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Sample GSM71894 Query DataSets for GSM71894
Status Public on Aug 26, 2005
Title 1223c mutant 10 hr
Sample type RNA
 
Channel 1
Source name RNA pool of all tp, three strains;2ug RNA
Organism Campylobacter jejuni
Characteristics RNA pool of all tp, three strains;2ug RNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 1223c mt + pRY108 10hr;2ug RNA
Organism Campylobacter jejuni
Characteristics 1223c mt + pRY108 10hr;2ug RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43065.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 Aug 25, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL2782
Series (1)
GSE3198 Cj1223c Mutant vs. Overexpressed, Time Course

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
1 474 397 215 122 259 275 432 335 407 284 217 213 0 0 163 171 1337 1130 0 0 0 0 534 430 .942 1.062 .982 1.198 1.084 2.102 52 312 1.056 .88 80 1690 42560 72 80 81 89 0 410 126 284 1.097 346 220 .912 1.014 .133 .02
2 759 467 206 123 553 344 728 451 211 125 522 328 0 0 282 156 41 32 100 100 100 100 897 850 1.608 .622 .628 .636 .645 1.594 52 420 .562 .85 90 1940 42560 71 80 105 114 0 482 127 355 .643 466 339 1.556 .649 -.638 -.623
3 600 323 216 123 384 200 578 319 222 128 362 196 0 0 170 109 42 36 100 100 100 88 584 558 1.92 .521 .541 .494 .473 1.736 52 420 .504 .78 90 2170 42560 71 80 128 137 0 334 127 207 .538 330 202 1.859 .559 -.894 -.838
4 467 314 222 128 245 186 430 286 227 131 208 158 0 0 167 100 45 37 94 96 84 90 431 366 1.317 .759 .76 .83 .755 1.935 52 332 .648 .76 80 2410 42560 72 80 153 161 0 324 132 192 .784 295 163 1.275 .785 -.351 -.35
5 572 397 232 137 340 260 547 375 234 140 315 238 0 0 159 135 45 40 100 100 100 96 600 553 1.308 .765 .756 .746 .771 1.743 32 236 .782 .81 70 2650 42560 72 79 177 184 0 410 142 269 .79 387 246 1.266 .781 -.34 -.358
6 883 501 230 134 653 367 743 470 235 138 513 336 0 0 575 236 47 41 100 98 100 96 1020 849 1.779 .562 .655 .56 .593 1.811 52 340 .43 .81 80 2890 42570 73 81 201 209 0 518 138 379 .581 486 347 1.722 .677 -.784 -.564
7 576 398 230 136 346 262 505 379 232 139 275 243 0 0 196 153 41 35 100 100 94 92 608 518 1.321 .757 .884 .752 .747 1.663 52 420 .726 .82 90 3130 42570 72 81 224 233 0 411 140 271 .782 392 251 1.278 .913 -.354 -.132
8 706 451 237 143 469 308 643 474 239 145 406 331 0 0 278 164 44 35 98 96 94 94 777 737 1.523 .657 .815 .651 .628 1.557 52 420 .625 .91 90 3370 42560 71 80 248 257 0 466 148 318 .678 490 342 1.474 .842 -.56 -.248
9 573 393 225 135 348 258 534 406 230 136 309 271 0 0 207 129 43 35 96 96 94 94 606 580 1.349 .741 .877 .782 .833 1.631 52 332 .686 .82 80 3610 42560 72 80 273 281 0 406 139 267 .766 419 280 1.306 .906 -.385 -.142
10 597 426 225 140 372 286 574 431 229 139 349 291 0 0 146 139 42 35 100 100 98 96 658 640 1.301 .769 .834 .729 .774 1.436 52 332 .811 .89 80 3860 42560 72 80 298 306 0 440 145 295 .794 445 301 1.259 .861 -.332 -.215
11 517 381 225 139 292 242 532 396 231 141 307 257 0 0 189 131 44 35 90 90 84 87 534 564 1.207 .829 .837 .843 .853 1.583 32 236 .698 .82 70 4100 42560 72 79 322 329 0 394 144 250 .856 409 265 1.168 .865 -.224 -.21
12 471 355 217 134 254 221 462 337 220 136 245 203 0 0 148 134 41 33 96 96 90 94 475 448 1.149 .87 .829 .887 .855 1.742 52 332 .878 .83 80 4330 42560 72 80 345 353 0 367 138 228 .899 348 210 1.113 .856 -.154 -.224
13 983 915 229 130 754 785 866 612 233 131 637 482 0 0 527 711 44 31 100 100 100 100 1539 1119 .961 1.041 .757 .96 .997 1.492 32 236 1.192 .95 70 4570 42570 73 80 369 376 0 945 134 811 1.076 632 498 .93 .782 .105 -.355
14 709 453 237 141 472 312 645 415 240 143 408 274 0 0 346 273 45 37 100 92 96 92 784 682 1.513 .661 .672 .581 .616 1.817 52 332 .706 .92 80 4810 42560 72 80 393 401 0 468 146 322 .683 429 283 1.464 .694 -.55 -.528
15 771 688 262 150 509 538 728 600 266 154 466 450 0 0 300 344 47 38 100 100 98 100 1047 916 .946 1.057 .966 1.068 1.179 1.638 52 340 1.108 .9 80 5040 42570 73 81 416 424 0 711 155 556 1.092 620 465 .916 .998 .127 -.004
16 1043 740 262 145 781 595 934 665 269 149 672 520 0 0 444 442 50 38 100 100 100 100 1376 1192 1.313 .762 .774 .719 .754 1.513 52 340 .826 .91 80 5290 42570 73 81 441 449 0 764 150 615 .787 687 537 1.271 .799 -.346 -.323
17 699 665 219 117 480 548 566 427 222 123 347 310 0 0 464 689 44 36 96 96 96 96 1028 657 .876 1.142 .893 1.002 .931 1.468 52 306 1.362 .94 80 1680 42810 97 105 80 88 0 687 121 566 1.179 441 320 .848 .923 .238 -.116
18 755 555 209 119 546 436 553 387 212 123 344 268 0 0 642 634 42 31 100 96 92 94 982 612 1.252 .799 .779 .704 .801 1.795 52 420 .922 .97 90 1920 42810 96 105 103 112 0 573 123 450 .825 400 277 1.212 .805 -.278 -.313
19 592 467 214 119 378 348 532 349 216 125 318 230 0 0 300 329 42 36 100 96 96 93 726 548 1.086 .921 .723 .802 .823 1.99 32 236 1.009 .91 70 2160 42810 97 104 128 135 0 482 123 359 .951 361 238 1.051 .747 -.072 -.421
20 586 516 211 123 375 393 530 407 214 125 319 284 0 0 257 326 42 34 98 98 92 96 768 603 .954 1.048 .89 1.015 1.102 1.657 52 340 1.16 .92 80 2420 42820 98 106 154 162 0 533 127 406 1.083 420 293 .924 .92 .115 -.121

Total number of rows: 3840

Table truncated, full table size 867 Kbytes.




Supplementary data files not provided
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