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Sample GSM88808 Query DataSets for GSM88808
Status Public on Dec 22, 2005
Title TC Motility_broth T=18.
Sample type RNA
 
Channel 1
Source name 1ug Motility_broth T=0
Organism Helicobacter pylori
Characteristics 1ug Motility_broth T=0
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 1ug Motility_broth T=18
Organism Helicobacter pylori
Characteristics 1ug Motility_broth T=18
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Environmental conditions, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31627.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 7895 5646 120 93 7775 5553 7417 5497 121 94 7297 5404 0 0 1628 974 18 18 100 100 100 100 13328 12701 1.4 .714 .741 .718 .712 1.088 52 400 .711 .99 90 1270 39600 27 36 34 43 0 4310 71 4239 .545 4196 4125 1.834 .565 -.875 -.823
2 1061 949 117 93 944 856 993 903 118 94 876 810 0 0 382 330 16 18 100 100 100 100 1800 1686 1.103 .907 .925 .916 .897 1.141 52 420 .9 .98 90 1510 39600 27 36 58 67 0 724 71 653 .692 689 618 1.445 .706 -.531 -.503
3 1844 1836 118 100 1726 1736 1695 1580 121 104 1577 1480 0 0 986 1044 19 26 100 100 100 100 3462 3057 .994 1.006 .938 .986 1.018 1.221 52 400 1.023 .99 90 1760 39580 25 34 83 92 0 1402 76 1325 .768 1206 1130 1.302 .716 -.381 -.481
4 472 520 139 136 333 384 401 401 143 144 262 265 0 0 322 374 29 42 84 81 81 71 717 527 .867 1.153 1.011 1.031 1.044 1.82 32 176 1.175 .97 60 1990 39620 31 37 108 114 0 397 104 293 .88 306 202 1.136 .772 -.184 -.373
5 652 791 170 214 482 577 678 840 171 206 508 626 0 0 128 169 36 55 100 100 100 100 1059 1134 .835 1.197 1.232 1.182 1.244 1.565 12 68 1.307 .93 40 2240 39600 30 34 134 138 0 604 163 440 .914 641 478 1.094 .941 -.13 -.088
6 862 765 201 214 661 551 848 675 223 218 647 461 0 0 349 318 126 105 100 100 100 91 1212 1108 1.2 .834 .713 .81 .765 1.237 12 98 1.029 .96 50 2460 39590 28 33 155 160 0 584 163 421 .636 515 352 1.572 .544 -.652 -.879
7 1185 1437 165 169 1020 1268 1139 1350 168 171 974 1181 0 0 581 729 30 43 100 100 100 100 2288 2155 .804 1.243 1.213 1.236 1.205 1.233 52 340 1.254 .98 80 2720 39600 28 36 180 188 0 1097 129 968 .949 1031 902 1.054 .926 -.076 -.112
8 1294 1769 177 175 1117 1594 1215 1699 178 179 1038 1524 0 0 612 863 31 45 100 100 100 100 2711 2562 .701 1.427 1.468 1.446 1.409 1.209 52 340 1.382 .92 80 2960 39600 28 36 204 212 0 1350 134 1217 1.089 1297 1163 .918 1.121 .123 .164
9 3418 4160 165 138 3253 4022 3527 4515 168 143 3362 4377 0 0 1553 1976 34 42 100 100 100 100 7275 7739 .809 1.236 1.302 1.225 1.249 1.121 52 415 1.251 .99 90 3190 39590 26 35 226 235 0 3176 105 3070 .944 3447 3341 1.06 .994 -.083 -.009
10 695 815 154 139 541 676 559 687 159 144 405 548 0 0 362 429 37 51 100 100 93 96 1217 953 .8 1.25 1.353 1.318 1.295 1.305 32 236 1.234 .97 70 3430 39610 29 36 251 258 0 622 106 516 .954 524 418 1.048 1.033 -.068 .047
11 759 1088 164 163 595 925 629 1110 169 164 465 947 0 0 311 384 33 47 100 100 100 100 1520 1412 .643 1.555 2.037 1.611 1.555 1.196 12 104 1.406 .96 50 3670 39590 28 33 276 281 0 831 124 706 1.187 847 723 .843 1.555 .247 .637
12 1065 1250 163 152 902 1098 1035 1281 177 165 872 1129 0 0 489 606 66 62 97 97 96 95 2000 2001 .821 1.217 1.295 1.208 1.214 1.398 80 656 1.232 .99 110 3920 39590 25 36 298 309 0 954 116 838 .929 978 862 1.076 .988 -.106 -.017
13 1032 1257 161 153 871 1104 854 910 162 155 693 757 0 0 511 695 27 32 100 100 100 100 1975 1450 .789 1.268 1.092 1.23 1.195 1.22 52 420 1.303 .98 90 4160 39590 26 35 323 332 0 960 117 843 .968 695 578 1.034 .834 -.048 -.262
14 1029 1377 187 190 842 1187 779 1017 198 206 592 827 0 0 734 1042 50 69 97 96 90 86 2029 1419 .709 1.41 1.397 1.39 1.382 1.423 80 552 1.42 .99 100 4390 39590 26 36 346 356 0 1051 145 906 1.076 776 631 .929 1.066 .106 .093
15 824 934 222 236 602 698 957 991 227 242 735 755 0 0 291 334 60 79 90 96 90 90 1300 1490 .862 1.159 1.027 1.318 1.226 1.634 32 170 1.175 .97 60 4640 39590 28 34 373 379 0 713 180 533 .885 756 576 1.13 .784 -.176 -.351
16 954 1761 165 166 789 1595 799 1655 169 172 634 1489 0 0 578 1104 34 46 100 100 100 100 2384 2123 .495 2.022 2.349 2.083 2.025 1.215 32 236 1.987 .99 70 4880 39590 27 34 396 403 0 1344 127 1218 1.543 1263 1137 .648 1.793 .626 .842
17 1336 1933 150 146 1186 1787 983 1520 153 150 833 1374 0 0 854 1284 22 30 100 100 100 100 2973 2207 .664 1.507 1.649 1.543 1.51 1.225 52 320 1.505 .98 80 5120 39580 26 34 420 428 0 1476 111 1364 1.15 1160 1049 .869 1.259 .202 .332
18 596 888 120 99 476 789 309 395 121 100 189 296 0 0 478 795 17 20 100 100 96 100 1265 485 .603 1.658 1.566 1.622 1.62 1.532 52 332 1.689 .97 80 1290 39840 52 60 37 45 0 678 76 602 1.265 302 226 .79 1.196 .339 .258
19 1644 1658 120 103 1524 1555 1414 1393 121 104 1294 1290 0 0 851 942 26 23 100 100 100 100 3079 2584 .98 1.02 .997 .972 .993 1.244 32 176 1.051 .98 60 1540 39820 51 57 63 69 0 1266 79 1187 .779 1063 985 1.284 .761 -.361 -.394
20 693 762 136 122 557 640 646 809 141 124 510 687 0 0 298 258 30 33 100 100 91 100 1197 1197 .87 1.149 1.347 1.388 1.114 1.837 12 68 1.083 .95 40 1780 39860 56 60 88 92 0 582 93 489 .877 618 524 1.14 1.028 -.189 .04

Total number of rows: 4608

Table truncated, full table size 1061 Kbytes.




Supplementary data files not provided
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