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Sample GSM322704 Query DataSets for GSM322704
Status Public on Sep 23, 2008
Title RRE2_14028s(delpreA)pBAD18_14028s(wt)pBAD18preA_LB10mMAra_OD0.74_6D071_1
Sample type RNA
 
Channel 1
Source Name RNA_14028s(delpreA)pBAD18
Organism(s) Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics Salmonella enterica subsp. enterica serovar Typhimurium 14028s
Salmonella typhimurium 14028s-preA mutant complemented with pBAD18 (vector control) grown in LB+10mM Ara at OD0.74
Extracted molecule total RNA
Extraction protocol Promega SV RNA isolation kit
Label Cy3
Label protocol incorporation of Cy3-dCTP with SuperscriptII and random hexamers
 
Channel 2
Source Name RNA_14028s(wt)pBAD18preA
Organism(s) Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics Salmonella enterica subsp. enterica serovar Typhimurium 14028s
Salmonella typhimurium 14028s complemented with pBAD18+preA grown in LB+10mM Ara at OD0.74
Extracted molecule total RNA
Extraction protocol Promega SV RNA isolation kit
Label Cy5
Label protocol incorporation of Cy5-dCTP with SuperscriptII 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 STv6_01_050607
Description biological replicate, Date_of_Scan = Fri Nov 04 11:41:50 2005
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 Sep 19, 2008
Contact name Michael McClelland
E-mail(s) mcclelland.michael@gmail.com
Phone 858-450-5990
Fax 858-550-3998
Organization name Sidney Kimmel Cancer Center
Department
Street address 10835 Road to the Cure
City San Diego
State/province CA
ZIP/Postal code 92121
Country USA
 
Platform ID GPL3788
Series (1)
GSE12866 PreA overexpression in Salmonella typhimurium

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 -[INV_VALUE]
INV_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 INV_VALUE
1 2130 3800 11748 912 1902.9375 1062.160522 97.066856 8100 17.863211 0.97046 0.907898 0.964798 11.060475 0.899423 3184 346 765.734924 203.487457 97.066856 8100 17.863211 0.97046 0.974472 0.994232 15.647156 0.943334 1 1 1 1 1 1 1 1 1 1 1 1 1 10836 2838 0.046239073 0.029336584 1.576157366 -0.1976 0.197599576
2 2360 3800 10706 880 2298.716797 218.063156 97.066856 8100 14.563643 0.97046 0.911514 0.992752 49.095868 0.94101 5002 278 1166.179688 184.41011 97.066856 8100 14.563643 0.97046 0.955902 0.994873 27.124326 0.965664 1 1 1 1 1 1 1 1 1 1 1 1 1 9826 4724 0.041929229 0.048832284 0.85863748 0.0661902 -0.066190158
3 2600 3800 1800 832 0 180.792862 0 100 17.863211 1 1 0.993073 9.956145 0.5 766 254 190.474518 150.620255 68.636635 2600 17.863211 0.866634 0.995026 0.995575 5.085637 0.821611 0 0 1 1 1 1 1 1 1 1 1 1 1 968 512 0.004130622 0.005292576 0.780455898 0.107652 -0.107651633
4 2830 3800 2024 828 134.350296 207.867767 0 200 14.563643 1 0.99855 0.993332 9.736959 0.5 578 200 159.305725 184.125687 79.788467 2900 14.563643 0.844417 0.996536 0.995056 3.13916 0.805416 0 0 1 1 1 1 1 1 1 1 1 1 1 1196 378 0.005103537 0.00390741 1.306117807 -0.115982 0.11598235
5 3070 3800 1270 900 0 284.989197 0 100 17.863211 1 1 0.990234 4.456309 0.5 596 222 145.275116 189.218079 46.524269 800 17.863211 0.632136 0.996597 0.99472 3.149805 0.722441 0 0 1 1 1 1 0 0 0 1 1 1 1 370 374 0.001578854 0.003866061 0.408388113 0.388927 -0.388926907
6 3300 3800 1740 762 105.897751 191.27803 17.841244 400 14.563643 0.210515 0.998184 0.994171 9.096706 0.240589 690 290 177.943817 194.664536 19.544102 400 14.563643 0.399994 0.997162 0.993927 3.544559 0.457136 0 0 0 1 1 1 0 0 0 1 1 1 1 978 400 0.004173294 0.004134825 1.009303627 -0.00402183 0.004021834
7 3540 3800 2498 906 370.78244 296.175385 92.016548 6600 17.863211 0.942821 0.989059 0.988419 8.434192 0.904161 914 304 287.227936 185.935684 87.403885 5100 17.863211 0.916686 0.992264 0.994446 4.915678 0.855401 1 1 1 1 1 1 1 1 1 1 1 1 1 1592 610 0.006793337 0.006305608 1.07734847 -0.0323562 0.032356199
8 3770 3800 4612 792 885.89679 252.581787 97.066856 8100 14.563643 0.97046 0.970108 0.991104 18.259432 0.95064 2160 216 449.004181 164.811569 97.066856 8100 14.563643 0.97046 0.984543 0.995148 13.105876 0.933801 1 1 1 1 1 1 1 1 1 1 1 1 1 3820 1944 0.016300596 0.02009525 0.811166624 0.0908899 -0.090889927
9 4010 3800 2068 806 249.076431 295.956818 85.934807 4700 17.863211 0.894838 0.99176 0.990204 6.987506 0.888734 1102 260 301.1008 200.255524 92.705818 7600 17.863211 0.934498 0.990265 0.993317 5.502969 0.866719 1 1 1 1 1 1 1 1 1 1 1 1 1 1262 842 0.005385171 0.008703807 0.618714414 0.20851 -0.208509766
10 4240 3800 8422 798 2266.361328 287.886963 97.066856 8100 14.563643 0.97046 0.924042 0.991501 29.254538 0.949361 3498 210 1250.079712 179.194534 97.066856 8100 14.563643 0.97046 0.958954 0.994781 19.520685 0.953533 1 1 1 1 1 1 1 1 1 1 1 1 1 7624 3288 0.032532917 0.033988262 0.957180956 0.019006 -0.019005951
11 4480 3800 2140 828 190.589508 232.655426 37.424107 1300 17.863211 0.811844 0.995392 0.99295 9.198152 0.687121 864 286 281.459869 194.605621 71.809616 2100 17.863211 0.874295 0.990829 0.993912 4.439748 0.804635 0 0 1 1 1 1 1 1 1 1 1 1 1 1312 578 0.005598529 0.005974822 0.93702023 0.028251 -0.028251033
12 4710 3800 1742 758 167.11554 237.944992 43.701942 1200 14.563643 0.654247 0.996231 0.99176 7.32102 0.71851 690 226 145.061172 140.942825 75.693985 3800 14.563643 0.837165 0.995911 0.99617 4.895602 0.85498 0 0 0 1 1 1 1 1 1 1 1 1 1 984 464 0.004198897 0.004796397 0.875427305 0.0577799 -0.057779911
13 4950 3800 1858 772 147.45929 272.918396 79.388519 3200 17.863211 0.885511 0.996719 0.991379 6.807896 0.841983 682 194 297.765839 145.812119 89.562332 6200 17.863211 0.899552 0.992416 0.996323 4.677252 0.850238 1 1 1 1 1 1 1 1 1 1 1 1 1 1086 488 0.004634148 0.005044487 0.918656123 0.036847 -0.036847026
14 5180 3800 2182 808 423.177094 262.309296 88.489685 6500 14.563643 0.916456 0.985229 0.991226 8.318424 0.903086 832 228 235.209396 139.038651 86.672455 6300 14.563643 0.903828 0.99408 0.995132 5.983948 0.874749 1 1 1 1 1 1 1 1 1 1 1 1 1 1374 604 0.005863094 0.006243586 0.939058752 0.0273072 -0.027307235
15 5420 3800 2194 922 111.72287 226.188492 0 200 17.863211 0 0.998795 0.993378 9.699875 0 684 202 243.649933 171.910385 94.069214 6000 17.863211 0.948274 0.992416 0.994431 3.978817 0.832743 0 0 0 1 1 1 1 1 1 1 1 1 1 1272 482 0.005427842 0.004982464 1.089389146 -0.037183 0.037183044
16 5650 3800 1418 874 0 282.140991 0 100 14.563643 1 1 0.990356 5.025856 0.5 514 194 98.577148 172.062943 65.79525 1100 14.563643 0.739744 0.997299 0.995605 2.987279 0.770682 0 0 1 1 1 1 1 0 1 1 1 0 1 544 320 0.002321341 0.00330786 0.701765303 0.153808 -0.153808108
17 5890 3800 2648 814 636.380981 222.628189 78.176407 4600 17.863211 0.885264 0.983002 0.993134 11.894271 0.889517 870 236 328.854309 200.057373 76.530403 4400 17.863211 0.884673 0.988571 0.993622 4.348752 0.842489 1 1 1 1 1 1 1 1 1 1 1 1 1 1834 634 0.007825993 0.006553698 1.194133945 -0.077053 0.077053044
18 6120 3800 1664 784 0 297.47226 0 100 14.563643 1 1 0.991241 5.593799 0.5 526 210 85.415512 146.410019 57.536282 1500 14.563643 0.811338 0.99794 0.99617 3.59265 0.784263 0 0 1 1 1 1 0 0 1 1 1 1 1 880 316 0.003755111 0.003266512 1.149578308 -0.0605386 0.06053856
19 6360 3800 2722 882 440.062988 244.694626 95.078926 7400 17.863211 0.950954 0.987274 0.991776 11.124069 0.923804 978 174 414.994629 120.350861 97.066856 8000 17.863211 0.97046 0.988617 0.99646 8.12624 0.901247 1 1 1 1 1 1 1 1 1 1 1 1 1 1840 804 0.007851596 0.008310998 0.944723557 0.0246953 -0.024695255
20 2130 4030 1700 684 176.258255 199.212494 64.327515 1700 14.957706 0.755431 0.995682 0.993744 8.533601 0.791054 718 214 192.267761 184.037964 88.129242 4800 14.957706 0.889802 0.993942 0.994385 3.901369 0.830548 1 0 1 1 1 1 1 1 1 1 1 1 1 1016 504 0.004335446 0.00520988 0.83215867 0.0797939 -0.079793858

Total number of rows: 5776

Table truncated, full table size 1650 Kbytes.




Supplementary data files not provided
Raw data included within Sample table
Processed data included within Sample table
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