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Sample GSM24408 Query DataSets for GSM24408
Status Public on Sep 02, 2004
Title RH_RRE2_14028_cheB_2h_+glucose_broth_2D_2
Sample type RNA
 
Channel 1
Source name cheB 2h +glucose in broth
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Extracted molecule total RNA
 
Channel 2
Source name 14028 2h +glucose in broth
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Extracted molecule total RNA
 
 
Description Salmonella typhimurium 14028 vs cheB at 2h incubation with glucose in broth
User - TWang
Date_of_Scan = 2003/11/07 15:14:05
 
Submission date May 28, 2004
Last update date May 27, 2005
Contact name Rasika Harshey
E-mail(s) [email protected]
Phone (512)471-6881
Fax (512)471-7088
Organization name Institute of Cellular and Molecular Biology
Department Section of Molecular Genetics and Microbiology
Lab [email protected]
Street address
City Austin
State/province TX
ZIP/Postal code 78712
Country USA
 
Platform ID GPL548
Series (1)
GSE1632 14028 versus che mutants

Data table header descriptions
ID_REF Number
X_LOCATION X-coordinate of spot
Y_LOCATION Y-coordinate of spot
CH1_MEAN Cy5 (635nm) mean of signals
CH1_BKD_MEAN Cy5 (635nm) mean of background
CH1_SD Cy5 (635nm) standard deviation of signals
CH1_BKD_SD Cy5 (635nm) standard deviation
CH1_MEDIAN Cy5 (635nm) median of signals
CH1_BKD_MEDIAN Cy5 (635nm) median of background
CH1%>CH1_BKD+1SD Percent of Cy5 (635nm) signal pixels over one standard deviation over background levels
CH1%>CH1_BKD+2SD Percent of Cy5 (635nm) signal pixels over two standard deviation over background levels
CH1%_SAT Percent of saturated Cy5 (635nm) signal pixels
CH1_MEDIAN_BKGR_CORR median pixel intensity Cy5 (635nm) minus median background of the spot
CH1_SIGNAL_NOISE Cy5(635nm) signal/noise ratio
CH1_INTENSITY total Cy5 (632nm) intensity of all pixels of the spot
CH2_MEAN Cy3 (532nm) mean of signals
CH2_BKD_MEAN Cy3 (532nm) mean of background
CH2_SD Cy3 (532nm) standard deviation of signals
CH2_BKD_SD Cy3 (532nm) standard deviation
CH2%>CH2_BKD+1SD Percent of Cy3 (532nm) signal pixels over one standard deviation over background levels
CH2%>CH2_BKD+2SD Percent of Cy3 (532nm) signal pixels over two standard deviation over background levels
CH2%_SAT Percent of saturated Cy3 (532nm) signal pixels
CH2_MEDIAN Cy3 (532nm) median of signals
CH2_BKD_MEDIAN Cy3 (532nm) median of background
CH2_MEDIAN_BKGR_CORR median pixel intensity Cy3 (532nm) minus median background of the spot
CH2_SIGNAL_NOISE Cy3 (532nm) signal/noise ratio
CH2_INTENSITY total Cy3 (532nm) intensity of all pixels of the spot
DIAMETER Spot diameter
MEDIANS_CH1/CH2 Cy5/Cy3 background corrected ratio of median intensity value of the whole feature
MEANS_CH1/CH2 Cy5/Cy3 background corrected ratio of mean intensity value of the whole feature
MEDIAN_OF_RATIOS_CH1/CH2 median of the Cy5/Cy3 background corrected ratios of each pixel of the feature
MEAN_OF_RATIOS_CH1/CH2 mean of the Cy5/Cy3 background corrected ratios of each pixel of the feature
RATIOS_SD_CH1/CH2 standard deviation of the Cy5/Cy3 background corrected ratios of each pixel of the feature
REGRESSION_RATIO_CH1/CH2 slope of the least squares best-fit regression line in a scatter plot of Cy5/Cy3 for each pixel
REGRESSION_RSQUARE_CH1/CH2 Square of correlation coefficient of the least-squares regression fit, proportion of regression pixels that can be described by the regression fit
NUMBER_OF_PIXELS Number of pixels in the spot
NUMBER_OF_BKD_PIXELS number of pixels that comprise the background for the spot
SUM_OF_MEDIANS sum of background subtracted median pixel intensities of both wavelengths
SUM_OF_MEANS sum of background subtracted mean pixel intensities of both wavelengths
LOG_RATIO_CH1/CH2 log2 of means_ch1/ch2
CH1_MEAN_BKGR_CORR mean pixel intensity Cy5 (635nm) minus median background of the spot
CH2_MEAN_BKGR_CORR mean pixel intensity Cy3 (532nm) minus median background of the spot
CH1%_OF_TOTAL Channel 1 (Cy5 = 635nm) % of total
CH2%_OF_TOTAL Channel 2 (Cy3 = 532nm) % of total
PRE-VALUE Cy5 [635nm] % of total / Cy3 [532nm] % of total
VALUE log of Cy5 [635nm] % of total / Cy3 [532nm] % of total
FLAGS Feature quality assessment

Data table
ID_REF X_LOCATION Y_LOCATION CH1_MEAN CH1_BKD_MEAN CH1_SD CH1_BKD_SD CH1_MEDIAN CH1_BKD_MEDIAN CH1%>CH1_BKD+1SD CH1%>CH1_BKD+2SD CH1%_SAT CH1_MEDIAN_BKGR_CORR CH1_SIGNAL_NOISE CH1_INTENSITY CH2_MEAN CH2_BKD_MEAN CH2_SD CH2_BKD_SD CH2%>CH2_BKD+1SD CH2%>CH2_BKD+2SD CH2%_SAT CH2_MEDIAN CH2_BKD_MEDIAN CH2_MEDIAN_BKGR_CORR CH2_SIGNAL_NOISE CH2_INTENSITY DIAMETER MEDIANS_CH1/CH2 MEANS_CH1/CH2 MEDIAN_OF_RATIOS_CH1/CH2 MEAN_OF_RATIOS_CH1/CH2 RATIOS_SD_CH1/CH2 REGRESSION_RATIO_CH1/CH2 REGRESSION_RSQUARE_CH1/CH2 NUMBER_OF_PIXELS NUMBER_OF_BKD_PIXELS SUM_OF_MEDIANS SUM_OF_MEANS LOG_RATIO_CH1/CH2 CH1_MEAN_BKGR_CORR CH2_MEAN_BKGR_CORR CH1%_OF_TOTAL CH2%_OF_TOTAL PRE-VALUE VALUE FLAGS
1 1740 21720 2992 38 1819 17 2387 35 100 100 0 2351 169 239368 16577 76 17685 235 100 100 6 7876 51 7825 70.107 1326207 110 0.3 0.179 0.257 0.237 1.773 0.122 0.868 80 656 10176 19482 -1.735 2956 16526 0.040444036 0.249377198 0.162180169 -0.790002252 0
2 1980 21720 667 35 257 8 621 34 100 100 0 586 76.75 53362 767 52 464 13 100 100 0 630 50 579 52.5 61420 110 1.011 0.882 0.943 0.932 1.309 0.789 0.925 80 656 1165 1348 0.016 632 716 0.008647033 0.010804434 0.800322677 -0.096734877 0
3 2210 21720 70 34 22 9 68 33 90 73 0 34 3.889 3688 106 51 26 13 96 86 0 104 50 53 4 5529 90 0.654 0.668 0.551 0.614 2.46 0.619 0.392 52 420 87 92 -0.614 37 55 0.000506235 0.00082995 0.609958238 -0.214699899 0
4 2450 21710 1005 34 185 9 959 33 100 100 0 925 104.889 80483 1015 50 169 13 100 100 0 993 48 944 70.857 81210 110 0.98 1.005 1.006 1.003 1.213 1.018 0.968 80 656 1869 1937 -0.029 971 966 0.013285236 0.014576932 0.911387715 -0.04029683 0
5 2690 21720 187 34 47 8 190 33 100 100 0 156 18.5 14939 202 50 55 12 100 100 0 198 49 148 12 16172 100 1.05 1.003 1.079 1.027 1.563 0.96 0.79 80 560 304 305 0.071 153 152 0.002093348 0.002293679 0.912659775 -0.03969109 0
6 2930 21720 133 34 40 8 130 33 99 98 0 96 12 16031 166 50 45 12 98 96 0 164 49 114 9.154 19899 120 0.842 0.855 0.889 0.861 1.706 0.82 0.757 120 793 210 215 -0.248 99 116 0.001354519 0.001750439 0.77381701 -0.111361728 0
7 3170 21710 1751 34 376 8 1837 32 100 100 0 1804 208.625 140110 1683 50 291 12 100 100 0 1743 49 1694 129.154 134662 110 1.065 1.052 1.048 1.038 1.217 1.068 0.978 80 650 3498 3351 0.091 1718 1633 0.023505702 0.024641956 0.953889441 -0.020501959 0
8 3390 21710 199 34 97 8 173 33 100 100 0 139 20 15976 226 50 123 12 100 100 0 201 49 151 13.923 18107 110 0.922 0.935 0.943 0.962 1.556 0.875 0.865 80 650 290 342 -0.118 165 177 0.002257532 0.002670928 0.845223853 -0.073028255 0
9 3630 21710 197 34 119 9 175 33 100 98 0 141 17.556 15824 228 50 164 12 100 100 0 204 48 155 14.077 18273 110 0.912 0.909 0.929 0.929 1.682 0.809 0.859 80 656 296 342 -0.133 163 179 0.002230168 0.002701108 0.825649344 -0.08320436 0
10 3870 21710 467 35 128 8 485 33 99 99 0 451 52.5 56116 498 51 126 12 100 100 0 507 49 458 35.385 59925 120 0.985 0.966 0.951 0.937 1.468 0.963 0.921 120 786 909 882 -0.021 433 449 0.005924312 0.006775406 0.874384846 -0.058297378 0
11 4110 21710 18043 37 4225 9 19170 34 100 100 0 19135 1945.889 2165204 15728 51 3547 12 100 100 0 16651 50 16600 1239.923 1887369 120 1.153 1.149 1.154 1.133 1.231 1.153 0.991 120 772 35735 33685 0.205 18008 15677 0.246385725 0.236565796 1.041510351 0.01766359 0
12 4340 21710 1474 35 428 8 1594 34 100 100 0 1559 174.875 176933 1524 51 460 12 99 99 0 1652 50 1601 116.462 182916 120 0.974 0.977 0.983 1.009 1.353 0.972 0.976 120 774 3160 2912 -0.038 1439 1473 0.019688419 0.022227557 0.88576622 -0.052680886 0
13 4570 21710 17155 96 3935 643 16042 35 100 100 0 16006 26.503 1372460 15276 109 3019 670 100 100 0 14548 50 14498 22.633 1222118 110 1.104 1.124 1.121 1.112 1.203 1.143 0.986 80 650 30504 32344 0.143 17119 15225 0.234222413 0.229745119 1.019488092 0.008382157 0
14 4820 21710 81 35 27 9 78 33 96 86 0 44 4.889 6522 108 50 30 12 95 86 0 109 49 60 4.615 8679 110 0.733 0.797 0.811 0.799 2.365 0.692 0.428 80 650 104 106 -0.448 47 59 0.000643055 0.000890309 0.722282201 -0.141293087 0
15 5050 21710 110 34 32 8 115 33 98 95 0 81 9.125 13195 145 48 40 11 99 96 0 142 47 95 8.333 17489 120 0.852 0.775 0.819 0.766 1.991 0.718 0.66 120 774 176 174 -0.231 76 98 0.001039833 0.001478819 0.703150975 -0.152951417 0
16 5280 21710 7122 35 2267 9 7938 33 100 100 0 7904 765.778 854726 5731 48 1848 11 100 100 0 6392 47 6345 486.917 687798 120 1.246 1.247 1.255 1.275 1.295 1.246 0.989 120 772 14249 12771 0.317 7088 5683 0.096978122 0.085756421 1.130855513 0.05340712 0
17 5520 21710 5269 37 867 14 5337 34 100 100 0 5302 363.5 632298 4723 50 715 29 100 100 0 4813 48 4764 160.167 566898 120 1.113 1.12 1.109 1.114 1.193 1.123 0.985 120 792 10066 9909 0.154 5234 4675 0.071611666 0.07054571 1.015110149 0.00651317 0
18 5760 21710 86 35 24 16 83 33 93 77 0 49 3.063 6875 106 51 35 34 76 31 0 105 48 56 1.629 8570 100 0.875 0.899 0.992 0.962 2.652 0.701 0.447 80 560 105 110 -0.193 52 58 0.000711465 0.00087522 0.812898677 -0.089963583 0
19 5990 21710 105 35 31 9 99 33 100 100 0 65 7.556 8458 111 48 28 11 95 90 0 112 47 65 5.417 8949 100 1.01 1.121 1.147 1.182 2.094 1.07 0.531 80 560 130 135 0.014 71 64 0.000971423 0.000965759 1.005864409 0.002539441 0
20 1760 21960 69 35 20 9 67 34 89 77 0 32 3.667 8417 105 51 26 20 90 73 0 102 48 53 2.619 12595 120 0.615 0.62 0.622 0.575 2.952 0.516 0.345 120 792 85 90 -0.701 34 56 0.000465189 0.00084504 0.550493198 -0.259248043 0

Total number of rows: 5776

Table truncated, full table size 1296 Kbytes.




Supplementary data files not provided

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