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Sample GSM24262 Query DataSets for GSM24262
Status Public on Sep 02, 2004
Title RH_RRE2_mRNA from swarming cells on 0.6% agar plates_3h_6h_2D_2
Sample type RNA
 
Channel 1
Source name mRNA from swarming cells on 0.6% agar plates 6h
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 6h incubation
User - TWang
Date_of_Scan = 2003/09/30 11:23:58
 
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 1650 21770 2259 38 404 19 2158 36 100 100 0 2121 112.15 180758 5483 83 1627 50 100 100 0 4979 78 4900 106.92 438726 110 0.433 0.411 0.425 0.42 1.146 0.243 0.782 80 656 7021 7626 -1.208 2222 5404 0.037302001 0.104147936 0.358163611 -0.44591854 0
2 1900 21770 1137 36 258 8 1111 35 100 100 0 1076 123.556 91002 612 79 255 17 100 100 0 561 78 482 31 49003 110 2.229 2.066 2.193 2.148 1.278 2.015 0.846 80 656 1558 1634 1.156 1101 533 0.018483125 0.010272178 1.799338432 0.255112856 0
3 2130 21780 64 37 16 9 64 35 86 69 0 28 2.7 3366 119 81 27 17 80 50 0 115 79 35 2.176 6223 90 0.812 0.729 0.702 0.739 3.098 0.393 0.184 52 420 63 67 -0.3 28 39 0.000470052 0.000751623 0.625383143 -0.203853829 0
4 2360 21760 379 37 65 10 384 36 100 100 0 347 31.364 30295 496 80 89 18 100 100 0 507 79 427 22.889 39755 110 0.813 0.821 0.82 0.826 1.287 0.809 0.898 80 656 774 759 -0.298 342 417 0.005741352 0.008036582 0.714402223 -0.146057203 0
5 2600 21770 107 36 34 9 105 35 100 94 0 70 7.2 5592 178 81 38 19 100 92 0 178 79 98 5.053 9305 90 0.71 0.73 0.821 0.695 1.876 0.656 0.516 52 420 168 170 -0.494 72 98 0.001208706 0.001888693 0.639969338 -0.193840833 0
6 2840 21770 124 38 38 10 119 36 100 98 0 83 7.909 10009 171 82 45 23 97 86 0 164 80 83 3.826 13772 110 0.992 0.969 0.981 0.992 1.874 0.845 0.488 80 656 166 178 -0.012 88 90 0.001477307 0.001734514 0.85171228 -0.069707091 0
7 3070 21770 1496 37 286 9 1557 35 100 100 0 1521 147.4 119715 1436 83 291 19 100 100 0 1509 83 1425 70.474 114922 100 1.068 1.08 1.07 1.089 1.167 1.071 0.957 80 560 2946 2813 0.094 1461 1352 0.024526653 0.026056256 0.941296124 -0.026273729 0
8 3300 21770 442 37 114 9 417 35 100 100 0 382 40.9 35402 245 80 151 18 100 93 0 199 78 121 9.056 19667 110 3.153 2.441 3.16 3.078 1.764 2.077 0.66 80 656 503 572 1.657 406 166 0.006815757 0.003199215 2.13044679 0.328470692 0
9 3540 21770 367 37 158 9 348 36 100 100 0 311 33.3 29350 268 79 240 17 100 98 0 211 78 132 11 21490 100 2.357 1.741 2.236 2.184 1.652 1.151 0.665 80 560 443 519 1.237 330 189 0.005539901 0.00364248 1.520914786 0.182104882 0
10 3780 21770 149 38 47 11 144 36 97 97 0 107 9.333 17886 296 77 80 18 100 99 0 294 76 218 12.056 35657 120 0.495 0.513 0.505 0.492 1.649 0.489 0.796 120 794 325 332 -1.016 112 220 0.001880209 0.004239923 0.443453501 -0.353151912 0
11 4010 21770 37522 41 1799 42 37583 37 100 100 0 37545 880.419 3001777 13039 78 819 19 100 100 0 12949 77 12871 675.316 1043142 110 2.917 2.892 2.914 2.894 1.032 2.923 0.973 80 650 50416 50445 1.544 37484 12961 0.629265619 0.249789305 2.519185598 0.401260165 0
12 4240 21780 1040 37 139 10 1041 36 100 100 0 1004 92.091 83223 677 79 133 19 100 100 0 687 77 610 31.158 54245 110 1.647 1.673 1.685 1.7 1.204 1.714 0.922 80 656 1614 1602 0.72 1003 599 0.016837942 0.011544155 1.45856859 0.163926857 0
13 4480 21770 4607 38 562 16 4523 36 100 100 0 4486 271.471 368592 1642 78 222 19 100 100 0 1596 76 1520 81.474 131357 110 2.952 2.92 2.915 2.927 1.089 2.944 0.955 80 656 6006 6135 1.561 4570 1565 0.076719237 0.030161273 2.5436339 0.405454604 0
14 4720 21780 128 37 42 9 131 36 98 97 0 95 9.2 10296 133 76 36 17 88 71 0 131 75 55 3.294 10697 100 1.711 1.599 1.53 1.679 2.319 1.538 0.45 80 560 150 149 0.775 92 57 0.001544457 0.001098526 1.405936539 0.147965718 0
15 4950 21770 224 37 43 9 224 36 100 100 0 188 18.9 17967 171 76 43 17 100 95 0 169 75 93 5.529 13770 110 2.002 1.96 2.06 2.11 1.617 1.905 0.681 80 656 281 283 1.002 188 95 0.003156065 0.001830876 1.723800452 0.23648699 0
16 5190 21780 609 37 106 10 619 36 100 100 0 583 52.545 48806 747 75 104 16 100 100 0 732 74 657 41.563 59777 110 0.887 0.852 0.849 0.847 1.229 0.851 0.927 80 650 1240 1245 -0.173 573 672 0.009619283 0.012951039 0.742742192 -0.129161905 0
17 5420 21780 1053 37 289 9 1112 35 100 100 0 1077 102.6 126462 2739 75 757 17 100 100 0 2906 75 2831 155.118 328728 120 0.38 0.382 0.38 0.384 1.318 0.374 0.948 120 786 3908 3680 -1.394 1017 2663 0.017072968 0.051322345 0.332661493 -0.477997467 0
18 5660 21780 84 37 27 9 82 35 93 85 0 46 4.7 6698 147 74 42 17 93 81 0 138 74 63 4.235 11761 100 0.731 0.667 0.663 0.667 2.184 0.561 0.529 80 560 109 120 -0.452 48 72 0.000805804 0.001387611 0.580712918 -0.236038513 0
19 5890 21780 67 36 22 9 66 34 82 67 0 31 3.1 5397 193 75 47 17 97 97 0 194 73 121 6.882 15481 100 0.261 0.272 0.253 0.234 2.22 0.24 0.446 80 560 152 152 -1.936 32 120 0.000537203 0.002312685 0.232285167 -0.633978522 0
20 1670 22000 174 37 40 9 168 36 100 100 0 131 13.8 13968 123 80 29 17 82 57 0 119 79 39 2.471 9833 110 3.343 3.168 3.373 3.721 2.284 3.274 0.43 80 656 170 180 1.741 137 43 0.002299898 0.000828712 2.775267551 0.443304858 0

Total number of rows: 5776

Table truncated, full table size 1289 Kbytes.




Supplementary data files not provided

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