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Sample GSM84342 Query DataSets for GSM84342
Status Public on Nov 22, 2005
Title TC2 6HR
Sample type RNA
 
Channel 1
Source name Original SS1 RNA
Organism Helicobacter pylori
Characteristics Original SS1 RNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name T6 RNA
Organism Helicobacter pylori
Characteristics T6 RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Environmental conditions, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15191.gif
Measurement: time(absolute) 6 h
name: 15191_Elapsed Time
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 Nov 18, 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)
GSE3636 Growth phase dependent gene expression and motility_3 time courses

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 6538 2794 188 120 6350 2674 5765 2781 190 127 5577 2661 0 0 2548 789 49 50 100 100 100 100 9024 8238 2.375 .421 .477 .439 .43 1.577 52 420 .362 .9 90 1490 14250 60 69 24 33 0 2599 112 2487 .392 2586 2475 2.553 .444 -1.352 -1.172
2 491 414 173 119 318 295 477 405 179 129 304 286 0 0 65 84 42 52 100 100 100 100 613 590 1.078 .928 .941 .909 .879 1.352 12 68 .903 .76 40 1750 14250 63 67 53 57 0 385 111 274 .863 377 266 1.159 .875 -.213 -.193
3 2771 1144 175 129 2596 1015 2639 1110 177 134 2464 981 0 0 1033 363 40 52 100 100 100 100 3611 3445 2.558 .391 .398 .401 .409 1.422 52 332 .355 .89 80 1960 14240 60 68 72 80 0 1064 120 944 .364 1032 912 2.75 .37 -1.459 -1.433
4 641 772 162 128 479 644 614 713 166 126 452 585 0 0 373 379 43 29 83 100 83 100 1123 1037 .744 1.344 1.294 1.908 1.389 3.015 12 54 1.169 .86 40 2200 14230 61 65 98 102 0 718 119 599 1.25 663 544 .8 1.204 .322 .268
5 614 749 155 123 459 626 583 843 163 123 428 720 0 0 239 264 36 36 100 100 100 100 1085 1148 .733 1.364 1.682 1.428 1.265 1.993 12 54 1.311 .77 40 2440 14230 61 65 122 126 0 697 114 582 1.268 784 670 .788 1.565 .343 .646
6 626 465 188 150 438 315 600 448 191 155 412 298 0 0 154 131 42 52 100 99 100 94 753 710 1.39 .719 .723 .696 .729 1.623 156 1088 .743 .86 140 2680 14240 57 71 141 155 0 432 140 293 .669 417 277 1.495 .673 -.58 -.572
7 592 569 157 137 435 432 549 542 164 141 392 405 0 0 139 246 31 43 100 100 100 100 867 797 1.007 .993 1.033 .897 .908 1.677 12 48 1.15 .79 40 2920 14220 60 64 170 174 0 529 127 402 .924 504 377 1.083 .961 -.115 -.058
8 664 802 160 128 504 674 677 892 167 135 517 764 0 0 312 251 36 41 91 100 91 100 1178 1281 .748 1.337 1.478 1.71 1.458 2.225 12 98 1.067 .83 50 3150 14230 60 65 192 197 0 746 119 627 1.244 830 711 .804 1.374 .315 .459
9 1248 914 179 141 1069 773 387 290 181 146 208 149 0 0 1522 1049 39 42 78 75 67 63 1842 357 1.383 .723 .716 .867 .797 2.825 80 543 .684 .95 100 3390 14230 58 68 214 224 0 850 131 719 .673 270 139 1.487 .666 -.572 -.586
10 603 767 175 142 428 625 701 848 182 151 526 706 0 0 250 227 44 49 91 100 91 100 1053 1232 .685 1.46 1.342 1.759 1.25 2.288 12 98 1.293 .84 50 3620 14230 60 65 239 244 0 713 132 581 1.358 789 657 .736 1.248 .442 .32
11 393 526 163 134 230 392 367 451 166 138 204 317 0 0 161 274 35 41 84 93 81 90 622 521 .587 1.704 1.554 1.913 1.713 2.245 32 160 1.783 .86 60 3880 14220 59 65 265 271 0 489 125 365 1.585 419 295 .631 1.445 .665 .531
12 423 436 165 130 258 306 419 414 169 134 254 284 0 0 119 130 36 37 100 100 100 98 564 538 .843 1.186 1.118 1.184 1.072 1.589 52 400 1.33 .8 90 4120 14220 57 66 287 296 0 406 121 285 1.103 385 264 .907 1.04 .142 .056
13 530 660 167 139 363 521 521 650 170 142 354 511 0 0 145 175 37 40 100 100 100 100 884 865 .697 1.435 1.444 1.461 1.503 1.477 32 220 1.397 .89 70 4360 14220 58 65 312 319 0 614 129 485 1.335 605 475 .749 1.343 .417 .425
14 1559 1177 209 167 1350 1010 1225 998 233 178 1016 831 0 0 858 597 168 82 100 96 96 96 2360 1847 1.337 .748 .818 .711 .747 1.772 32 220 .685 .91 70 4590 14220 58 65 335 342 0 1095 155 939 .696 928 773 1.437 .761 -.523 -.395
15 574 391 172 127 402 264 579 378 166 134 407 251 0 0 76 98 33 38 100 100 100 100 666 658 1.523 .657 .617 .634 .575 1.484 12 90 .626 .79 50 4860 14220 59 64 363 368 0 364 118 246 .611 352 233 1.637 .574 -.711 -.802
16 560 756 162 145 398 611 478 775 166 146 316 630 0 0 230 342 34 43 100 96 100 93 1009 946 .651 1.535 1.994 1.331 1.474 2.327 32 170 1.614 .88 60 5100 14230 60 66 387 393 0 703 135 568 1.428 721 586 .7 1.854 .514 .891
17 775 1640 161 139 614 1501 702 1405 161 145 541 1266 0 0 399 820 35 45 100 100 96 100 2115 1807 .409 2.445 2.34 2.726 2.411 1.639 52 420 2.385 .94 90 5330 14240 59 68 408 417 0 1525 129 1396 2.274 1307 1177 .44 2.176 1.185 1.122
18 264 225 179 128 85 97 201 164 794 790 22 36 0 0 169 154 4409 4767 0 0 0 0 182 58 .876 1.141 1.636 .799 .675 3.908 52 420 1.077 .93 90 1490 14470 82 91 24 33 0 209 119 90 1.061 153 33 .942 1.522 .086 .606
19 654 495 175 123 479 372 552 415 176 128 377 292 0 0 299 237 39 38 100 100 100 100 851 669 1.288 .777 .775 .787 .724 1.635 32 176 .744 .83 60 1740 14480 85 91 51 57 0 460 114 346 .722 386 272 1.384 .72 -.469 -.473
20 202 190 173 127 29 63 160 131 175 130 -13 4 0 0 150 196 34 38 13 26 11 17 92 -9 .46 2.172 null 1.777 1.583 4.31 80 650 1.432 .76 110 1970 14480 82 93 71 82 0 177 118 59 2.02 122 4 .495 null 1.015 null

Total number of rows: 4608

Table truncated, full table size 1033 Kbytes.




Supplementary data files not provided
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