NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM24283 Query DataSets for GSM24283
Status Public on Sep 02, 2004
Title RH_RRE2_14028_cheY_4h_+glucose_broth_2D_2
Sample type RNA
 
Channel 1
Source name cheY 4h +glucose in broth
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Extracted molecule total RNA
 
Channel 2
Source name 14028 4h +glucose in broth
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Extracted molecule total RNA
 
 
Description Salmonella typhimurium 14028 vs cheY at 4h incubation with glucose in broth
User - TWang
Date_of_Scan = 2003/10/10 11:46:16
 
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)
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 1830 21020 1721 40 1024 12 1584 38 100 99 0 1545 137.75 206663 15278 58 17640 16 100 100 1 5279 56 5223 910.529 1833435 120 0.296 0.111 0.223 0.161 2.597 0.065 0.669 120 789 6768 16905 -1.757 1683 15222 0.058248012 0.573358168 0.101590969 -0.993144897 0
2 2070 21020 511 39 172 12 477 37 100 100 0 439 38.667 40908 593 58 180 17 100 100 0 556 57 499 30.222 47508 110 0.88 0.883 0.872 0.885 1.351 0.848 0.872 80 656 938 1009 -0.185 473 536 0.016370356 0.020189198 0.810847264 -0.091060944 0
3 2330 21030 58 39 25 12 51 37 53 34 0 14 1.583 3044 92 59 22 16 76 48 0 92 58 33 1.941 4823 90 0.426 0.639 0.589 0.501 3.238 0.519 0.116 52 420 47 54 -1.231 21 33 0.000726802 0.001242992 0.584720149 -0.23305194 0
4 2540 21020 236 39 68 12 228 37 100 100 0 191 16.167 18948 228 61 58 16 100 97 0 224 59 164 9.941 18220 110 1.164 1.186 1.226 1.216 1.694 1.252 0.79 80 650 355 367 0.22 199 168 0.006887317 0.006327958 1.088394904 0.0367865 0
5 2790 21020 104 39 29 12 99 38 98 94 0 61 5.333 5459 123 58 28 15 100 92 0 117 57 60 4.188 6417 90 1.001 0.989 1.088 0.971 2.213 1.062 0.376 52 420 121 132 0.002 66 66 0.002284236 0.002485983 0.918845949 -0.036757295 0
6 3020 21030 80 39 34 12 74 37 85 73 0 36 3.333 6403 117 58 36 15 92 78 0 107 57 50 3.75 9329 110 0.73 0.712 0.703 0.682 2.499 0.596 0.302 80 656 86 101 -0.454 42 59 0.001453605 0.002222318 0.654093726 -0.184360016 0
7 3250 21030 1811 40 356 13 1874 37 100 100 0 1836 133.923 144943 1094 58 176 14 100 100 0 1128 57 1071 70.2 87526 110 1.714 1.71 1.727 1.694 1.268 1.754 0.949 80 656 2907 2810 0.777 1773 1037 0.061362879 0.039060072 1.570987336 0.196172684 0
8 3500 21030 296 40 153 12 264 37 100 97 0 226 21 35684 241 58 99 15 99 98 0 222 58 164 11.625 29045 120 1.381 1.411 1.378 1.347 1.724 1.496 0.806 120 791 390 442 0.466 259 183 0.008963895 0.006892954 1.300443173 0.114091379 0
9 3730 21020 254 40 228 12 207 38 100 100 0 168 17.5 20350 259 59 161 15 100 100 0 227 58 169 12.688 20743 110 0.998 1.07 1.043 1.018 1.684 1.265 0.733 80 650 337 416 -0.002 215 201 0.007441071 0.007570949 0.982845169 -0.007514893 0
10 3960 21020 192 41 73 15 182 38 100 100 0 143 9.867 15381 190 62 49 17 100 96 0 184 60 123 7.222 15274 110 1.158 1.183 1.129 1.178 1.729 1.257 0.666 80 656 266 282 0.211 153 129 0.005295274 0.004858968 1.089794032 0.037344425 0
11 4200 21030 2046 40 388 13 2100 39 100 100 0 2060 151.692 245576 2793 59 602 15 100 100 0 2909 57 2852 173.75 335251 120 0.722 0.733 0.728 0.74 1.39 0.721 0.954 120 772 4912 4742 -0.469 2006 2736 0.069426923 0.103055311 0.673686028 -0.17154246 0
12 4440 21030 674 40 197 12 669 38 100 99 0 630 51.917 80930 600 60 147 15 100 100 0 596 58 537 34.313 72076 120 1.172 1.173 1.172 1.147 1.419 1.202 0.899 120 760 1167 1176 0.23 635 541 0.021977117 0.02037753 1.078497555 0.032819165 0
13 4660 21030 3962 40 1234 13 3602 38 100 100 0 3563 296.615 475533 1856 62 593 16 100 100 0 1740 60 1679 107.294 222802 120 2.122 2.186 2.125 2.218 1.34 2.195 0.941 120 756 5242 5718 1.086 3923 1795 0.135773589 0.067611215 2.008151898 0.30279656 0
14 4910 21030 94 40 31 12 91 38 95 83 0 52 4.417 7569 135 61 27 16 98 96 0 134 59 74 4.412 10891 100 0.708 0.739 0.715 0.668 2.061 0.735 0.453 80 560 126 130 -0.499 55 75 0.00190353 0.002824981 0.673820362 -0.171455869 0
15 5140 21030 118 40 38 13 116 37 98 95 0 79 5.923 14279 152 59 38 16 99 94 0 154 58 96 5.529 18234 120 0.823 0.862 0.822 0.843 2.097 0.836 0.535 120 764 175 175 -0.28 81 94 0.00280338 0.003540643 0.791771509 -0.10140013 0
16 5380 21030 3967 40 1017 13 4133 38 100 100 0 4094 297 476087 2058 59 565 16 100 100 0 2168 58 2110 119.588 247029 120 1.94 1.964 1.959 1.981 1.53 1.976 0.958 120 760 6204 5928 0.956 3928 2000 0.135946637 0.07533283 1.804613443 0.256384188 0
17 5600 21030 421 40 148 12 401 37 100 100 0 364 31.167 50574 442 59 109 15 100 100 0 423 58 365 24.313 53139 130 0.995 0.997 0.985 0.965 1.425 1.04 0.88 120 851 729 767 -0.007 383 384 0.013255489 0.014463903 0.916453121 -0.037889746 0
18 5840 21030 77 40 30 12 77 38 81 65 0 38 3 6214 106 58 24 15 88 73 0 105 58 47 3 8459 110 0.819 0.802 0.952 0.865 2.831 0.695 0.222 80 656 85 86 -0.288 38 48 0.001315166 0.001807988 0.727419709 -0.138214936 0
19 6090 21030 63 41 19 13 61 38 71 38 0 22 1.615 3293 90 59 21 16 76 42 0 89 58 30 1.824 4684 80 0.734 0.776 0.678 0.704 3.045 0.497 0.15 52 340 52 55 -0.446 24 31 0.000830631 0.001167659 0.711364605 -0.147907747 0
20 1840 21260 57 40 25 12 52 38 50 32 0 14 1.417 6933 92 56 27 14 78 50 0 86 55 31 2.467 11121 130 0.453 0.517 0.602 0.583 3.95 0.39 0.082 120 876 45 56 -1.144 19 37 0.000657583 0.001393657 0.471839812 -0.326205418 0

Total number of rows: 5776

Table truncated, full table size 1278 Kbytes.




Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap