 .73 1.37 1.351 1.369 1.404 1.401 52 340 1.398 .95 80 5190 40700 26 34 427 435 0 1929 113 1815 1.413 1436 1323 .708 1.392 .499 .477
18 801 877 135 104 666 773 771 840 136 107 636 736 0 0 511 515 20 24 100 100 100 100 1439 1372 .862 1.161 1.157 1.234 1.311 1.65 32 176 1.109 .84 60 1340 40960 53 59 43 49 0 904 107 797 1.197 866 759 .836 1.193 .259 .255
19 1505 1275 135 105 1370 1170 1293 1199 138 108 1158 1094 0 0 916 774 23 26 100 100 100 100 2540 2252 1.171 .854 .945 .859 .906 1.326 32 236 .851 .99 70 1600 40950 51 58 68 75 0 1314 108 1206 .88 1236 1128 1.136 .974 -.184 -.038
20 401 408 121 94 280 314 369 324 125 95 248 230 0 0 210 217 20 20 96 100 96 96 594 478 .892 1.121 .927 1.212 1.136 1.514 32 176 1.104 .94 60 1820 40950 52 58 91 97 0 421 97 324 1.156 334 237 .865 .956 .209 -.065

Total number of rows: 4608

Table truncated, full table size 1057 Kbytes.




Supplementary data files not provided
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