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Sample GSM100310 Query DataSets for GSM100310
Status Public on Mar 15, 2006
Title 129SvJ_P3_29day_liver3
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_liver3
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics P3_29day_liver3
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Comparative genomics, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64908.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 1957 1849 362 224 1595 1625 2002 1872 367 226 1640 1648 0 0 322 380 58 53 100 100 100 100 3220 3288 .982 1.019 1.005 1.007 1.016 1.132 120 768 1.037 .99 120 1830 6510 37 49 49 61 0 1724 209 1515 .95 1746 1537 1.053 .937 -.074 -.094
2 1644 1473 380 238 1264 1235 1603 1448 385 241 1223 1210 0 0 350 369 62 57 100 100 100 100 2499 2433 1.023 .977 .989 .972 .963 1.199 120 754 .983 .97 120 2060 6520 38 50 72 84 0 1374 222 1152 .911 1350 1128 1.098 .923 -.134 -.116
3 1307 1185 373 231 934 954 1279 1181 380 239 906 950 0 0 209 239 73 68 100 100 100 100 1888 1856 .979 1.021 1.049 1.016 1.021 1.196 120 784 1.024 .97 120 2300 6500 36 48 96 108 0 1105 215 890 .952 1101 886 1.05 .978 -.07 -.032
4 1107 987 375 235 732 752 1115 986 383 241 740 751 0 0 112 139 72 58 100 100 100 100 1484 1491 .973 1.027 1.015 1.022 1.016 1.192 80 656 1.023 .95 110 2540 6500 36 47 120 131 0 920 219 701 .958 919 700 1.044 .946 -.062 -.08
5 1688 1717 376 232 1312 1485 1662 1720 378 236 1286 1488 0 0 289 298 74 59 100 100 100 100 2797 2774 .884 1.132 1.157 1.136 1.147 1.153 120 782 1.12 .98 120 2780 6510 37 49 144 156 0 1601 216 1385 1.055 1604 1388 .947 1.079 .078 .11
6 2168 1856 372 232 1796 1624 2113 1833 373 237 1741 1601 0 0 406 370 84 64 100 100 100 100 3420 3342 1.106 .904 .92 .903 .916 1.134 120 874 .894 .98 130 3020 6510 36 49 167 180 0 1731 216 1514 .843 1709 1493 1.186 .858 -.246 -.222
7 990 929 357 223 633 706 973 905 375 248 616 682 0 0 134 163 132 130 100 100 100 100 1339 1298 .897 1.115 1.107 1.111 1.124 1.156 52 420 1.055 .94 90 3250 6510 38 47 192 201 0 866 208 658 1.04 844 636 .962 1.032 .057 .046
8 1639 1610 306 199 1333 1411 1662 1605 321 211 1356 1406 0 0 345 334 93 89 100 100 99 100 2744 2762 .945 1.059 1.037 1.076 1.047 1.267 120 889 1.047 .98 130 3500 6510 36 49 215 228 0 1501 186 1316 .987 1497 1311 1.013 .967 -.019 -.049
9 2085 2192 298 193 1787 1999 2113 2224 307 199 1815 2031 0 0 346 390 71 64 100 100 100 100 3786 3846 .894 1.119 1.119 1.117 1.111 1.138 120 752 1.12 .99 120 3740 6530 39 51 240 252 0 2044 180 1864 1.043 2074 1894 .959 1.043 .061 .061
10 1746 1857 294 190 1452 1667 1776 1862 298 193 1482 1672 0 0 258 285 52 49 100 100 100 100 3119 3154 .871 1.148 1.128 1.151 1.154 1.151 120 750 1.143 .99 120 3980 6530 39 51 264 276 0 1732 177 1554 1.071 1736 1559 .934 1.052 .098 .073
11 1207 1043 317 204 890 839 1205 1050 320 209 888 846 0 0 148 151 61 52 100 100 100 100 1729 1734 1.061 .943 .953 .939 .939 1.178 120 822 .94 .97 130 4220 6530 38 51 287 300 0 973 190 782 .879 979 789 1.138 .888 -.186 -.171
12 2156 1371 374 242 1782 1129 2204 1383 383 246 1830 1141 0 0 324 206 79 61 100 100 100 100 2911 2971 1.578 .634 .623 .634 .638 1.167 120 822 .633 .98 130 4460 6530 38 51 311 324 0 1278 226 1053 .591 1290 1064 1.693 .581 -.759 -.782
13 4437 5352 441 284 3996 5068 4283 5230 443 286 3842 4946 0 0 1322 1718 74 65 100 100 100 100 9064 8788 .788 1.268 1.287 1.262 1.257 1.168 120 822 1.279 .98 130 4700 6530 38 51 335 348 0 4991 265 4726 1.183 4877 4612 .846 1.2 .242 .264
14 3715 3636 439 278 3276 3358 3580 3444 440 283 3141 3166 0 0 816 963 76 65 100 100 100 100 6634 6307 .976 1.025 1.008 1.02 1.005 1.148 120 752 1.036 .98 120 4940 6530 39 51 360 372 0 3391 259 3131 .956 3211 2952 1.046 .94 -.065 -.089
15 2443 3120 383 246 2060 2874 2420 3021 391 249 2037 2775 0 0 711 1005 69 59 100 100 100 100 4934 4812 .717 1.395 1.362 1.398 1.408 1.195 120 889 1.402 .98 130 5180 6510 36 49 383 396 0 2909 229 2680 1.301 2817 2588 .769 1.27 .38 .345
16 3636 4181 349 213 3287 3968 3503 3924 352 215 3154 3711 0 0 1065 1389 50 46 100 100 100 100 7255 6865 .828 1.207 1.177 1.203 1.182 1.127 120 764 1.22 .99 120 1820 6740 60 72 48 60 0 3899 199 3700 1.126 3659 3460 .888 1.097 .171 .134
17 2567 2510 394 237 2173 2273 2595 2514 397 238 2201 2277 0 0 708 822 58 52 99 100 99 100 4446 4478 .956 1.046 1.035 1.061 1.03 1.277 120 816 1.059 .99 130 2060 6750 60 73 71 84 0 2341 221 2120 .975 2344 2123 1.025 .965 -.036 -.052
18 2566 2821 425 255 2141 2566 2447 2629 434 263 2022 2374 0 0 723 854 72 68 100 100 100 100 4707 4396 .834 1.199 1.174 1.203 1.199 1.152 120 836 1.2 .98 130 2300 6740 59 72 95 108 0 2631 238 2393 1.118 2452 2214 .895 1.095 .16 .131
19 2650 2724 448 271 2202 2453 2606 2578 459 281 2158 2307 0 0 822 1043 78 73 100 100 100 100 4655 4465 .898 1.114 1.069 1.109 1.092 1.169 120 767 1.146 .97 120 2540 6740 60 72 120 132 0 2540 253 2287 1.039 2404 2151 .963 .997 .055 -.005
20 1814 1789 459 280 1355 1509 1823 1793 468 288 1364 1513 0 0 390 477 73 66 100 100 99 100 2864 2877 .898 1.114 1.109 1.116 1.11 1.217 120 824 1.124 .98 130 2780 6750 60 73 143 156 0 1668 261 1407 1.038 1672 1411 .963 1.034 .054 .049

Total number of rows: 6528

Table truncated, full table size 1509 Kbytes.




Supplementary data files not provided
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