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Sample GSM43877 Query DataSets for GSM43877
Status Public on Aug 23, 2005
Title RH_RRE2_14028_cheB_3h_plate_4D_2
Sample type RNA
 
Channel 1
Source name Typhimurium 14028 wt
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Extracted molecule total RNA
 
Channel 2
Source name Typhimurium 14028 cheB mutant
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Extracted molecule total RNA
 
 
Description Typhimurium 14028 wt and cheB mutant transcripts after 3h growth on plate
User - TWang
Date_of_Scan = 2004/01/22 11:49:19
 
Submission date Feb 24, 2005
Last update date Jun 16, 2005
Contact name Rasika Harshey
E-mail(s) wqf@mail.utexas.edu
Phone (512)471-6881
Fax (512)471-7088
Organization name Institute of Cellular and Molecular Biology
Department Section of Molecular Genetics and Microbiology
Lab rasika@uts.cc.utexas.edu
Street address
City Austin
State/province TX
ZIP/Postal code 78712
Country USA
 
Platform ID GPL548
Series (1)
GSE2341 Transcription profiles of che and flgM mutants of Typhimurium 14028 at 3h on agar 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 1830 21170 3903 38 3176 10 2704 37 100 100 0 2666 353.455 468480 27416 65 21077 17 100 100 11 14950 64 14886 1599.412 3289873 120 0.179 0.141 0.168 0.15 1.565 0.129 0.797 120 779 17552 31217 -2.481 3866 27351 0.055390264 0.403649388 0.137223702 -0.862570867 0
2 2070 21160 832 38 166 12 835 36 100 100 0 798 61.385 99864 2183 65 472 22 100 100 0 2127 64 2063 95.727 262078 130 0.387 0.375 0.376 0.375 1.206 0.36 0.935 120 838 2861 2914 -1.37 795 2119 0.011390393 0.03127246 0.364230797 -0.438623336 0
3 2290 21170 85 38 25 12 83 36 93 77 0 46 3.615 10228 122 63 31 21 90 70 0 121 61 60 2.81 14749 130 0.774 0.794 0.83 0.776 2.364 0.669 0.413 120 824 106 109 -0.369 48 61 0.000687722 0.000900245 0.763927061 -0.116948105 0
4 2530 21170 1179 37 230 10 1127 36 100 100 0 1090 104.364 141501 1247 61 251 16 100 100 0 1185 60 1125 73.688 149709 130 0.969 0.962 0.945 0.965 1.159 0.954 0.959 120 850 2215 2328 -0.046 1142 1186 0.016362049 0.017503132 0.934806896 -0.029278093 0
5 2770 21170 170 37 53 10 168 35 99 98 0 132 12.182 20472 197 61 51 16 99 96 0 197 60 136 8.438 23653 120 0.966 0.988 0.971 0.956 1.708 0.972 0.727 120 752 268 271 -0.049 135 136 0.001934218 0.002007105 0.963685562 -0.016064647 0
6 3000 21170 238 37 65 10 234 36 100 100 0 197 18.364 28640 273 63 68 17 100 100 0 265 62 203 12.294 32828 120 0.974 0.955 0.988 0.952 1.466 0.949 0.811 120 764 400 412 -0.039 201 211 0.002879835 0.003113964 0.924813359 -0.033945905 0
7 3240 21170 1352 37 452 10 1358 36 100 100 0 1322 120.182 162212 1383 63 452 16 100 100 0 1421 62 1358 82 166029 120 0.973 0.996 0.976 0.994 1.308 0.995 0.951 120 774 2680 2635 -0.04 1315 1320 0.018840713 0.019480721 0.96714661 -0.014507686 0
8 3480 21170 341 37 99 10 336 35 100 100 0 300 27.818 41057 378 62 94 17 100 100 0 379 60 318 18.471 45441 120 0.942 0.963 0.963 0.964 1.343 0.974 0.895 120 752 618 623 -0.087 306 317 0.004384227 0.004678325 0.937136076 -0.028197343 0
9 3710 21170 175 38 65 10 175 36 99 99 0 139 12.545 21084 204 62 76 18 99 96 0 192 60 131 7.833 24471 120 1.056 0.968 1.003 0.973 1.569 0.922 0.814 120 762 270 282 0.079 139 143 0.001991528 0.002110411 0.943668059 -0.025180745 0
10 3950 21170 276 39 79 10 275 37 100 100 0 237 21.636 22140 304 63 75 18 100 100 0 315 62 253 13.333 24350 110 0.937 0.984 0.976 0.99 1.405 0.973 0.817 80 656 490 480 -0.093 238 242 0.003409954 0.003571465 0.954777297 -0.020097917 0
11 4190 21170 18306 39 4651 10 18887 37 100 100 0 18849 1670.455 2196843 17270 65 4289 18 100 100 0 17887 64 17822 950.222 2072479 120 1.058 1.062 1.061 1.06 1.186 1.066 0.983 120 762 36671 35475 0.081 18269 17206 0.261749799 0.253928243 1.030802231 0.01317535 0
12 4420 21170 1875 38 372 10 1884 36 100 100 0 1848 168 225087 1883 64 358 17 100 100 0 1898 63 1834 106.353 225963 120 1.007 1.011 1.003 1.004 1.164 1.013 0.971 120 742 3682 3658 0.01 1839 1819 0.026348343 0.026845023 0.981498234 -0.008110477 0
13 4650 21170 3643 38 871 11 3847 36 100 100 0 3810 302.167 437212 3835 64 966 17 100 100 0 4024 62 3962 220.529 460252 130 0.962 0.956 0.944 0.958 1.151 0.948 0.977 120 838 7772 7379 -0.056 3606 3773 0.051665104 0.055682393 0.927853498 -0.03252059 0
14 4890 21170 738 38 203 10 738 37 100 100 0 700 64 88679 823 62 241 17 100 100 0 810 60 750 44.529 98882 120 0.934 0.918 0.915 0.913 1.295 0.906 0.945 120 763 1450 1463 -0.099 700 763 0.010029277 0.011260447 0.890664196 -0.050286006 0
15 5130 21180 149 37 49 10 149 36 100 99 0 112 10.182 17930 180 63 43 17 100 97 0 180 61 118 6.824 21556 120 0.946 0.946 1.009 0.922 1.648 0.959 0.695 120 741 230 230 -0.079 112 118 0.001604684 0.001741458 0.921460043 -0.035523492 0
16 5360 21180 1034 38 264 10 1092 36 100 100 0 1055 91.091 124174 1022 62 274 16 99 99 0 1070 60 1009 59.625 122687 120 1.045 1.038 1.047 1.034 1.245 1.033 0.956 120 755 2064 1959 0.064 998 961 0.014298883 0.014182555 1.008202212 0.003547646 0
17 5600 21170 5714 38 1769 10 6016 36 100 100 0 5979 519 685673 5958 61 1705 16 100 100 0 6141 60 6080 366.438 715136 130 0.983 0.963 0.958 0.95 1.165 0.976 0.977 120 864 12059 11575 -0.024 5677 5898 0.081337436 0.087043402 0.93444688 -0.029445382 0
18 5840 21180 612 38 237 9 588 36 100 100 0 551 57.7 73461 658 61 232 16 98 98 0 663 59 604 37.125 79047 120 0.913 0.96 0.93 0.947 1.431 0.975 0.927 120 756 1155 1174 -0.132 575 599 0.008238335 0.008840115 0.931926185 -0.030618485 0
19 6070 21180 143 51 51 150 139 36 13 0 0 102 0.609 17134 171 72 51 134 32 0 0 163 58 105 0.731 20521 120 0.969 0.944 0.927 0.936 1.803 0.936 0.701 120 770 207 218 -0.045 106 112 0.001518719 0.00165291 0.918815547 -0.036771665 0
20 1830 21400 82 38 26 10 81 36 87 75 0 44 4 9905 104 63 29 17 79 59 0 99 61 38 2.412 12562 120 1.17 1.057 1.107 0.961 3.322 0.879 0.312 120 768 82 88 0.227 45 43 0.000644739 0.000634599 1.015978577 0.006884551 0

Total number of rows: 5776

Table truncated, full table size 1305 Kbytes.




Supplementary data files not provided

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