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Sample GSM654634 Query DataSets for GSM654634
Status Public on Feb 01, 2011
Title RRE2_SKY_HCl45_03_7DE1571
Sample type RNA
 
Channel 1
Source name SKY 3795 total RNA after 10min exposure to HCl pH4.5 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 pH4.5
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 Fri Apr 24 11:39:30 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) mcclelland.michael@gmail.com
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 1170 540 761 153 804.377563 93.737892 97.066856 7600 10.028674 0.97046 0.96978 0.997101 8.118382 0.90117 1013 128 401.992554 103.745087 97.066856 8100 10.028674 0.97046 0.988762 0.998459 9.764318 0.914997 1 1 1 1 1 1 1 1 1 1 1 1 1 608 885 0.001820469 0.004490298 0.405422815 -0.392091816
2 1400 530 4636 160 1610.470459 91.921867 97.066856 8100 1.154804 0.97046 0.951874 0.997246 50.434136 0.967916 7214 131 2187.537842 29.450304 97.066856 8100 1.154804 0.97046 0.939491 0.999016 244.955026 0.959661 1 1 1 1 1 1 1 1 1 1 1 1 1 4476 7083 0.013402007 0.035937605 0.372924325 -0.428379288
3 1630 530 497 146 131.751709 74.584648 86.672455 6200 5.546596 0.92253 0.996185 0.997627 6.66357 0.884574 335 132 59.498272 36.776176 79.388519 4600 5.546596 0.894048 0.998459 0.99884 9.109158 0.889517 1 1 1 1 1 1 1 1 1 1 1 1 1 351 203 0.001050962 0.001029978 1.020372991 0.008758954
4 1870 520 423 161 58.901962 93.892525 53.523727 1700 11.075274 0.718861 0.998024 0.996666 4.505151 0.767619 446 139 77.654716 32.881008 67.702759 4300 11.075274 0.892682 0.997665 0.999016 13.564061 0.838514 0 0 1 1 1 1 1 1 1 1 1 1 1 262 307 0.000784479 0.001557651 0.503629072 -0.297889208
5 2120 520 424 155 78.42363 3974.929688 80.582397 1200 18.285738 0.886879 0.997849 0.996872 0.106669 0.028445 366 137 0 30.715723 0 100 18.285738 1 1 0.99894 11.915721 0.5 1 0 1 1 1 0 0 0 1 1 1 1 1 269 229 0.000805438 0.001161896 0.693209768 -0.159135327
6 2360 520 728 255 115.396416 106.921021 7.978847 300 22.470806 0.060131 0.998299 0.996788 6.808764 0.068721 432 150 86.52742 40.748192 60.238968 2700 22.470806 0.808573 0.997803 0.998726 10.601697 0.801195 0 0 0 1 1 1 1 1 1 1 1 1 1 473 282 0.001416253 0.001430807 0.989828395 -0.004440092
7 2570 520 1459 203 609.080383 98.88414 89.562332 6600 12.332593 0.918803 0.983177 0.996971 14.754641 0.940315 939 154 287.691895 43.940239 74.848213 5300 12.332593 0.924653 0.992386 0.998459 21.369934 0.874241 1 1 1 1 1 1 1 1 1 1 1 1 1 1256 785 0.003760706 0.00398292 0.944208397 -0.024932142
8 2810 530 2802 160 1018.646362 88.279091 95.078926 8000 1.154804 0.950954 0.969566 0.997475 31.740245 0.967303 2927 140 988.269531 34.033451 97.066856 8100 1.154804 0.97046 0.974472 0.99881 86.00362 0.980307 1 1 1 1 1 1 1 1 1 1 1 1 1 2642 2787 0.007910657 0.014140633 0.559427383 -0.25225628
9 3050 530 9749 164 2132.822266 97.738503 97.066856 8100 4.680002 0.97046 0.921913 0.996582 99.745748 0.947942 4342 143 841.492554 34.694592 97.066856 8100 4.680002 0.97046 0.970558 0.998917 125.149189 0.980307 1 1 1 1 1 1 1 1 1 1 1 1 1 9585 4199 0.028699338 0.021304815 1.347082265 0.129394118
10 3270 530 1702 147 726.730957 79.24511 96.408768 8000 10.497422 0.963834 0.979012 0.997597 21.477666 0.957406 1953 141 704.707947 33.455524 94.743553 7900 10.497422 0.955337 0.981102 0.998825 58.376009 0.970225 1 1 1 1 1 1 1 1 1 1 1 1 1 1555 1812 0.00465597 0.009193695 0.506430759 -0.295479924
11 3520 530 384 165 0 72.79528 0 100 4.680002 1 1 0.997498 5.275067 0.5 292 141 0 33.195381 0 100 4.680002 1 1 0.998848 8.796404 0.5 0 0 1 1 1 1 0 0 1 1 1 1 1 219 151 0.000655728 0.000766141 0.855884267 -0.067584957
12 3750 530 2574 162 1242.818237 89.426765 94.406982 7900 1.154804 0.943981 0.968719 0.997299 28.783329 0.962654 1095 143 398.334778 35.692696 88.489685 7100 1.154804 0.955203 0.990334 0.999031 30.678546 0.942448 1 1 1 1 1 1 1 1 1 1 1 1 1 2412 952 0.007221993 0.004830241 1.495161932 0.174688231
13 3990 530 1222 167 445.703705 81.345512 94.406982 7900 4.680002 0.943981 0.987671 0.997284 15.022341 0.941254 1600 146 611.19751 47.271606 95.078926 7800 4.680002 0.950954 0.984131 0.99839 33.846956 0.967303 1 1 1 1 1 1 1 1 1 1 1 1 1 1055 1454 0.003158873 0.00737728 0.428189417 -0.368364071
14 4220 540 802 182 286.857605 77.742867 89.562332 6100 8.944576 0.936095 0.992622 0.997543 10.316059 0.918805 554 148 112.793465 34.8783 81.368584 5900 8.944576 0.943464 0.996887 0.998863 15.883802 0.906843 1 1 1 1 1 1 1 1 1 1 1 1 1 620 406 0.0018564 0.002059956 0.901184123 -0.045186468
15 4450 530 3834 162 1499.205078 78.184402 96.408768 7900 5.546596 0.963834 0.959732 0.997513 49.037914 0.973155 1965 146 637.647583 30.880594 94.406982 7900 5.546596 0.943981 0.981934 0.99897 63.632195 0.962654 1 1 1 1 1 1 1 1 1 1 1 1 1 3672 1819 0.010994676 0.009229211 1.191290969 0.076017849
16 4680 530 351 147 48.443863 79.72113 71.809616 1300 10.497422 0.749301 0.998856 0.997002 4.402848 0.777472 288 133 0 34.401325 0 100 10.497422 1 1 0.998734 8.371771 0.5 1 0 1 1 1 1 0 0 1 1 1 1 1 204 155 0.000610815 0.000786436 0.776687553 -0.109753655
17 4920 550 1121 157 428.842163 77.35849 90.622276 6300 19.700468 0.939847 0.988846 0.997498 14.490976 0.939361 605 145 136.930328 39.9361 75.272285 5100 19.700468 0.931952 0.996094 0.998695 15.149201 0.876361 1 1 1 1 1 1 1 1 1 1 1 1 1 964 460 0.002886402 0.00233394 1.236707738 0.092267078
18 5160 540 405 157 117.434235 74.01429 50.462654 500 8.944576 0.472537 0.997902 0.997688 5.471916 0.540043 284 141 0 38.861691 0 100 8.944576 1 1 0.998596 7.307968 0.5 0 0 0 1 1 1 0 0 1 1 1 1 1 248 143 0.00074256 0.000725551 1.023442668 0.010063519
19 5410 530 811 164 211.678589 92.149529 88.489685 7000 14.595894 0.944831 0.994537 0.997406 8.800913 0.907415 877 145 169.725922 37.595448 94.406982 7800 14.595894 0.959758 0.99408 0.998924 23.327292 0.960517 1 1 1 1 1 1 1 1 1 1 1 1 1 647 732 0.001937243 0.003714009 0.521604195 -0.282658925
20 1170 750 419 148 110.442589 80.708694 89.562332 4900 16.700138 0.927395 0.995949 0.997627 5.19151 0.860947 394 138 70.208122 30.639406 93.048538 7300 16.700138 0.956099 0.99807 0.999039 12.859257 0.932702 1 1 1 1 1 1 1 1 1 1 1 1 1 271 256 0.000811426 0.001298888 0.624708193 -0.204322799

Total number of rows: 17328

Table truncated, full table size 4813 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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