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Sample GSM100308 Query DataSets for GSM100308
Status Public on Mar 15, 2006
Title 129SvJ_P3_29day_spleenpool_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_spleenpool_a
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics P3_29day_spleenpool_a
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Comparative genomics, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64924.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 1289 2996 325 241 964 2755 1422 3358 362 268 1097 3117 0 0 392 1137 150 132 96 96 89 95 3719 4214 .35 2.858 2.841 2.736 2.871 1.691 156 1006 2.978 .94 140 1500 6720 37 51 47 61 0 3063 246 2816 2.922 3433 3186 .342 2.905 1.547 1.538
2 1382 1261 349 268 1033 993 1291 1151 363 282 942 883 0 0 520 686 97 96 99 97 97 94 2026 1825 1.04 .961 .937 .882 .845 1.744 120 742 1.075 .82 120 1740 6720 38 50 72 84 0 1289 274 1015 .983 1177 903 1.018 .958 -.025 -.062
3 1132 1069 337 240 795 829 1103 996 344 249 766 756 0 0 277 362 68 70 100 100 99 98 1624 1522 .959 1.043 .987 1.006 .981 1.539 120 785 1.095 .91 120 1980 6700 36 48 96 108 0 1093 245 847 1.066 1018 773 .938 1.009 .092 .013
4 860 851 328 239 532 612 878 860 343 249 550 621 0 0 91 129 70 75 100 100 100 100 1144 1171 .869 1.15 1.129 1.143 1.134 1.271 80 656 1.2 .91 110 2220 6700 36 47 120 131 0 870 244 626 1.176 879 635 .85 1.154 .234 .207
5 1217 1187 348 241 869 946 1284 1253 358 252 936 1012 0 0 298 328 72 72 98 100 96 99 1815 1948 .919 1.089 1.081 1.122 1.062 1.681 120 776 1.095 .93 120 2470 6700 36 48 145 157 0 1213 246 967 1.113 1281 1035 .899 1.105 .154 .144
6 1586 1449 344 237 1242 1212 1594 1324 359 253 1250 1087 0 0 305 540 93 86 100 100 100 100 2454 2337 1.025 .976 .87 .922 .935 1.392 80 656 1.054 .91 110 2710 6700 36 47 169 180 0 1481 242 1239 .998 1354 1111 1.002 .889 -.003 -.17
7 763 660 342 229 421 431 763 653 349 242 421 424 0 0 122 153 65 69 100 100 100 97 852 845 .977 1.024 1.007 1.006 1.008 1.415 80 560 1.057 .86 100 2950 6710 38 48 194 204 0 675 234 441 1.047 668 433 .956 1.03 .066 .042
8 1385 1321 343 233 1042 1088 1377 1336 354 247 1034 1103 0 0 267 316 74 74 100 100 100 100 2130 2137 .958 1.044 1.067 1.032 1.013 1.315 120 762 1.054 .95 120 3180 6710 37 49 216 228 0 1350 238 1112 1.067 1366 1128 .937 1.091 .094 .125
9 1414 1534 376 264 1038 1270 1447 1552 425 308 1071 1288 0 0 386 447 527 511 86 97 51 68 2308 2359 .817 1.224 1.203 1.243 1.228 1.364 120 818 1.074 .87 130 3430 6710 36 49 240 253 0 1568 270 1298 1.251 1587 1317 .8 1.229 .323 .298
10 1248 1204 368 257 880 947 1231 1217 386 274 863 960 0 0 129 186 102 96 100 100 100 100 1827 1823 .929 1.076 1.112 1.068 1.066 1.196 80 614 1.095 .94 110 3660 6720 38 49 264 275 0 1231 263 968 1.1 1244 981 .909 1.137 .138 .185
11 993 815 319 214 674 601 1020 829 332 226 701 615 0 0 189 204 72 74 100 100 100 99 1275 1316 1.121 .892 .877 .87 .877 1.336 120 728 .911 .94 120 3900 6720 38 50 288 300 0 833 219 614 .912 847 629 1.097 .897 -.134 -.157
12 1474 2013 326 234 1148 1779 1542 1995 337 239 1216 1761 0 0 307 399 71 69 99 100 99 100 2927 2977 .645 1.55 1.448 1.594 1.576 1.293 120 792 1.527 .95 130 4150 6740 39 52 312 325 0 2058 239 1819 1.584 2039 1800 .631 1.48 .664 .566
13 3569 5162 349 270 3220 4892 3367 4639 391 472 3018 4369 0 0 1422 2897 413 3147 100 66 100 22 8112 7387 .658 1.519 1.448 1.442 1.44 1.431 80 631 1.716 .9 110 4370 6710 37 48 335 346 0 5277 276 5001 1.553 4742 4466 .644 1.48 .635 .566
14 2212 2506 377 270 1835 2236 2276 2560 423 301 1899 2290 0 0 668 900 175 147 99 100 99 99 4071 4189 .821 1.219 1.206 1.2 1.206 1.408 120 883 1.308 .94 130 4630 6700 35 48 360 373 0 2562 276 2286 1.246 2617 2341 .803 1.233 .317 .302
15 2013 2499 364 234 1649 2265 1828 2199 365 239 1464 1965 0 0 735 1104 48 65 100 100 100 100 3914 3429 .728 1.374 1.342 1.342 1.356 1.392 80 644 1.465 .91 110 4860 6690 35 46 384 395 0 2555 239 2315 1.404 2248 2009 .712 1.372 .49 .456
16 3469 4153 317 232 3152 3921 3559 4243 354 257 3242 4011 0 0 1443 1788 149 126 98 100 94 97 7073 7253 .804 1.244 1.237 1.305 1.222 1.655 120 726 1.263 .96 120 1500 6940 60 72 48 60 0 4246 237 4008 1.272 4338 4100 .786 1.265 .347 .339
17 1867 2029 337 251 1530 1778 2063 2054 374 274 1726 1803 0 0 977 1408 193 118 97 96 82 92 3308 3529 .861 1.162 1.045 1.08 1.051 1.658 156 946 1.305 .88 140 1740 6950 60 74 71 85 0 2074 257 1818 1.188 2100 1843 .842 1.068 .249 .095
18 2019 2599 337 242 1682 2357 2054 2640 354 259 1717 2398 0 0 635 987 88 102 100 100 100 100 4039 4115 .714 1.401 1.397 1.398 1.376 1.457 120 760 1.47 .95 120 1990 6940 60 72 97 109 0 2657 247 2410 1.433 2699 2451 .698 1.428 .519 .514
19 1972 2230 331 244 1641 1986 2033 2218 354 261 1702 1974 0 0 712 939 109 106 99 100 98 100 3627 3676 .826 1.21 1.16 1.247 1.212 1.529 120 746 1.248 .95 120 2230 6940 60 72 121 133 0 2280 249 2030 1.237 2267 2018 .808 1.186 .307 .246
20 1225 1207 374 268 851 939 1303 1155 390 281 929 887 0 0 479 622 98 93 93 94 87 91 1790 1816 .906 1.103 .955 1.101 1.056 1.638 156 915 1.187 .91 140 2470 6930 58 72 144 158 0 1234 274 960 1.128 1181 907 .887 .976 .174 -.035

Total number of rows: 6528

Table truncated, full table size 1501 Kbytes.




Supplementary data files not provided
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