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Sample GSM100306 Query DataSets for GSM100306
Status Public on Mar 15, 2006
Title 129SvJ_P3_29day_liverpool_a
Sample type RNA
 
Channel 1
Source name 10X library
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics 10X library
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name P3_29day_liverpool_a
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics P3_29day_liverpool_a
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Comparative genomics, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64915.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 Mar 13, 2006
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 GPL3545
Series (1)
GSE4461 Genome-wide screen for salmonella genes required for long-term systemic infection of the mouse.

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
1 756 3216 148 93 608 3123 766 3241 149 99 618 3148 0 0 157 869 24 39 100 100 100 100 3731 3766 .195 5.137 5.094 5.074 5.04 1.229 120 850 5.346 .97 130 1710 6910 32 45 36 49 0 3098 90 3009 4.948 3122 3033 .202 4.907 2.307 2.295
2 889 793 152 117 737 676 896 808 153 121 744 691 0 0 220 200 30 37 100 100 99 100 1413 1435 1.09 .917 .929 .935 .91 1.501 120 836 .891 .94 130 1940 6930 34 47 59 72 0 764 113 651 .884 778 666 1.132 .895 -.179 -.16
3 417 311 152 103 265 208 467 330 158 143 315 227 0 0 333 229 93 733 59 0 57 0 473 542 1.274 .785 .721 .548 .613 1.862 120 865 7.318 .52 130 2190 6910 32 45 84 97 0 300 99 200 .756 318 219 1.323 .694 -.403 -.527
4 521 504 151 98 370 406 513 494 153 102 362 396 0 0 95 187 25 32 100 100 100 98 776 758 .911 1.097 1.094 .984 1.117 1.587 80 650 1.25 .91 110 2420 6900 32 43 108 119 0 486 94 391 1.057 476 381 .946 1.054 .08 .076
5 665 651 146 98 519 553 663 642 154 104 517 544 0 0 122 176 90 69 100 99 100 98 1072 1061 .939 1.066 1.052 1.032 1.038 1.347 120 782 1.103 .95 120 2660 6910 33 45 132 144 0 627 94 533 1.026 618 524 .974 1.014 .038 .02
6 604 459 156 105 448 354 761 549 161 111 605 444 0 0 429 319 87 68 68 67 65 63 802 1049 1.266 .79 .734 .597 .642 1.865 120 848 .778 .88 130 2910 6910 32 45 156 169 0 442 101 341 .761 529 428 1.314 .707 -.394 -.5
7 403 314 166 111 237 203 412 314 174 117 246 203 0 0 71 61 63 46 96 99 93 98 440 449 1.167 .857 .825 .853 .841 1.56 120 741 .857 .84 120 3140 6920 34 46 180 192 0 302 107 196 .825 302 196 1.212 .795 -.277 -.331
8 708 721 166 109 542 612 680 673 168 113 514 564 0 0 146 244 30 35 100 100 100 100 1154 1078 .886 1.129 1.097 1.091 1.138 1.305 120 809 1.2 .93 130 3380 6910 32 45 203 216 0 695 105 590 1.088 648 543 .919 1.057 .121 .08
9 789 840 163 108 626 732 818 818 165 112 655 710 0 0 224 296 27 35 99 99 99 98 1358 1365 .855 1.169 1.084 1.166 1.169 1.549 156 954 1.21 .95 140 3620 6920 33 47 227 241 0 809 104 705 1.126 788 684 .888 1.044 .172 .062
10 671 694 164 111 507 583 683 685 167 114 519 574 0 0 128 125 28 34 99 100 99 100 1090 1093 .87 1.15 1.106 1.192 1.09 1.439 120 727 1.143 .94 120 3860 6930 35 47 252 264 0 669 107 562 1.108 660 553 .903 1.065 .148 .091
11 573 469 167 111 406 358 570 437 168 114 403 326 0 0 110 179 29 37 100 98 100 95 764 729 1.134 .882 .809 .786 .807 1.632 120 728 .971 .88 120 4100 6920 34 46 276 288 0 452 107 345 .849 421 314 1.177 .779 -.235 -.36
12 1066 1437 169 115 897 1322 1059 1441 170 121 890 1326 0 0 241 351 34 44 100 100 100 100 2219 2216 .679 1.474 1.49 1.475 1.495 1.225 156 1012 1.487 .97 150 4340 6940 34 49 298 313 0 1384 111 1274 1.42 1388 1277 .704 1.435 .506 .521
13 1060 1317 154 111 906 1206 959 1074 157 119 805 963 0 0 356 871 32 46 100 99 100 98 2112 1768 .751 1.331 1.196 1.13 1.198 1.646 120 810 1.63 .92 130 4580 6920 33 46 323 336 0 1269 107 1162 1.282 1035 928 .78 1.152 .359 .205
14 1156 1153 138 100 1018 1053 1135 1050 147 110 997 950 0 0 344 413 58 66 99 100 99 100 2071 1947 .967 1.034 .953 1.051 .994 1.498 120 823 1.05 .94 130 4820 6930 34 47 347 360 0 1111 96 1014 .996 1012 915 1.004 .918 -.005 -.124
15 1113 1599 132 87 981 1512 998 1250 132 90 866 1163 0 0 433 1577 22 29 100 100 100 100 2493 2029 .649 1.541 1.343 1.366 1.393 1.491 120 780 2.587 .77 120 5060 6910 33 45 372 384 0 1540 84 1457 1.485 1204 1120 .673 1.294 .57 .372
16 1071 1503 145 86 926 1417 1068 1458 147 91 923 1372 0 0 486 720 24 33 92 98 92 98 2343 2295 .653 1.53 1.486 1.456 1.488 2.098 156 956 1.546 .95 140 1710 7140 55 69 36 50 0 1448 83 1365 1.474 1405 1322 .678 1.432 .56 .518
17 996 1078 148 102 848 976 987 1020 150 107 839 918 0 0 332 389 24 35 97 99 97 99 1824 1757 .869 1.151 1.094 1.244 1.083 1.923 120 691 1.159 .94 120 1940 7150 57 69 60 72 0 1038 98 940 1.109 983 884 .902 1.054 .149 .076
18 1210 1123 150 103 1060 1020 990 1048 153 107 840 945 0 0 1995 511 25 34 100 99 100 99 2080 1785 1.039 .962 1.125 1.015 1.102 1.767 120 747 .308 .57 120 2180 7140 56 68 84 96 0 1082 99 983 .927 1010 910 1.079 1.084 -.109 .116
19 1051 1171 149 96 902 1075 1026 1156 150 99 877 1060 0 0 259 369 24 30 100 100 100 99 1977 1937 .839 1.192 1.209 1.135 1.172 1.465 120 747 1.219 .94 120 2420 7140 56 68 108 120 0 1128 92 1036 1.148 1114 1021 .871 1.164 .199 .22
20 843 779 146 94 697 685 841 742 147 97 695 648 0 0 158 307 25 30 100 100 100 98 1382 1343 1.018 .983 .932 .889 .946 1.646 120 746 1.072 .92 120 2660 7140 56 68 132 144 0 750 91 660 .947 715 624 1.056 .898 -.079 -.155

Total number of rows: 6528

Table truncated, full table size 1493 Kbytes.




Supplementary data files not provided
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