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Sample GSM86059 Query DataSets for GSM86059
Status Public on Dec 03, 2005
Title LB_o/n-->LB-->M9pH5_4.0hr
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_4.0hr
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics LB_o/n-->LB-->M9pH5_4.0hr
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Media comparisons, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20240.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 1362 748 614 274 748 474 1368 686 618 282 754 412 0 0 160 210 122 77 100 100 100 100 1222 1166 1.578 .634 .546 .596 .572 1.673 12 62 .549 .79 40 2230 18150 44 48 45 49 0 1968 721 1247 1.668 1805 1084 .6 1.438 .738 .524 .524
2 1911 1578 673 287 1238 1291 1900 1605 678 300 1227 1318 0 0 541 439 134 97 100 100 100 100 2529 2545 .959 1.043 1.074 1.071 1.108 1.405 52 420 .994 .91 90 2510 18150 41 50 70 79 0 4153 755 3397 2.744 4224 3468 .364 2.827 1.456 1.499 1.499
3 1424 946 648 292 776 654 1395 971 642 315 747 679 0 0 174 215 127 124 100 100 100 100 1430 1426 1.187 .843 .909 .812 .842 1.506 12 68 .729 .7 40 2790 18160 45 49 101 105 0 2489 768 1721 2.218 2555 1787 .451 2.392 1.149 1.258 1.258
4 1716 1723 734 310 982 1413 1762 1702 1524 459 1028 1392 0 0 418 371 5372 1040 0 80 0 1 2395 2420 .695 1.439 1.354 1.5 1.41 1.531 52 340 1.312 .85 80 3050 18160 43 51 125 133 0 4534 816 3718 3.787 4479 3663 .264 3.563 1.921 1.833 1.833
5 1643 1264 735 295 908 969 1677 1319 751 314 942 1024 0 0 503 459 160 105 96 100 88 100 1877 1966 .937 1.067 1.087 1.137 1.018 1.603 52 340 .947 .88 80 3330 18160 43 51 153 161 0 3326 776 2550 2.808 3471 2695 .356 2.861 1.49 1.516 1.516
6 1767 1664 760 275 1007 1389 1832 1652 775 298 1072 1377 0 0 320 444 168 129 100 100 100 100 2396 2449 .725 1.379 1.285 1.388 1.459 1.351 32 176 1.304 .89 60 3600 18160 44 50 181 187 0 4379 724 3655 3.63 4347 3624 .275 3.38 1.86 1.757 1.757
7 1479 1041 800 271 679 770 1540 1053 814 282 740 782 0 0 418 396 140 88 87 96 81 96 1449 1522 .882 1.134 1.057 1.121 1.032 2.085 32 176 1.073 .77 60 3870 18170 45 51 208 214 0 2739 713 2026 2.984 2771 2058 .335 2.781 1.577 1.476 1.476
8 1457 864 786 279 671 585 1388 843 791 274 602 564 0 0 296 241 146 80 100 96 96 96 1256 1166 1.147 .872 .937 .861 .853 1.709 32 236 .815 .77 70 4140 18150 42 49 234 241 0 2274 734 1539 2.294 2218 1484 .436 2.465 1.198 1.302 1.302
9 1857 2294 771 358 1086 1936 1844 2253 789 369 1073 1895 0 0 201 557 149 113 100 100 100 100 3022 2968 .561 1.783 1.766 1.74 1.762 1.377 12 98 1.958 .89 50 4420 18140 42 47 263 268 0 6037 942 5095 4.691 5929 4987 .213 4.648 2.23 2.216 2.216
10 1797 953 730 330 1067 623 1743 886 779 374 1013 556 0 0 299 183 204 152 100 100 100 100 1690 1569 1.713 .584 .549 .586 .602 1.39 12 104 .568 .81 50 4680 18160 44 49 289 294 0 2508 868 1639 1.537 2332 1463 .651 1.444 .62 .53 .53
11 892 407 676 293 216 114 792 309 704 304 116 16 0 0 292 201 168 93 40 46 31 34 330 132 1.895 .528 .138 .91 .815 2.684 32 170 .56 .76 60 4950 18150 43 49 316 322 -50 1071 771 300 1.389 813 42 .72 .363 .474 -1.462
12 2379 1314 756 353 1623 961 1638 1058 922 371 882 705 0 0 4051 1460 2485 147 7 90 3 84 2584 1587 1.689 .592 .799 .723 .803 1.977 52 420 .188 .69 90 5240 18150 41 50 343 352 0 3458 929 2529 1.558 2784 1855 .642 2.103 .64 1.073 1.073
13 1610 515 743 320 867 195 1502 428 1051 386 759 108 0 0 681 292 2915 573 0 13 0 0 1062 867 4.446 .225 .142 .192 .218 2.756 80 560 .262 .67 100 5520 18160 42 52 371 381 0 1355 842 513 .592 1126 284 1.69 .374 -.757 -1.417 -1.417
14 1394 511 726 341 668 170 1271 418 740 346 545 77 0 0 703 271 154 119 80 42 67 30 838 622 3.929 .254 .141 .315 .341 2.268 52 332 .299 .77 80 5810 18150 42 50 401 409 0 1345 897 447 .67 1100 203 1.493 .372 -.578 -1.427 -1.427
15 1540 613 838 325 702 288 1470 457 1093 327 632 132 0 0 473 329 2431 108 0 53 0 43 990 764 2.438 .41 .209 .345 .423 2.595 32 236 .275 .54 70 6050 18150 42 49 425 432 0 1613 855 758 1.08 1203 347 .926 .55 .111 -.863 -.863
16 1797 493 720 319 1077 174 1595 457 1785 466 875 138 0 0 875 129 6486 845 0 0 0 0 1251 1013 6.19 .162 .158 .212 .179 4.233 12 98 .114 .99 50 6350 18170 45 50 456 461 0 1297 839 458 .425 1203 363 2.352 .415 -1.234 -1.269 -1.269
17 2099 1289 839 306 1260 983 2163 1396 846 323 1324 1090 0 0 713 492 154 99 96 96 90 93 2243 2414 1.282 .78 .823 .799 .789 1.593 32 236 .768 .89 70 2230 18440 71 78 43 50 0 3392 805 2587 2.053 3674 2868 .487 2.166 1.038 1.115 1.115
18 2025 1388 756 325 1269 1063 2104 1575 776 340 1348 1250 0 0 893 749 153 98 87 84 84 81 2332 2598 1.194 .838 .927 .627 .739 2.199 32 236 .809 .83 70 2510 18430 70 77 71 78 0 3653 855 2797 2.204 4145 3289 .454 2.44 1.14 1.287 1.287
19 1195 351 717 282 478 69 967 357 719 294 250 75 0 0 660 108 142 87 65 40 46 21 547 325 6.928 .144 .3 .259 .23 3.696 32 176 .119 .5 60 2780 18420 70 76 99 105 0 924 742 182 .38 939 197 2.632 .789 -1.396 -.341 -.341
20 1123 406 666 302 457 104 1049 392 673 300 383 90 0 0 281 102 117 73 83 58 83 41 561 473 4.394 .228 .235 .274 .226 4.334 12 68 .104 .22 40 3040 18420 71 75 126 130 0 1068 795 274 .599 1032 237 1.67 .618 -.74 -.693 -.693

Total number of rows: 7680

Table truncated, full table size 1786 Kbytes.




Supplementary data files not provided
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