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Sample GSM24395 Query DataSets for GSM24395
Status Public on Sep 02, 2004
Title RH_RRE2_14028_cheA_2.5h_+glucose_broth_2D_1
Sample type RNA
 
Channel 1
Source name cheA 2.5h +glucose in broth
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Extracted molecule total RNA
 
Channel 2
Source name 14028 2.5h +glucose in broth
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Extracted molecule total RNA
 
 
Description Salmonella typhimurium 14028 vs cheA at 2.5h incubation with glucose in broth
User - TWang
Date_of_Scan = 2003/11/07 15:30:09
 
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 1930 2290 2962 36 2330 9 1970 34 100 100 0 1936 314.222 355600 23068 53 21909 13 100 100 10 10182 51 10131 1701.286 2768215 120 0.191 0.127 0.17 0.155 2.023 0.106 0.827 120 781 12067 25944 -2.387 2928 23016 0.055149458 0.435225424 0.126714698 -0.897173007 0
2 2160 2290 733 37 252 44 660 34 100 100 0 626 15.651 58724 885 53 340 16 100 100 0 779 51 728 50.647 70779 110 0.859 0.839 0.842 0.848 1.307 0.82 0.927 80 650 1354 1532 -0.219 699 833 0.013165803 0.015751772 0.835829979 -0.077882056 0
3 2400 2290 67 36 18 8 64 35 92 77 0 28 3.75 5365 97 53 27 13 91 70 0 96 52 44 3.286 7822 100 0.652 0.706 0.774 0.69 2.853 0.463 0.248 80 560 72 77 -0.617 32 45 0.000602726 0.000850936 0.708309773 -0.149776766 0
4 2620 2300 729 36 169 9 692 34 100 100 0 658 74.444 58403 665 52 135 13 100 100 0 659 50 609 45.357 53292 110 1.079 1.13 1.151 1.126 1.286 1.144 0.944 80 650 1267 1310 0.11 695 615 0.013090462 0.011629459 1.125629479 0.051395458 0
5 2870 2290 115 35 31 8 120 34 97 96 0 85 9.75 9268 129 53 30 13 100 96 0 126 52 74 5.643 10326 100 1.154 1.058 1.045 1.045 2.017 1.015 0.635 80 560 159 158 0.207 81 77 0.001525651 0.001456046 1.047804027 0.020280063 0
6 3100 2290 146 35 39 8 140 33 100 100 0 107 13.5 11738 158 52 42 13 100 100 0 150 50 100 7.857 12706 110 1.071 1.052 1.061 1.057 1.645 1.039 0.734 80 656 207 221 0.099 113 108 0.002128377 0.002042247 1.042174536 0.017940458 0
7 3340 2290 2132 35 272 8 2156 33 100 100 0 2123 253.375 170596 1514 51 229 13 100 100 0 1509 50 1459 108.143 121151 100 1.455 1.434 1.415 1.44 1.201 1.438 0.976 80 560 3582 3562 0.541 2099 1463 0.03953508 0.027664876 1.42907125 0.155053882 0
8 3570 2290 305 36 63 9 306 34 100 100 0 272 28.889 24460 330 52 64 14 100 100 0 336 50 286 19.2 26444 110 0.952 0.968 0.983 0.971 1.412 0.969 0.879 80 656 558 551 -0.072 271 280 0.005104339 0.005294713 0.964044384 -0.015902971 0
9 3810 2290 392 35 128 9 373 33 100 100 0 340 38.333 31412 334 52 142 13 100 100 0 309 50 258 20.857 26753 110 1.315 1.264 1.248 1.301 1.391 1.188 0.906 80 656 598 643 0.395 359 284 0.006761836 0.005370352 1.259104796 0.100061878 0
10 4050 2290 282 35 87 8 290 34 99 99 0 256 29.875 33954 281 51 86 12 99 97 0 277 50 227 18.308 33746 120 1.13 1.075 1.073 1.082 1.572 1.059 0.88 120 772 483 478 0.177 248 230 0.004671129 0.004349229 1.074013189 0.031009614 0
11 4280 2290 19122 36 4224 8 20567 35 100 100 0 20532 2305.375 2294732 19178 52 4742 13 100 100 0 20800 50 20749 1413.857 2301479 120 0.99 0.998 0.986 1.01 1.263 0.99 0.985 120 758 41281 38215 -0.015 19087 19128 0.359507414 0.36170455 0.993925608 -0.00264612 0
12 4510 2300 1450 36 356 8 1541 35 100 100 0 1506 170.875 174105 817 53 236 13 99 99 0 867 51 816 56.5 98043 120 1.845 1.848 1.814 1.912 1.535 1.836 0.948 120 773 2322 2181 0.884 1415 766 0.026651804 0.014484823 1.83998143 0.26481344 0
13 4750 2310 18456 36 4850 9 18235 35 100 100 0 18200 1977.667 2214769 9228 53 2839 13 100 100 0 9475 52 9423 678.286 1107467 120 1.931 2.007 1.955 2.126 1.563 1.985 0.973 120 773 27623 27597 0.95 18421 9176 0.346963173 0.173515315 1.999611231 0.300945567 0
14 4990 2290 107 36 43 9 103 34 97 88 0 69 7.667 8572 110 53 30 13 93 86 0 109 51 57 4.214 8843 100 1.196 1.247 1.25 1.112 2.629 1.31 0.475 80 560 126 131 0.258 73 58 0.001374969 0.001096762 1.253662503 0.098180636 0
15 5220 2290 142 37 36 9 138 35 100 100 0 103 11.333 11444 185 52 38 13 100 100 0 188 51 137 9.857 14829 110 0.754 0.801 0.812 0.797 1.617 0.767 0.758 80 656 240 241 -0.407 107 134 0.002015366 0.002533898 0.795361837 -0.099435251 0
16 5450 2300 17748 41 1883 43 17946 36 100 100 0 17909 407.381 1419878 6768 54 784 28 100 100 0 6837 50 6787 239.621 541512 110 2.639 2.636 2.658 2.642 1.157 2.657 0.981 80 656 24696 24430 1.4 17712 6718 0.333609018 0.127035297 2.626112783 0.419313374 0
17 5690 2300 2243 38 411 20 2299 35 100 100 0 2264 106.55 269293 2942 52 515 17 100 100 0 3005 50 2954 166.167 353130 120 0.766 0.764 0.761 0.763 1.243 0.76 0.977 120 808 5218 5100 -0.384 2208 2892 0.041588116 0.054686823 0.760477817 -0.11891345 0
18 5930 2300 99 36 48 8 93 35 92 91 0 57 7.625 7966 134 50 44 13 100 93 0 127 48 79 6.214 10755 100 0.731 0.746 0.699 0.664 2.263 0.799 0.612 80 560 136 149 -0.451 64 85 0.001205453 0.001607324 0.749975054 -0.124953182 0
19 6160 2300 81 36 23 8 82 34 97 93 0 48 5.5 6511 113 50 28 12 98 96 0 109 49 59 5 9045 100 0.812 0.746 0.76 0.721 2.081 0.633 0.525 80 560 107 110 -0.301 47 63 0.000885254 0.00119131 0.743092842 -0.128956922 0
20 1940 2530 64 36 16 8 62 35 93 78 0 26 3.375 7744 95 52 24 13 94 78 0 90 50 40 3.214 11486 120 0.663 0.638 0.614 0.599 2.575 0.486 0.321 120 786 66 73 -0.593 28 45 0.000527386 0.000850936 0.619771051 -0.207768713 0

Total number of rows: 5776

Table truncated, full table size 1286 Kbytes.




Supplementary data files not provided

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