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Sample GSM24403 Query DataSets for GSM24403
Status Public on Sep 02, 2004
Title RH_RRE2_14028_cheA_3h_+glucose_broth_2D_3
Sample type RNA
 
Channel 1
Source name cheA 3h +glucose in broth
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Extracted molecule total RNA
 
Channel 2
Source name 14028 3h +glucose in broth
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Extracted molecule total RNA
 
 
Description Salmonella typhimurium 14028 vs cheA at 3h incubation with glucose in broth
User - TWang
Date_of_Scan = 2003/11/07 15:58:59
 
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 1750 40700 2221 39 1554 76 1673 32 100 100 0 1641 28.592 177727 15583 172 19788 1576 97 93 5 6087 52 6034 9.773 1246677 110 0.272 0.141 0.242 0.213 1.829 0.095 0.872 80 648 7675 17720 -1.878 2189 15531 0.044545977 0.330724828 0.134691965 -0.870658312 0
2 1990 40700 770 32 285 7 691 30 100 100 0 660 105 61675 938 52 436 16 100 100 0 803 50 752 52.353 75122 110 0.878 0.834 0.85 0.851 1.237 0.787 0.905 80 656 1412 1627 -0.187 740 887 0.015058942 0.018888219 0.797266372 -0.098396554 0
3 2230 40700 58 31 18 7 58 30 88 81 0 28 3.857 4699 95 51 23 12 96 78 0 92 50 41 3.385 7670 110 0.673 0.628 0.703 0.588 2.594 0.455 0.321 80 656 69 72 -0.572 28 44 0.000569798 0.000936958 0.608135983 -0.215999299 0
4 2460 40690 1002 32 251 18 982 30 100 100 0 952 53.667 80170 1009 52 322 29 100 100 0 939 49 889 32.033 80766 110 1.07 1.013 1.017 1.029 1.235 0.928 0.87 80 656 1841 1931 0.098 972 959 0.019780123 0.020421422 0.968596743 -0.013856996 -50
5 2700 40690 178 32 62 7 171 31 100 100 0 140 20.857 14327 207 48 71 10 100 100 0 198 47 150 14.455 16570 100 0.936 0.927 0.876 0.936 1.578 0.901 0.804 80 560 290 306 -0.096 147 159 0.002991438 0.003385825 0.883518316 -0.053784443 0
6 2940 40690 116 31 30 6 117 30 100 100 0 87 14.167 14019 137 49 32 11 99 98 0 138 48 89 7.333 16427 120 0.975 0.975 1.005 1.003 1.783 0.936 0.649 120 786 176 174 -0.036 86 88 0.001750093 0.001873916 0.933923118 -0.029688874 0
7 3170 40690 1473 31 271 6 1525 30 100 100 0 1495 239.333 117862 1294 49 298 11 100 100 0 1342 47 1295 104.167 103526 110 1.155 1.158 1.169 1.183 1.209 1.13 0.958 80 650 2790 2689 0.208 1443 1246 0.029364936 0.026532943 1.106734977 0.044043635 0
8 3410 40680 264 32 79 7 273 30 99 99 0 243 33 31695 335 48 98 11 99 99 0 333 47 285 24 40317 120 0.851 0.814 0.83 0.796 1.478 0.8 0.89 120 784 528 521 -0.233 234 287 0.004761882 0.006111521 0.779164769 -0.108370693 0
9 3640 40680 382 32 179 6 344 31 100 100 0 313 58.167 30606 371 48 194 11 100 100 0 331 47 283 27 29738 110 1.105 1.087 1.133 1.109 1.345 1.034 0.877 80 650 596 674 0.144 351 323 0.007142822 0.006878122 1.038484313 0.016399941 0
10 3880 40680 261 32 69 7 260 31 100 100 0 229 32.571 31301 343 49 90 11 100 100 0 332 48 283 24.583 41192 120 0.807 0.781 0.779 0.776 1.452 0.758 0.832 120 786 512 524 -0.309 230 294 0.004680482 0.006260582 0.747611292 -0.126324148 0
11 4120 40680 10978 33 2872 7 11768 32 100 100 0 11736 1556.571 1317444 10694 49 2307 15 100 100 0 11261 47 11213 668.313 1283357 120 1.047 1.028 1.043 0.988 1.322 1.049 0.964 120 763 22949 21593 0.066 10946 10647 0.222750235 0.226722507 0.982479588 -0.007676464 0
12 4350 40680 1079 32 303 7 1095 31 100 100 0 1064 149 129590 1093 49 318 15 100 100 0 1110 47 1063 65.5 131187 120 1.001 1.003 0.993 1.01 1.267 0.998 0.964 120 773 2127 2093 0.002 1048 1045 0.021326717 0.022252749 0.95838573 -0.018459661 0
13 4590 40670 22793 32 6027 7 23104 31 100 100 0 23073 3237 2735148 23925 49 6348 10 100 100 0 24012 48 23964 2180.273 2871031 120 0.963 0.953 0.957 0.951 1.472 0.951 0.962 120 783 47037 46638 -0.055 22762 23876 0.463204901 0.508427404 0.91105416 -0.040455805 0
14 4830 40670 152 32 78 7 133 31 98 98 0 102 17.143 12206 197 48 86 11 100 100 0 195 48 146 12.417 15798 110 0.7 0.819 0.764 0.778 1.6 0.836 0.817 80 650 248 269 -0.514 121 148 0.00246234 0.003151586 0.781302118 -0.107180998 0
15 5060 40670 148 32 43 7 141 31 99 99 0 110 16.571 17795 173 47 43 10 98 98 0 173 46 126 11.455 20824 120 0.874 0.93 0.92 0.914 1.702 0.908 0.728 120 783 236 243 -0.194 117 126 0.002380941 0.002683107 0.887382098 -0.051889337 0
16 5290 40660 20964 45 1315 158 21093 32 100 100 0 21061 131.804 1677127 19203 69 1874 298 100 100 0 19285 47 19237 64.067 1536257 110 1.095 1.093 1.091 1.097 1.103 1.072 0.975 80 650 40298 40086 0.131 20931 19155 0.425944196 0.407896085 1.044246836 0.018803168 0
17 5530 40670 1426 33 234 14 1447 31 100 100 0 1416 99.071 171111 1319 49 196 22 100 100 0 1334 46 1288 55.435 158244 120 1.099 1.097 1.104 1.091 1.26 1.103 0.958 120 794 2704 2667 0.137 1395 1272 0.02838814 0.0270866 1.048051063 0.020382443 0
18 5760 40670 70 31 22 7 69 30 98 94 0 39 5.571 3672 96 48 23 10 96 86 0 93 47 45 4.364 5030 90 0.855 0.824 0.871 0.818 2.106 0.714 0.474 52 420 84 88 -0.225 40 48 0.000813997 0.001022136 0.79636855 -0.098885899 0
19 6010 40660 56 36 16 57 52 31 3 0 0 21 0.351 4497 71 82 18 441 0 0 0 70 47 22 -0.025 5766 110 0.921 1.051 1.023 1.017 2.613 0.58 0.158 80 656 43 48 -0.118 25 23 0.000508748 0.000489773 1.038741587 0.016507519 0
20 1780 40940 56 32 29 8 52 31 80 60 0 21 3 6758 89 51 28 20 71 39 0 84 50 33 1.81 10732 120 0.623 0.647 0.592 0.591 3.288 0.6 0.296 120 785 54 63 -0.682 25 38 0.000508748 0.000809191 0.628712013 -0.201548241 0

Total number of rows: 5776

Table truncated, full table size 1287 Kbytes.




Supplementary data files not provided

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