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Sample GSM88815 Query DataSets for GSM88815
Status Public on Dec 22, 2005
Title TC Motility_broth T=30.
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 1 ug Motility_broth T=30
Organism Helicobacter pylori
Characteristics 1 ug Motility_broth T=30
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Environmental conditions, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31629.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 6850 4067 102 84 6748 3983 7068 4330 103 85 6966 4246 0 0 1941 1039 16 18 100 100 100 100 10731 11212 1.694 .59 .61 .59 .603 1.397 80 522 .575 .97 100 1390 40890 28 38 46 56 0 2676 55 2620 .388 2849 2793 2.575 .401 -1.365 -1.318
2 1002 899 99 80 903 819 958 862 100 84 859 782 0 0 368 315 16 39 100 100 100 100 1722 1641 1.103 .907 .91 .925 .943 1.249 52 420 .899 .97 90 1630 40890 28 37 70 79 0 591 53 539 .597 567 514 1.676 .599 -.745 -.74
3 1426 1042 95 76 1331 966 973 734 96 76 878 658 0 0 1085 805 14 17 100 100 98 98 2297 1536 1.378 .726 .749 .707 .729 1.62 80 560 .727 .97 100 1880 40890 28 38 95 105 0 686 50 636 .477 483 433 2.094 .493 -1.066 -1.02
4 327 356 95 74 232 282 245 297 95 76 150 223 0 0 244 229 12 18 100 100 100 100 514 373 .823 1.216 1.487 1.472 1.377 1.611 32 236 1.062 .95 70 2120 40900 30 37 120 127 0 234 49 186 .8 195 147 1.25 .978 -.323 -.032
5 221 267 98 78 123 189 209 253 100 79 111 175 0 0 97 117 16 19 83 100 66 100 312 286 .651 1.537 1.577 1.818 1.764 1.712 12 104 1.374 .93 50 2350 40890 30 35 144 149 0 176 51 124 1.011 166 115 .989 1.037 .016 .053
6 339 257 100 82 239 175 174 148 102 84 74 66 0 0 353 236 17 23 84 78 73 60 414 140 1.366 .732 .892 .869 .789 2.264 120 787 .682 .97 120 2600 40870 25 37 166 178 0 169 54 115 .482 97 43 2.076 .587 -1.054 -.769
7 730 823 106 93 624 730 592 770 108 97 486 677 0 0 493 528 18 33 98 100 98 98 1354 1163 .855 1.17 1.393 1.312 1.214 1.69 80 552 1.157 .94 100 2850 40870 26 36 192 202 0 541 61 480 .77 507 445 1.299 .916 -.378 -.126
8 704 1144 108 94 596 1050 596 1010 110 107 488 916 0 0 370 651 23 68 98 98 98 96 1646 1404 .568 1.762 1.877 1.769 1.737 1.296 80 552 1.788 .97 100 3100 40870 26 36 217 227 0 753 62 691 1.159 664 603 .863 1.235 .213 .304
9 2610 2968 104 85 2506 2883 2827 3278 107 96 2723 3193 0 0 1324 1416 18 52 100 100 100 100 5389 5916 .869 1.15 1.173 1.187 1.166 1.266 80 560 1.13 .98 100 3330 40880 27 37 240 250 0 1953 56 1897 .757 2157 2101 1.321 .771 -.402 -.374
10 401 608 108 84 293 524 339 522 109 86 231 438 0 0 179 311 16 22 100 100 98 100 817 669 .559 1.788 1.896 1.793 1.907 1.557 52 340 1.83 .94 80 3580 40880 28 36 266 274 0 400 55 345 1.177 343 288 .85 1.247 .235 .319
11 415 656 128 102 287 554 367 549 128 103 239 447 0 0 237 431 17 23 98 100 94 98 841 686 .518 1.93 1.87 2.056 1.985 1.53 52 332 1.903 .95 80 3820 40870 27 35 290 298 0 432 67 364 1.27 361 294 .787 1.23 .345 .299
12 948 1517 137 110 811 1407 932 1473 138 115 795 1363 0 0 344 597 20 29 100 100 100 100 2218 2158 .576 1.735 1.714 1.755 1.735 1.323 80 538 1.752 .98 100 4060 40860 25 35 313 323 0 998 72 926 1.141 969 897 .876 1.128 .191 .174
13 731 1268 132 101 599 1167 545 981 134 107 413 880 0 0 426 798 23 37 100 100 97 98 1766 1293 .513 1.948 2.131 1.969 1.918 1.328 80 552 1.942 .98 100 4300 40870 26 36 337 347 0 834 66 768 1.282 645 579 .78 1.402 .358 .487
14 736 1003 136 108 600 895 344 404 161 130 208 296 0 0 659 1008 531 286 37 52 20 40 1495 504 .67 1.492 1.423 1.392 1.452 1.397 120 856 .889 .87 130 4530 40860 23 36 358 371 0 660 71 589 .981 266 195 1.019 .936 -.027 -.095
15 380 488 138 112 242 376 217 227 162 130 79 115 0 0 333 523 524 282 19 32 3 22 618 194 .644 1.554 1.456 1.556 1.575 2.027 120 877 1.512 .95 130 4750 40880 25 38 380 393 0 321 74 247 1.022 149 76 .978 .958 .032 -.062
16 611 1358 128 105 483 1253 618 1309 130 107 490 1204 0 0 306 802 20 24 96 100 96 100 1736 1694 .385 2.594 2.457 2.654 2.573 1.477 52 332 2.657 .98 80 5010 40870 27 35 409 417 0 893 69 824 1.707 861 792 .586 1.617 .771 .693
17 1357 1349 124 102 1233 1247 1002 967 125 104 878 865 0 0 918 924 17 20 100 100 100 100 2480 1743 .989 1.011 .985 1.038 1.016 1.217 52 400 .969 .97 90 5250 40850 24 33 432 441 0 888 67 820 .665 636 569 1.503 .648 -.588 -.626
18 506 880 115 99 391 781 292 473 117 105 177 374 0 0 400 682 20 28 100 100 100 100 1172 551 .501 1.997 2.113 2.174 2.214 1.469 32 220 1.94 .91 70 1390 41120 52 59 47 54 0 579 65 514 1.314 311 246 .761 1.39 .394 .475
19 1138 1264 109 93 1029 1171 886 970 109 96 777 877 0 0 699 801 22 24 100 100 100 100 2200 1654 .879 1.138 1.129 1.132 1.138 1.257 32 236 1.114 .98 70 1650 41120 52 59 73 80 0 832 61 770 .749 638 577 1.336 .743 -.418 -.429
20 450 634 101 83 349 551 390 542 100 86 289 459 0 0 207 269 12 17 100 100 100 100 900 748 .633 1.579 1.588 1.678 1.549 1.435 12 104 1.435 .94 50 1890 41120 53 58 98 103 0 417 55 363 1.039 357 302 .963 1.045 .055 .063

Total number of rows: 4608

Table truncated, full table size 1054 Kbytes.




Supplementary data files not provided
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