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Sample GSM24258 Query DataSets for GSM24258
Status Public on Sep 02, 2004
Title RH_RRE2_mRNA from swarming cells on 0.6% agar plates_3h_5h_2D_1
Sample type RNA
 
Channel 1
Source name mRNA from swarming cells on 0.6% agar plates 5h
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Extracted molecule total RNA
 
Channel 2
Source name mRNA from swarming cells on 0.6% agar plates 3h
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Extracted molecule total RNA
 
 
Description mRNA from swarming cells on 0.6% agar plates 3h vs 5h incubation
User - TWang
Date_of_Scan = 2003/09/30 11:04:27
 
Submission date May 27, 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)
GSE1625 14028 time course on swarming plates

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 1550 2300 2424 44 461 60 2390 39 100 100 0 2351 39.283 193952 5007 64 470 140 100 100 0 4932 54 4877 35.155 400587 110 0.482 0.482 0.475 0.475 1.173 0.485 0.907 80 656 7228 7337 -1.053 2385 4952 0.044139733 0.107406237 0.410960615 -0.386199797 0
2 1800 2290 1064 39 271 11 1071 38 100 100 0 1033 92.273 85194 510 55 191 12 100 100 0 492 54 437 35.385 40871 100 2.361 2.248 2.287 2.337 1.334 2.162 0.913 80 560 1470 1482 1.239 1026 456 0.018988414 0.009890397 1.919883932 0.283274974 0
3 2030 2290 80 40 24 11 80 38 90 78 0 42 3.636 6466 89 54 23 11 85 67 0 85 53 31 2.917 7136 100 1.339 1.19 1.133 1.223 2.554 1.152 0.388 80 560 73 77 0.421 42 35 0.000777303 0.000759131 1.023938097 0.010273702 0
4 2260 2300 473 39 77 11 466 38 100 100 0 428 39.091 37871 592 53 69 12 100 100 0 589 53 535 41.846 47363 110 0.799 0.808 0.799 0.801 1.236 0.812 0.925 80 656 963 973 -0.323 435 538 0.008050643 0.011668933 0.689921116 -0.161200563 0
5 2510 2300 103 39 45 10 90 38 93 82 0 52 6.3 8259 134 54 42 11 100 95 0 126 53 73 6.75 10786 100 0.717 0.796 0.79 0.678 2.169 0.845 0.606 80 560 125 145 -0.481 64 81 0.001184462 0.001756847 0.674197924 -0.171212589 0
6 2730 2290 187 39 45 10 184 38 100 100 0 146 14.7 15026 170 53 35 12 100 100 0 167 52 114 9.077 13608 110 1.275 1.268 1.289 1.263 1.612 1.305 0.745 80 650 260 266 0.35 149 117 0.002757577 0.002537668 1.086657952 0.036092862 0
7 2980 2290 1753 39 431 10 1879 37 100 100 0 1842 169.7 140234 1762 52 416 11 100 100 0 1905 51 1853 143.917 141014 100 0.994 1.003 1.013 1.001 1.222 1.004 0.967 80 560 3695 3426 -0.009 1715 1711 0.031739892 0.037110677 0.855276562 -0.067893429 0
8 3200 2300 382 40 102 10 364 38 100 100 0 326 33.9 30633 215 52 94 11 100 100 0 194 51 142 13.75 17236 110 2.288 2.095 2.228 2.321 1.573 2.096 0.767 80 650 468 508 1.194 344 164 0.006366486 0.003557072 1.789810495 0.25280705 0
9 3440 2300 438 40 132 10 428 39 100 100 0 388 39.4 35091 243 53 150 12 100 100 0 209 51 158 14.769 19516 100 2.454 2.077 2.29 2.281 1.491 1.786 0.73 80 560 546 590 1.295 398 192 0.007365876 0.004164378 1.768781956 0.247674299 0
10 3670 2300 159 40 48 10 153 39 99 98 0 114 11.8 19166 232 52 57 12 100 100 0 242 50 192 14 27962 120 0.594 0.66 0.657 0.651 1.587 0.663 0.808 120 786 306 302 -0.751 120 182 0.002220867 0.003947483 0.56260335 -0.249797686 0
11 3900 2310 41160 55 2293 165 41461 41 100 100 0 41420 248.183 3292882 14161 56 929 30 100 100 0 14377 52 14325 459.516 1132941 110 2.891 2.914 2.901 2.916 1.073 2.943 0.977 80 636 55745 55228 1.532 41119 14109 0.760998613 0.30601668 2.48678802 0.395638767 0
12 4140 2300 909 43 238 37 940 39 99 99 0 900 23.189 109160 507 54 224 17 99 99 0 506 52 454 25.444 60905 120 1.982 1.911 1.943 1.989 1.516 1.796 0.872 120 793 1354 1325 0.987 870 455 0.016101286 0.009868707 1.631549715 0.212600312 0
13 4380 2310 3567 40 918 10 3757 38 100 100 0 3719 349.2 428001 1667 53 434 10 100 100 0 1768 52 1715 148.182 200100 120 2.168 2.185 2.183 2.171 1.479 2.197 0.971 120 753 5434 5142 1.116 3528 1614 0.065293492 0.035006799 1.86516605 0.270717502 0
14 4610 2300 135 40 36 11 136 39 100 100 0 96 8.545 10801 109 53 27 11 97 86 0 104 53 51 4.75 8759 100 1.883 1.7 1.76 1.875 1.951 1.697 0.641 80 560 147 151 0.913 95 56 0.001758186 0.00121461 1.447531536 0.160628034 0
15 4850 2290 287 40 53 10 291 39 100 100 0 252 24.5 23021 151 51 33 11 100 100 0 151 50 100 8.417 12082 110 2.5 2.46 2.265 2.57 1.624 2.621 0.744 80 656 352 348 1.322 248 100 0.004589792 0.002168947 2.116138734 0.325544137 0
16 5080 2290 745 40 137 14 754 38 100 100 0 716 49.857 59635 770 52 166 11 100 100 0 801 51 749 60.417 61610 100 0.955 0.983 0.98 1 1.314 0.96 0.923 80 560 1465 1424 -0.066 706 718 0.013066101 0.015573037 0.839020771 -0.076227287 0
17 5310 2300 1840 41 249 11 1832 39 100 100 0 1793 161.909 147226 3780 51 443 11 100 100 0 3779 50 3729 313.833 302420 110 0.481 0.483 0.484 0.482 1.136 0.483 0.965 80 656 5522 5530 -1.056 1800 3730 0.033313006 0.080901709 0.411771353 -0.385343871 0
18 5550 2290 123 40 36 10 129 39 96 93 0 89 8.2 9852 118 52 30 11 98 95 0 111 50 61 5.583 9483 110 1.464 1.227 1.265 1.161 2.078 1.259 0.582 80 656 150 151 0.55 83 68 0.0015361 0.001474884 1.041505662 0.017661635 0
19 5790 2290 107 40 47 10 102 39 95 90 0 62 6.6 8569 208 51 42 10 100 100 0 212 50 162 14.455 16712 110 0.386 0.427 0.39 0.362 2.058 0.432 0.557 80 656 224 225 -1.375 67 158 0.001239984 0.003426936 0.361834665 -0.441489828 0
20 1560 2540 150 40 150 11 132 38 100 97 0 93 9.909 12073 96 54 20 12 91 75 0 95 53 41 3.231 7695 110 2.258 2.633 2.424 2.47 2.142 6.838 0.247 80 656 134 154 1.175 112 42 0.002072809 0.000910958 2.275417993 0.357061188 0

Total number of rows: 5776

Table truncated, full table size 1282 Kbytes.




Supplementary data files not provided

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