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Sample GSM654637 Query DataSets for GSM654637
Status Public on Feb 01, 2011
Title RRE2_SKY_HCl55_01_7DE1542
Sample type RNA
 
Channel 1
Source name SKY 3795 total RNA after 10min exposure to HCl pH5.5 in TSB
Organism Salmonella enterica subsp. enterica serovar Kentucky
Characteristics strain: Salmonella Kentucky 3795
condition: log phase culture after 10min exposure to acidic conditions HCl pH5.5
medium: TSB
Extracted molecule total RNA
Extraction protocol RNeasy kit (QIAGEN)
Label Cy5
Label protocol incorporation of Cy5-dCTP with Superscript RT and random hexamers
 
Channel 2
Source name SKY 3795 total RNA in TSB
Organism Salmonella enterica subsp. enterica serovar Kentucky
Characteristics strain: Salmonella Kentucky 3795
condition: log phase culture
medium: TSB
Extracted molecule total RNA
Extraction protocol RNeasy kit (QIAGEN)
Label Cy3
Label protocol incorporation of Cy3-dCTP with Superscript RT and random hexamers
 
 
Hybridization protocol overnight hyb on Corning UltraGAPS slides at 42°C in 25% formamide / 5xSSC / 0.1% BSA
Scan protocol Perkin Elmer ScanArray 5000 scanner, image acquisition with ScanArray Express 3.0.1 software, spot quantification using Quantarray 3.0 software, adaptive quantification, protocol STv5_SP040504_adapforsmallpins_040817
Description biological replicate, Date of Scan Wed Oct 14 08:44:26 2009
Data processing normalized based on total signal for each channel, background subtracted VALUE data obtained from log of normalized background subtracted ch1/ch2 signal.
 
Submission date Jan 12, 2011
Last update date Feb 01, 2011
Contact name Michael McClelland
E-mail(s) [email protected]
Phone 858-336-9554
Organization name University of California, Irvine
Department Microbiology & Molecular Genetics
Street address 132 Med Surge I
City Irvine
State/province CA
ZIP/Postal code 92697
Country USA
 
Platform ID GPL11279
Series (1)
GSE26597 Transcriptional profile of Salmonella enterica serovars Kentucky and Enteritidis in response to acidic conditions

Data table header descriptions
ID_REF Number
X_LOCATION X-coordinate of spot
Y_LOCATION Y-coordinate of spot
CH1_MEAN Channel 1 mean
CH1_BKD_MEAN Channel 1 mean background
CH1_SD Channel 1 standard deviation
CH1_BKD_SD Channel 1 background standard deviation
CH1_DIAMETER Channel 1 diameter
CH1_AREA Channel 1 area
CH1_FOOTPRINT Channel 1 footprint
CH1_CIRCULARITY Channel 1 circularity
CH1_SPOT_UNIFORMITY Channel 1 spot uniformity
CH1_BKD_UNIFORMITY Channel 1 background uniformity
CH1_SIGNAL_NOISE_RATIO Channel 1 signal to noise ratio
CH1_CONFIDENCE Channel 1 confidence
CH2_MEAN Channel 2 mean
CH2_BKD_MEAN Channel 2 mean background
CH2_SD Channel 2 standard deviation
CH2_BKD_SD Channel 2 background standard deviation
CH2_DIAMETER Channel 2 diameter
CH2_AREA Channel 2 area
CH2_FOOTPRINT Channel 2 footprint
CH2_CIRCULARITY Channel 2 circularity
CH2_SPOT_UNIFORMITY Channel 2 spot uniformity
CH2_BKD_UNIFORMITY Channel 2 background uniformity
CH2_SIGNAL_NOISE_RATIO Channel 2 signal to noise ratio
CH2_CONFIDENCE Channel 2 confidence
CH1_DIAMETER_FILTER Channel 1 diameter filter
CH1_AREA_FILTER Channel 1 area filter
CH1_CIRCULARITY_FILTER Channel 1 circularity filter
CH1_SPOT_UNIFORMITY_FILTER Channel 1 spot uniformity filter
CH1_BKD_UNIFORMITY_FILTER Channel 1 background uniformity filter
CH1_SIGNAL_NOISE_RATIO_FILTER Channel 1 signal to noise ratio filter
CH2_DIAMETER_FILTER Channel 2 diameter filter
CH2_AREA_FILTER Channel 2 area filter
CH2_CIRCULARITY_FILTER Channel 2 circularity filter
CH2_SPOT_UNIFORMITY_FILTER Channel 2 spot uniformity filter
CH2_BKD_UNIFORMITY_FILTER Channel 2 background uniformity filter
CH2_SIGNAL_NOISE_RATIO_FILTER Channel 2 signal to noise ratio filter
IGNORE_FILTER Ignore filter
CH1_BKD_CORR Channel 1 background correlation
CH2_BKD_CORR Channel 2 background correlation
CH1%_OF_TOTAL Channel 1 % of total
CH2%_OF_TOTAL Channel 2 % of total
PRE-VALUE ch1 % of total / ch2 % of total
VALUE log of ch1 % of total / ch2 % of total

Data table
ID_REF X_LOCATION Y_LOCATION CH1_MEAN CH1_BKD_MEAN CH1_SD CH1_BKD_SD CH1_DIAMETER CH1_AREA CH1_FOOTPRINT CH1_CIRCULARITY CH1_SPOT_UNIFORMITY CH1_BKD_UNIFORMITY CH1_SIGNAL_NOISE_RATIO CH1_CONFIDENCE CH2_MEAN CH2_BKD_MEAN CH2_SD CH2_BKD_SD CH2_DIAMETER CH2_AREA CH2_FOOTPRINT CH2_CIRCULARITY CH2_SPOT_UNIFORMITY CH2_BKD_UNIFORMITY CH2_SIGNAL_NOISE_RATIO CH2_CONFIDENCE CH1_DIAMETER_FILTER CH1_AREA_FILTER CH1_CIRCULARITY_FILTER CH1_SPOT_UNIFORMITY_FILTER CH1_BKD_UNIFORMITY_FILTER CH1_SIGNAL_NOISE_RATIO_FILTER CH2_DIAMETER_FILTER CH2_AREA_FILTER CH2_CIRCULARITY_FILTER CH2_SPOT_UNIFORMITY_FILTER CH2_BKD_UNIFORMITY_FILTER CH2_SIGNAL_NOISE_RATIO_FILTER IGNORE_FILTER CH1_BKD_CORR CH2_BKD_CORR CH1%_OF_TOTAL CH2%_OF_TOTAL PRE-VALUE VALUE
1 1360 2340 435 166 95.091347 76.857857 84.816299 2600 3.135624 0.850106 0.997437 0.997665 5.659799 0.821611 247 88 73.366821 27.386461 92.016548 4300 3.135624 0.927064 0.997627 0.999191 9.019055 0.879332 1 1 1 1 1 1 1 1 1 1 1 1 1 269 159 0.001518361 0.001561199 0.972560636 -0.012083312
2 1610 2340 1966 168 601.023926 83.043388 95.078926 7800 11.888586 0.950954 0.981377 0.997467 23.674371 0.961051 5294 92 1196.038208 25.419535 97.066856 8100 11.888586 0.97046 0.957016 0.999138 208.265024 0.971344 1 1 1 1 1 1 1 1 1 1 1 1 1 1798 5202 0.010148747 0.051077728 0.198692224 -0.701819128
3 1820 2340 1048 161 226.929398 81.88623 97.066856 8100 13.121023 0.97046 0.992294 0.997787 12.798245 0.932424 236 94 26.455465 68.859978 75.693985 2900 13.121023 0.866756 0.999275 0.99794 3.427245 0.815744 1 1 1 1 1 1 1 1 1 1 1 1 1 887 142 0.00500664 0.001394279 3.590846228 0.555196808
4 2070 2330 516 176 102.128548 83.209038 84.062363 5200 10.516246 0.919335 0.99707 0.996872 6.201249 0.878067 275 90 61.960079 27.212988 85.563599 5700 10.516246 0.907488 0.998253 0.999092 10.105469 0.917393 1 1 1 1 1 1 1 1 1 1 1 1 1 340 185 0.001919118 0.00181649 1.056498101 0.023868721
5 2310 2330 516 186 50.204582 82.860565 0 200 12.426861 0 0.999458 0.997238 6.227329 0 235 94 16.441816 26.447622 7.978847 300 12.426861 0.038246 0.999763 0.999184 8.885487 0.04371 0 0 0 1 1 1 0 0 0 1 1 1 1 330 141 0.001862673 0.00138446 1.345415292 0.128856359
6 2530 2330 474 179 130.098785 64.898537 52.320793 1600 13.149924 0.80287 0.995949 0.998009 7.303709 0.761604 276 94 63.168152 26.245293 67.230957 2400 13.149924 0.836213 0.998444 0.999077 10.516172 0.814821 0 0 1 1 1 1 1 1 1 1 1 1 1 295 182 0.001665117 0.001787033 0.931777373 -0.03068784
7 2760 2320 4199 167 1944.296875 66.791824 96.408768 7900 24.207621 0.963834 0.955109 0.9981 62.866976 0.970072 542 95 180.060059 26.329058 83.301605 6100 24.207621 0.947801 0.994713 0.999191 20.585621 0.916508 1 1 1 1 1 1 1 1 1 1 1 1 1 4032 447 0.022758481 0.004389032 5.185307696 0.714774532
8 3010 2340 4755 172 1203.131714 77.084236 97.066856 8100 1.915095 0.97046 0.96154 0.997612 61.685764 0.97436 2374 98 542.409851 41.822201 97.066856 8100 1.915095 0.97046 0.980125 0.998566 56.76411 0.980307 1 1 1 1 1 1 1 1 1 1 1 1 1 4583 2276 0.025868582 0.022347733 1.157548327 0.063539132
9 3240 2340 11776 173 2761.593994 77.218994 97.066856 8100 3.135624 0.97046 0.902313 0.997459 152.501339 0.934875 1820 96 267.387939 28.387541 97.066856 8100 3.135624 0.97046 0.990089 0.999115 64.112633 0.980307 1 1 1 1 1 1 1 1 1 1 1 1 1 11603 1724 0.065492723 0.016927721 3.86896288 0.587594563
10 3480 2340 678 173 170.377625 79.229195 84.062363 6300 1.915095 0.902217 0.994507 0.997864 8.557452 0.90528 1755 92 506.431091 29.481367 97.066856 8100 1.915095 0.97046 0.98336 0.9991 59.529125 0.980307 1 1 1 1 1 1 1 1 1 1 1 1 1 505 1663 0.002850455 0.01632877 0.174566402 -0.758039339
11 3710 2340 429 174 54.921154 77.254669 26.462839 300 3.135624 0.315548 0.999184 0.997604 5.553062 0.360626 235 97 9.899495 31.558048 0 200 3.135624 1 0.999893 0.998894 7.446595 0.5 0 0 0 1 1 1 0 0 1 1 1 1 1 255 138 0.001439338 0.001355003 1.062239939 0.026222626
12 3930 2340 824 158 574.79657 97.235237 93.389999 7200 18.119762 0.941627 0.981483 0.996971 8.474294 0.904528 308 95 95.474113 31.391144 80.582397 4100 18.119762 0.891942 0.997185 0.999008 9.811685 0.872541 1 1 1 1 1 1 1 1 1 1 1 1 1 666 213 0.003759213 0.002091418 1.797447267 0.254656158
13 4190 2340 795 180 195.116562 64.397102 89.91703 7200 6.892245 0.939309 0.994041 0.998055 12.345276 0.930291 1103 93 271.447906 27.921701 97.066856 8100 6.892245 0.97046 0.991058 0.999054 39.503323 0.975906 1 1 1 1 1 1 1 1 1 1 1 1 1 615 1010 0.003471346 0.009917052 0.350038065 -0.455884726
14 4420 2350 1552 180 533.83905 69.835938 92.361824 7600 9.83584 0.938643 0.984718 0.997536 22.223515 0.958718 565 95 185.628098 29.567719 89.562332 7200 9.83584 0.95593 0.994598 0.999176 19.108678 0.947812 1 1 1 1 1 1 1 1 1 1 1 1 1 1372 470 0.007744206 0.004614866 1.6780998 0.224817786
15 4650 2350 3156 183 612.153076 85.101944 97.066856 8100 10.144374 0.97046 0.978653 0.997551 37.084934 0.974415 1106 99 247.381516 37.188931 97.066856 8100 10.144374 0.97046 0.990227 0.998657 29.740032 0.968494 1 1 1 1 1 1 1 1 1 1 1 1 1 2973 1007 0.016780993 0.009887596 1.697176348 0.229726971
16 4890 2340 580 197 130.380081 89.978149 55.279068 600 1.915095 0.670182 0.997673 0.996895 6.446009 0.753705 252 97 142.061691 42.933048 66.277275 2700 1.915095 0.846928 0.995338 0.998894 5.869604 0.825007 0 0 0 1 1 1 1 1 1 1 1 1 1 383 155 0.00216183 0.001521924 1.42045869 0.152428608
17 5130 2340 730 162 344.547821 75.99929 86.30442 6200 6.892245 0.913438 0.990334 0.997551 9.605353 0.913833 336 90 404.652496 36.023266 82.147255 5700 6.892245 0.926411 0.985085 0.999092 9.327305 0.910736 1 1 1 1 1 1 1 1 1 1 1 1 1 568 246 0.003206056 0.00241544 1.327317318 0.122974761
18 5350 2340 399 170 36.06337 77.765335 66.755821 600 8.123835 0.831531 0.999268 0.997833 5.130821 0.753705 229 100 59.080452 33.389771 45.834984 800 8.123835 0.703564 0.998657 0.999039 6.858388 0.729175 1 0 1 1 1 1 0 0 1 1 1 1 1 229 129 0.001292582 0.001266633 1.020486595 0.008807304
19 5590 2350 694 188 167.915771 77.535362 93.048538 7600 10.144374 0.930384 0.995171 0.997665 8.950755 0.908682 688 102 138.602478 29.868614 97.066856 8100 10.144374 0.97046 0.994492 0.999031 23.034212 0.960055 1 1 1 1 1 1 1 1 1 1 1 1 1 506 586 0.002856099 0.005753854 0.496380181 -0.304185567
20 1370 2570 465 156 98.053436 77.699471 89.206215 5500 8.715788 0.897867 0.997292 0.997574 5.984597 0.874759 378 86 82.802948 25.109816 95.078926 8000 8.715788 0.950954 0.997047 0.999245 15.053874 0.941362 1 1 1 1 1 1 1 1 1 1 1 1 1 309 292 0.00174414 0.002867108 0.608327095 -0.21586284

Total number of rows: 17328

Table truncated, full table size 4818 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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