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Sample GSM322710 Query DataSets for GSM322710
Status Public on Sep 23, 2008
Title RRE2_14028s(delpreAB)pBAD18preA_14028s(delpreAB)pBAD18_LB10mMAra_OD0.74_6D069_1
Sample type RNA
 
Channel 1
Source Name RNA_14028s(delpreAB)pBAD18preA
Organism(s) Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics Salmonella enterica subsp. enterica serovar Typhimurium 14028s
Salmonella typhimurium 14028s-preAB mutant complemented with pBAD18+preA 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 Reverse Transcriptase
 
Channel 2
Source Name RNA_14028s(delpreAB)pBAD18
Organism(s) Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics Salmonella enterica subsp. enterica serovar Typhimurium 14028s
Salmonella typhimurium 14028s-preAB 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 Cy5
Label protocol incorporation of Cy5-dCTP with Reverse Transcriptase
 
 
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 09:50:46 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 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 2270 3950 3338 290 1222.977661 86.940102 97.066856 8100 27.211893 0.97046 0.945953 0.997452 38.39425 0.963969 988 140 204.973892 53.977264 94.406982 7900 27.211893 0.943981 0.991867 0.99826 18.304003 0.950749 1 1 1 1 1 1 1 1 1 1 1 1 1 3048 848 0.072159962 0.022780053 3.167681933 0.500741568
2 2500 3950 1438 304 261.443726 65.544899 93.730225 7800 23.079479 0.955854 0.991562 0.998123 21.93916 0.958227 950 122 232.592377 44.957214 97.066856 8100 23.079479 0.97046 0.991302 0.998596 21.131202 0.956768 1 1 1 1 1 1 1 1 1 1 1 1 1 1134 828 0.026846915 0.022242788 1.206994177 0.081705175
3 2740 3950 494 334 0 79.92868 0 100 27.211893 0 1 0.997437 6.18051 0 308 120 19.24877 77.499535 60.765083 1200 27.211893 0.692244 0.999573 0.997345 3.974217 0.774077 0 0 0 1 1 1 1 0 0 1 1 1 1 160 188 0.003787925 0.005050295 0.750040286 -0.124915409
4 2970 3950 522 344 0 60.721523 0 100 23.079479 1 1 0.997986 8.596622 0.5 346 130 45.617977 67.351936 30.901939 400 23.079479 0.285492 0.999222 0.997787 5.137195 0.326276 0 0 1 1 1 1 0 0 0 1 1 1 1 178 216 0.004214066 0.005802466 0.726254286 -0.138911292
5 3210 3950 474 318 0 51.665909 0 100 27.211893 1 1 0.998352 9.174328 0.5 258 110 12.165525 48.347176 47.873077 300 27.211893 0.586099 0.999832 0.998032 5.336403 0.669827 0 0 1 1 1 1 0 0 0 1 1 1 1 156 148 0.003693226 0.003975764 0.92893503 -0.03201466
6 3440 3950 574 348 0 74.496864 0 100 23.079479 1 1 0.997604 7.705022 0.5 268 106 58.854519 51.762951 51.089546 1100 23.079479 0.672824 0.998413 0.99823 5.177448 0.755448 0 0 1 1 1 1 0 0 0 1 1 1 1 226 162 0.005350443 0.00435185 1.229464184 0.089715882
7 3680 3950 598 346 0 57.425816 0 100 27.211893 1 1 0.997894 10.413435 0.5 442 112 124.903412 46.373867 97.066856 7800 27.211893 0.97046 0.996597 0.998611 9.53123 0.913279 0 0 1 1 1 1 1 1 1 1 1 1 1 252 330 0.005965981 0.008864879 0.672990693 -0.171990942
8 3910 3950 922 366 166.008026 73.031456 28.768141 400 23.079479 0.451103 0.997086 0.997482 12.624697 0.515547 586 154 134.257401 69.94976 94.406982 7700 23.079479 0.943981 0.996399 0.997757 8.377441 0.903637 0 0 0 1 1 1 1 1 1 1 1 1 1 556 432 0.013163038 0.011604933 1.134262312 0.054713502
9 4150 3960 796 354 19.681391 58.125858 44.424335 800 33.49934 0.651595 0.999588 0.997971 13.694421 0.722122 514 124 120.345642 53.408978 93.048538 7800 33.49934 0.930384 0.996521 0.998444 9.62385 0.91397 0 0 0 1 1 1 1 1 1 1 1 1 1 442 390 0.010464141 0.010476675 0.998803647 -0.00051988
10 4380 3960 1122 340 156.376114 53.40971 82.918602 6500 30.238735 0.944094 0.995422 0.998215 21.007416 0.914593 882 108 275.081604 61.796597 94.069214 7700 30.238735 0.948274 0.99147 0.997635 14.272631 0.938547 1 1 1 1 1 1 1 1 1 1 1 1 1 782 774 0.018513481 0.020792171 0.890406352 -0.05041175
11 4620 3960 570 332 0 64.263672 0 100 33.49934 1 1 0.997604 8.869708 0.5 300 118 73.367317 49.581993 41.459301 1100 33.49934 0.731691 0.997971 0.998276 6.050584 0.707296 0 0 1 1 1 1 0 0 1 1 1 1 1 238 182 0.005634538 0.004889115 1.152465747 0.061628026
12 4850 3960 652 366 0 145.18187 0 100 30.238735 1 1 0.994659 4.490919 0.5 352 124 55.856697 70.08699 53.523727 1700 30.238735 0.730366 0.998505 0.99765 5.02233 0.767619 0 0 1 1 1 1 0 0 1 1 1 1 1 286 228 0.006770915 0.006124826 1.105487009 0.043553643
13 5090 3960 562 364 0 60.529041 0 100 33.49934 1 1 0.997971 9.284799 0.5 372 138 61.736782 55.773869 84.44017 2700 33.49934 0.859473 0.998383 0.998306 6.66979 0.825007 0 0 1 1 1 1 1 1 1 1 1 1 1 198 234 0.004687557 0.006286005 0.74571313 -0.12742821
14 5320 3960 842 352 43.092922 60.048584 15.957693 400 30.238735 0.238639 0.999283 0.998108 14.021979 0.27273 380 118 99.095848 46.963158 88.848671 6500 30.238735 0.919773 0.997284 0.998535 8.091449 0.900906 0 0 0 1 1 1 1 1 1 1 1 1 1 490 262 0.011600519 0.007038177 1.648227842 0.217017246
15 5560 3960 1070 354 133.671646 58.806 90.972847 7000 33.49934 0.931855 0.995575 0.997757 18.195422 0.950484 372 144 76.604668 52.78561 79.788467 2800 33.49934 0.824282 0.997513 0.998474 7.047375 0.828402 1 1 1 1 1 1 1 1 1 1 1 1 1 716 228 0.016950962 0.006124826 2.767582861 0.442100633
16 5790 3960 680 334 0 60.376431 0 100 30.238735 1 1 0.998047 11.262673 0.5 292 126 25.53429 57.73217 35.682487 300 30.238735 0.470992 0.999619 0.998154 5.057839 0.538277 0 0 1 1 1 1 0 0 0 1 1 1 1 346 166 0.008191387 0.004459303 1.836920953 0.264090468
17 6030 3960 1384 390 353.057922 209.272217 47.873077 2400 33.49934 0.89731 0.991028 0.993454 6.613396 0.739365 366 132 70.872566 47.020321 69.098839 3900 33.49934 0.834184 0.99826 0.998337 7.783869 0.845494 0 1 1 1 1 1 1 1 1 1 1 1 1 994 234 0.023532481 0.006286005 3.743630563 0.573292984
18 6260 3960 588 332 0 68.800301 0 100 30.238735 1 1 0.997726 8.546474 0.5 296 120 9.865766 49.455826 7.978847 300 30.238735 0.539012 0.999863 0.998505 5.985139 0.539894 0 0 1 1 1 1 0 0 0 1 1 1 1 256 176 0.006060679 0.004727936 1.281887034 0.107849755
19 6500 3960 738 310 44.822338 61.513283 77.357788 2000 33.49934 0.870803 0.99852 0.997879 11.997409 0.80124 514 118 110.387497 59.495655 97.066856 8100 33.49934 0.97046 0.995712 0.998352 8.639286 0.906009 1 1 1 1 1 1 1 1 1 1 1 1 1 428 396 0.010132698 0.010637855 0.952513282 -0.02112896
20 2250 4190 568 320 0 69.660385 0 100 19.366146 1 1 0.997742 8.153845 0.5 336 134 26.098106 82.455276 41.459301 900 19.366146 0.638269 0.99939 0.997864 4.074936 0.707296 0 0 1 1 1 1 0 0 0 1 1 1 1 248 202 0.005871283 0.005426381 1.081988808 0.034222769

Total number of rows: 5776

Table truncated, full table size 1494 Kbytes.




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