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Sample GSM100298 Query DataSets for GSM100298
Status Public on Mar 15, 2006
Title 129SvJ_P3_29day_spleen4
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_spleen4
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics P3_29day_spleen4
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Comparative genomics, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64920.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 1225 1567 81 93 1144 1474 1213 1420 81 98 1132 1327 0 0 259 1617 13 37 100 100 100 100 2618 2459 .776 1.288 1.172 1.15 1.137 1.348 120 744 2.655 .67 120 1770 6680 42 54 43 55 0 1837 109 1728 1.51 1664 1555 .662 1.374 .595 .458
2 1032 910 81 94 951 816 1010 861 82 99 929 767 0 0 317 419 14 42 100 99 100 99 1767 1696 1.165 .858 .826 .788 .835 1.382 120 754 .93 .96 120 2000 6690 43 55 66 78 0 1067 110 956 1.006 1009 899 .994 .968 .008 -.047
3 880 1003 84 98 796 905 858 973 85 105 774 875 0 0 214 372 14 44 100 99 100 99 1701 1649 .88 1.137 1.13 1.054 1.142 1.439 120 874 1.215 .95 130 2240 6670 40 53 89 102 0 1176 115 1061 1.333 1140 1026 .75 1.325 .414 .406
4 507 620 88 99 419 521 529 639 90 108 441 540 0 0 122 157 14 47 99 99 99 99 940 981 .804 1.243 1.224 1.249 1.262 1.543 120 807 1.274 .95 130 2480 6680 41 54 113 126 0 727 116 611 1.457 749 633 .686 1.435 .543 .521
5 782 691 93 104 689 587 794 698 94 113 701 594 0 0 219 242 16 56 100 98 98 96 1276 1295 1.174 .852 .847 .812 .824 1.366 156 1011 .892 .96 140 2730 6660 39 53 138 152 0 810 122 688 .999 818 696 1.001 .993 -.002 -.01
6 1203 1105 101 110 1102 995 1183 1060 103 116 1082 950 0 0 383 595 17 47 100 98 100 98 2097 2032 1.108 .903 .878 .819 .859 1.529 120 837 1.014 .94 130 2960 6680 41 54 161 174 0 1295 129 1166 1.058 1242 1113 .945 1.029 .082 .041
7 439 412 112 115 327 297 457 408 113 121 345 293 0 0 93 113 18 48 100 98 100 95 624 638 1.101 .908 .849 .881 .915 1.429 120 837 .966 .9 130 3200 6690 42 55 185 198 0 483 135 348 1.065 478 343 .939 .995 .09 -.007
8 935 842 124 119 811 723 929 831 126 126 805 712 0 0 140 175 24 49 100 100 100 100 1534 1517 1.122 .891 .884 .877 .886 1.258 156 1038 .901 .95 150 3450 6670 39 54 209 224 0 987 139 847 1.045 974 835 .957 1.037 .063 .052
9 1025 1186 139 123 886 1063 1030 1185 142 157 891 1062 0 0 271 330 31 499 100 95 99 57 1949 1953 .833 1.2 1.192 1.202 1.215 1.311 156 954 1.21 .97 140 3680 6680 41 55 233 247 0 1390 144 1246 1.406 1389 1245 .711 1.397 .492 .482
10 932 1040 160 140 772 900 953 1012 163 182 793 872 0 0 172 233 32 574 100 92 100 15 1672 1665 .858 1.166 1.1 1.166 1.155 1.315 120 718 1.192 .95 120 3920 6700 44 56 258 270 0 1219 164 1055 1.366 1186 1022 .732 1.289 .45 .366
11 687 628 179 151 508 477 710 621 183 158 531 470 0 0 131 182 29 55 100 98 100 98 985 1001 1.065 .939 .885 .882 .915 1.621 156 927 .983 .92 140 4160 6710 44 58 281 295 0 736 177 559 1.101 728 551 .909 1.037 .138 .053
12 1219 781 208 167 1011 614 1256 768 208 174 1048 601 0 0 296 218 30 58 99 98 98 98 1625 1649 1.647 .607 .573 .602 .6 1.315 156 976 .612 .94 140 4410 6670 40 54 306 320 0 915 196 720 .712 900 704 1.405 .672 -.49 -.573
13 3072 3508 211 173 2861 3335 2913 3248 213 176 2702 3075 0 0 1238 1568 31 52 100 100 100 100 6196 5777 .858 1.166 1.138 1.173 1.143 1.304 120 718 1.19 .97 120 4640 6700 44 56 330 342 0 4112 203 3909 1.366 3807 3604 .732 1.334 .45 .416
14 2218 2260 189 159 2029 2101 2101 2157 200 175 1912 1998 0 0 589 681 95 109 100 100 100 100 4130 3910 .966 1.035 1.045 1.021 1.025 1.201 120 823 1.045 .97 130 4880 6700 43 56 353 366 0 2649 186 2463 1.214 2528 2342 .824 1.225 .279 .293
15 1432 1767 159 137 1273 1630 1461 1823 161 144 1302 1686 0 0 412 542 26 51 99 100 99 100 2903 2988 .781 1.28 1.295 1.323 1.279 1.488 120 780 1.289 .98 120 5120 6680 42 54 378 390 0 2071 161 1910 1.501 2137 1976 .666 1.518 .586 .602
16 1953 1748 84 95 1869 1653 1843 1637 89 103 1759 1542 0 0 1058 939 70 69 98 99 97 98 3522 3301 1.131 .884 .877 .906 .896 1.719 156 1012 .88 .97 150 1790 6900 62 77 43 58 0 2049 111 1937 1.037 1919 1807 .965 1.027 .052 .039
17 1971 2433 84 94 1887 2339 1917 2017 88 101 1833 1923 0 0 894 1954 61 61 98 100 98 100 4226 3756 .807 1.24 1.049 1.193 1.102 1.496 120 697 1.566 .91 120 2000 6920 66 78 66 78 0 2852 110 2741 1.453 2364 2254 .688 1.23 .539 .298
18 1893 2747 84 98 1809 2649 1881 2665 87 122 1797 2567 0 0 609 844 32 251 100 100 99 100 4458 4364 .683 1.464 1.428 1.536 1.427 1.504 120 769 1.463 .97 120 2250 6920 66 78 91 103 0 3220 115 3105 1.716 3124 3009 .583 1.674 .779 .744
19 1306 1245 85 97 1221 1148 1399 1336 87 106 1314 1239 0 0 508 542 17 58 100 100 100 98 2369 2553 1.064 .94 .943 .915 .932 1.334 156 950 .978 .97 150 2500 6890 61 76 114 129 0 1459 114 1346 1.102 1566 1452 .907 1.105 .14 .144
20 1171 1461 90 100 1081 1361 1210 1364 91 106 1120 1264 0 0 401 652 16 46 98 100 97 100 2442 2384 .794 1.259 1.129 1.35 1.194 1.927 120 810 1.333 .94 130 2730 6920 65 78 138 151 0 1712 117 1595 1.476 1599 1482 .678 1.323 .561 .404

Total number of rows: 6528

Table truncated, full table size 1484 Kbytes.




Supplementary data files not provided
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