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Sample GSM86049 Query DataSets for GSM86049
Status Public on Dec 03, 2005
Title LB_o/n-->LB-->M9pH5_2.0hr
Sample type RNA
 
Channel 1
Source name pool of all time points
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics pool of all time points
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name LB_o/n-->LB-->M9pH5_2.0hr
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics LB_o/n-->LB-->M9pH5_2.0hr
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Media comparisons, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20238.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 02, 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 GPL3048
Series (1)
GSE3735 Switch from LB pH7 to M9 pH5

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 same as UNF_VALUE but with flagged values removed
UNF_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 UNF_VALUE
1 1051 733 362 327 689 406 1023 704 367 337 661 377 0 0 130 155 77 107 100 100 100 91 1095 1038 1.697 .589 .57 .553 .589 1.67 12 104 .601 .74 50 2180 18150 43 48 39 44 0 1333 595 738 1.071 1280 685 .933 1.037 .099 .052 .052
2 1507 1139 395 337 1112 802 1311 1109 398 351 916 772 0 0 621 427 87 111 100 98 100 93 1914 1688 1.387 .721 .843 .718 .713 1.489 80 656 .69 .9 110 2460 18150 40 51 64 75 0 2071 613 1458 1.311 2016 1404 .763 1.532 .391 .616 .616
3 1124 1256 368 352 756 904 1157 1214 375 377 789 862 0 0 225 430 86 195 100 100 100 100 1660 1651 .836 1.196 1.093 1.14 1.083 1.547 12 104 1.247 .86 50 2730 18140 42 47 94 99 0 2284 640 1644 2.174 2207 1567 .46 1.986 1.12 .99 .99
4 1182 1174 397 365 785 809 1267 1185 401 383 870 820 0 0 445 433 85 112 98 98 90 94 1594 1690 .97 1.031 .943 1.106 1.086 1.476 52 420 1.024 .88 90 3010 18140 40 49 120 129 0 2135 664 1471 1.874 2155 1491 .534 1.714 .906 .777 .777
5 945 1127 397 359 548 768 819 952 401 369 422 593 0 0 365 506 79 109 97 97 90 94 1316 1015 .714 1.401 1.405 1.377 1.345 1.788 120 940 1.449 .87 130 3290 18150 39 52 146 159 0 2049 653 1396 2.548 1731 1078 .392 2.555 1.349 1.353 1.353
6 1620 1795 399 371 1221 1424 1686 1855 405 373 1287 1484 0 0 361 467 86 110 100 100 100 100 2645 2771 .857 1.166 1.153 1.147 1.16 1.374 32 236 1.185 .93 70 3560 18140 41 48 176 183 0 3264 675 2589 2.12 3373 2698 .472 2.096 1.084 1.068 1.068
7 1318 1437 390 347 928 1090 1289 1341 396 354 899 994 0 0 379 547 83 100 100 100 96 100 2018 1893 .851 1.175 1.106 1.153 1.112 1.625 32 176 1.224 .91 60 3830 18140 42 48 204 210 0 2613 631 1982 2.136 2438 1807 .468 2.01 1.095 1.007 1.007
8 1224 1296 430 348 794 948 1302 1338 431 369 872 990 0 0 362 591 93 151 100 96 100 81 1742 1862 .838 1.194 1.135 1.035 1.07 1.651 32 236 1.31 .86 70 4100 18130 40 47 230 237 0 2356 633 1724 2.171 2433 1800 .461 2.064 1.118 1.046 1.046
9 2242 3204 427 392 1815 2812 2372 3339 426 393 1945 2947 0 0 575 1109 86 110 100 100 96 100 4627 4892 .645 1.549 1.515 1.529 1.603 1.538 32 230 1.636 .94 70 4370 18120 39 46 257 264 0 5825 713 5113 2.817 6071 5358 .355 2.755 1.494 1.462 1.462
10 966 798 422 374 544 424 797 686 430 398 375 312 0 0 415 373 89 218 91 66 81 36 968 687 1.283 .779 .832 .62 .789 2.923 80 552 .883 .77 100 4650 18120 38 48 284 294 0 1451 680 771 1.417 1247 567 .706 1.513 .503 .597 .597
11 1282 1267 455 387 827 880 1326 1297 456 402 871 910 0 0 216 316 106 120 100 100 100 100 1707 1781 .94 1.064 1.045 1.041 1.107 1.602 12 100 1.15 .84 50 4930 18120 40 45 314 319 0 2304 704 1600 1.935 2358 1655 .517 1.9 .952 .926 .926
12 1296 1590 443 378 853 1212 1235 1441 451 435 792 1063 0 0 437 594 92 809 100 70 97 30 2065 1855 .704 1.421 1.342 1.433 1.377 1.436 80 538 1.411 .92 100 5200 18110 37 47 339 349 0 2891 687 2204 2.583 2620 1933 .387 2.44 1.369 1.287 1.287
13 1080 698 449 398 631 300 929 594 460 412 480 196 0 0 401 346 96 125 97 58 92 41 931 676 2.103 .475 .408 .402 .472 2.562 80 560 .613 .68 100 5460 18130 39 49 365 375 0 1269 724 545 .864 1080 356 1.157 .742 -.21 -.43 -.43
14 1486 1138 495 431 991 707 1551 1124 499 437 1056 693 0 0 450 372 114 115 100 100 91 83 1698 1749 1.402 .713 .656 .711 .67 1.796 12 104 .773 .73 50 5750 18120 40 45 396 401 0 2069 784 1285 1.297 2044 1260 .771 1.193 .375 .255 .255
15 1013 792 497 435 516 357 894 659 503 453 397 224 0 0 367 352 99 127 92 67 80 46 873 621 1.445 .692 .564 .686 .742 3.303 52 332 .854 .7 80 6020 18120 39 47 422 430 0 1440 791 649 1.258 1198 407 .795 1.026 .331 .037 .037
16 1340 1215 478 385 862 830 1291 1048 470 413 813 663 0 0 349 470 90 125 100 100 100 100 1692 1476 1.039 .963 .815 .93 .897 1.553 12 62 1.07 .75 40 6300 18120 41 45 452 456 0 2209 700 1509 1.751 1905 1205 .571 1.483 .808 .568 .568
17 1845 1804 565 386 1280 1418 1942 1847 1611 819 1377 1461 0 0 761 924 4722 2178 0 28 0 0 2698 2838 .903 1.108 1.061 1.083 1.064 1.821 32 176 .754 .89 60 2190 18420 70 76 40 46 0 3280 702 2578 2.014 3358 2656 .496 1.929 1.01 .948 .948
18 1229 674 450 338 779 336 780 534 447 358 330 196 0 0 788 389 97 112 98 57 76 48 1115 526 2.318 .431 .594 .492 .52 2.598 52 340 .416 .75 80 2460 18410 68 76 66 74 0 1225 615 611 .784 971 356 1.275 1.08 -.351 .111 .111
19 660 464 396 343 264 121 549 465 405 345 153 122 0 0 341 157 85 94 53 56 50 31 385 275 2.182 .458 .797 .785 .537 5.736 32 176 .375 .47 60 2740 18420 70 76 95 101 0 844 624 220 .833 845 222 1.2 1.45 -.263 .536 .536
20 867 637 403 343 464 294 870 599 418 356 467 256 0 0 182 157 81 101 100 100 100 66 758 723 1.578 .634 .548 .619 .544 1.607 12 104 .615 .48 50 3010 18410 69 74 122 127 0 1158 624 535 1.152 1089 465 .868 .997 .204 -.005 -.005

Total number of rows: 7680

Table truncated, full table size 1773 Kbytes.




Supplementary data files not provided
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