NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM100307 Query DataSets for GSM100307
Status Public on Mar 15, 2006
Title 129SvJ_P3_29day_liver2
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_liver2
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics P3_29day_liver2
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Comparative genomics, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64907.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 1924 2188 158 105 1766 2083 1951 2214 159 107 1793 2109 0 0 298 402 29 36 100 100 100 100 3849 3902 .848 1.18 1.176 1.174 1.185 1.165 120 794 1.19 .98 120 1790 6550 41 53 45 57 0 1926 92 1833 1.038 1949 1856 .963 1.035 .054 .05
2 1684 2099 154 95 1530 2004 1616 1864 149 100 1462 1769 0 0 555 1512 39 36 100 100 100 100 3534 3231 .763 1.31 1.21 1.21 1.209 1.247 120 717 1.671 .91 120 2020 6560 42 54 68 80 0 1847 84 1764 1.153 1641 1557 .867 1.065 .205 .091
3 37 61 54 70 -17 -9 36 57 85 75 -18 -13 0 0 9 22 58 32 0 3 0 1 -26 -31 null null null .88 1 2.654 156 1077 .597 .42 150 2260 6540 38 53 90 105 -50 54 62 -8 null 50 -11 null null null null
4 834 906 159 97 675 809 836 880 147 102 677 783 0 0 105 159 55 48 100 100 100 100 1484 1460 .834 1.199 1.157 1.19 1.177 1.189 80 650 1.189 .96 110 2500 6540 40 51 116 127 0 797 85 712 1.055 775 689 .948 1.018 .077 .026
5 1475 1761 166 104 1309 1657 1488 1777 169 108 1322 1673 0 0 330 402 28 35 100 100 100 100 2966 2995 .79 1.266 1.266 1.278 1.228 1.25 120 756 1.265 .98 120 2750 6550 41 53 141 153 0 1550 92 1458 1.114 1564 1472 .898 1.114 .156 .156
6 1778 1741 169 102 1609 1639 1784 1754 171 108 1615 1652 0 0 365 448 31 35 100 100 100 100 3248 3267 .982 1.019 1.023 1.005 1.033 1.192 120 860 1.035 .97 130 2980 6550 40 53 163 176 0 1532 90 1443 .897 1544 1454 1.115 .9 -.158 -.151
7 563 496 178 113 385 383 578 502 181 116 400 389 0 0 78 97 33 34 100 100 100 99 768 789 1.005 .995 .973 .978 .995 1.296 120 762 1.016 .94 120 3230 6550 41 53 189 201 0 437 99 337 .876 442 342 1.142 .856 -.192 -.224
8 1470 1573 188 120 1282 1453 1447 1566 243 162 1259 1446 0 0 256 322 642 421 100 100 46 96 2735 2705 .882 1.133 1.149 1.125 1.136 1.155 120 850 1.146 .98 130 3460 6550 40 53 211 224 0 1384 106 1279 .998 1378 1273 1.002 1.011 -.004 .016
9 1954 2299 200 127 1754 2172 1982 2377 203 133 1782 2250 0 0 446 694 49 64 100 100 100 100 3926 4032 .808 1.238 1.263 1.209 1.247 1.178 120 847 1.275 .98 130 3700 6560 41 54 235 248 0 2023 112 1912 1.09 2092 1980 .918 1.111 .124 .152
10 1374 1463 221 127 1153 1336 1382 1452 226 130 1161 1325 0 0 284 365 52 41 100 100 100 100 2489 2486 .863 1.159 1.141 1.157 1.155 1.182 120 821 1.168 .98 130 3950 6570 42 55 260 273 0 1288 112 1176 1.02 1278 1166 .981 1.004 .028 .006
11 1046 922 212 123 834 799 1057 922 217 128 845 799 0 0 139 169 52 40 100 100 100 100 1633 1644 1.044 .958 .946 .949 .947 1.184 120 824 .968 .97 130 4180 6560 41 54 283 296 0 812 108 703 .843 812 703 1.186 .832 -.246 -.265
12 2098 1320 210 134 1888 1186 2131 1311 212 137 1921 1177 0 0 397 331 37 40 100 100 100 100 3074 3098 1.592 .628 .613 .615 .62 1.219 120 750 .635 .97 120 4420 6560 42 54 308 320 0 1162 118 1044 .553 1154 1036 1.809 .539 -.855 -.891
13 4455 6771 222 146 4233 6625 4348 6560 226 149 4126 6414 0 0 1130 2138 42 43 100 100 100 100 10858 10540 .639 1.565 1.555 1.534 1.571 1.187 120 736 1.613 .98 120 4660 6560 42 54 332 344 0 5960 129 5831 1.378 5774 5645 .726 1.368 .462 .452
14 3364 4044 234 155 3130 3889 3208 3935 239 157 2974 3780 0 0 935 1490 48 43 100 100 100 100 7019 6754 .805 1.242 1.271 1.202 1.241 1.191 120 847 1.297 .98 130 4900 6560 41 54 355 368 0 3559 136 3423 1.094 3463 3327 .914 1.119 .129 .162
15 1913 3494 216 152 1697 3342 1870 3452 224 155 1654 3300 0 0 552 1094 49 44 100 100 99 100 5039 4954 .508 1.969 1.995 2.005 1.951 1.242 120 887 1.994 .98 130 5150 6550 40 53 380 393 0 3075 134 2941 1.733 3038 2905 .577 1.756 .794 .812
16 5828 6149 158 99 5670 6050 4757 4628 191 215 4599 4529 0 0 3229 4135 312 434 100 100 100 91 11720 9128 .937 1.067 .985 .899 1.203 2.236 12 104 1.264 .85 50 1760 6820 71 76 45 50 -50 5412 87 5325 .939 4073 3986 1.065 .867 -.091 -.206
17 53 67 160 91 -107 -24 43 66 150 104 -117 -25 0 0 35 24 90 109 0 0 0 0 -131 -142 null null null .237 .281 2.358 156 1024 .359 .55 150 2020 6780 62 77 66 81 -50 59 80 -21 null 58 -22 null null null null
18 41 66 138 81 -97 -15 38 63 120 85 -100 -18 0 0 19 23 71 39 0 1 0 0 -112 -118 null null null .221 .255 2.036 156 972 .365 .56 150 2260 6780 62 77 90 105 -50 58 71 -13 null 55 -16 null null null null
19 2673 3327 163 99 2510 3228 2646 3272 149 102 2483 3173 0 0 597 935 60 40 100 100 100 100 5738 5656 .778 1.286 1.278 1.259 1.317 1.248 120 746 1.312 .97 120 2500 6780 64 76 116 128 0 2928 87 2841 1.132 2880 2793 .883 1.125 .179 .17
20 1275 1488 172 108 1103 1380 1346 1504 174 112 1174 1396 0 0 371 459 29 35 98 99 98 99 2483 2570 .799 1.251 1.189 1.302 1.203 1.579 156 993 1.264 .96 150 2740 6780 62 77 138 153 0 1310 95 1215 1.101 1324 1229 .908 1.047 .139 .066

Total number of rows: 6528

Table truncated, full table size 1523 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap