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Sample GSM289190 Query DataSets for GSM289190
Status Public on Dec 13, 2008
Title FH_RDE2_14028s_smpB_LBstat_2_7DS672
Sample type mixed
 
Channel 1
Source Name 14028s smpB RNA LBstat 061019
Organism(s) Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics Salmonella typhimurium 14028s smpB mutant RNA harvested from LB stat culture
Extracted molecule total RNA
Extraction protocol RNeasy kit (QIAGEN)
Label Cy3
Label protocol incorporation of Cy3-dCTP with Superscript RT and random hexamers
 
Channel 2
Source Name 14028s gDNA
Organism(s) Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics Salmonella typhimurium 14028s genomic DNA from stationary culture grown in LB at 37C with aeration
Extracted molecule genomic DNA
Extraction protocol SIGMA GenElute bacterial genomic DNA extraction
Label Cy5
Label protocol incorporation of Cy5-dCTP using Klenow enzyme 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 STv7S_01_051201
Description biological replicate, Date of Scan Fri Mar 02 11:27:32 2007
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 May 16, 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 GPL6868
Series (1)
GSE11486 Transcriptional profiles of Salmonella typhimurium wt, hfq and smpB mutants in four different growth 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 log10 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 1660 2280 65535 309 5342.777832 358.253448 97.066856 8100 24.397734 0.97046 0.633141 0.990189 182.929153 0.723589 51118 0 6349.232422 175.714569 97.066856 8100 24.397734 0.97046 0.68203 0.99427 290.914978 0.779463 1 1 1 0 1 1 1 1 1 0 1 1 1 65226 51118 1.382556171 0.025611396 53.98206906 1.732249526
2 1890 2290 643 159 331.539612 277.691254 93.048538 5500 14.429089 0.948563 0.990654 0.992271 2.315521 0.617472 22451 0 4663.443359 542.046814 97.066856 8100 14.429089 0.97046 0.830856 0.985916 41.418932 0.887238 1 1 1 1 1 0 1 1 1 1 1 1 1 484 22451 0.010259056 0.011248512 0.912036682 -0.039987694
3 2130 2290 770 212 238.017609 335.32663 86.30442 3300 18.997337 0.907422 0.992554 0.99073 2.296269 0.612338 18355 0 3838.186523 444.940277 97.066856 8100 18.997337 0.97046 0.843506 0.988388 41.252727 0.895671 1 1 1 1 1 0 1 1 1 1 1 1 1 558 18355 0.011827589 0.009196314 1.28612282 0.109282444
4 2360 2290 914 331 217.208298 332.875458 63.830772 900 14.429089 0.790816 0.994469 0.990883 2.745772 0.732206 22011 0 4273.63623 158.504654 97.066856 8100 14.429089 0.97046 0.836403 0.996506 138.866585 0.890935 1 0 1 1 1 0 1 1 1 1 1 1 1 583 22011 0.012357499 0.011028061 1.120550451 0.049431415
5 2600 2290 732 234 228.008911 276.267792 79.388519 1800 18.997337 0.88395 0.992355 0.992302 2.649603 0.706561 14143 0 3113.979736 157.989517 97.066856 8100 18.997337 0.97046 0.877884 0.994514 89.518597 0.918589 1 0 1 1 1 0 1 1 1 1 1 1 1 498 14143 0.010555806 0.007085997 1.489671247 0.173090435
6 2830 2290 627 231 109.468369 301.439972 76.113342 1800 14.429089 0.867003 0.997581 0.991501 2.080016 0.554671 10241 0 3532.815186 141.372284 97.066856 8100 14.429089 0.97046 0.884277 0.996101 72.439942 0.922852 1 0 1 1 1 0 1 1 1 1 1 1 1 396 10241 0.008393773 0.005130997 1.635895108 0.213755454
7 3070 2290 346 94 272.360291 267.817108 85.934807 3300 18.997337 0.910034 0.993584 0.993538 1.291926 0.344514 27402 0 5316.073242 77.286369 97.066856 8100 18.997337 0.97046 0.756599 0.997925 354.551524 0.837733 1 1 1 1 1 0 1 1 1 1 1 1 1 252 27402 0.005341492 0.013729087 0.389063879 -0.409979087
8 3300 2290 572 131 432.270935 279.432159 86.30442 2900 14.429089 0.924076 0.983864 0.992188 2.047008 0.545869 27670 0 6512.993652 144.53093 97.066856 8100 14.429089 0.97046 0.76564 0.994843 191.446911 0.84376 1 1 1 1 1 0 1 1 1 1 1 1 1 441 27670 0.009347611 0.013863362 0.674267247 -0.171167936
9 3540 2290 543 119 366.88089 285.677979 82.918602 2800 18.997337 0.887324 0.989357 0.991241 1.900742 0.506864 24339 0 4727.408691 142.875183 97.066856 8100 18.997337 0.97046 0.78096 0.995628 170.351488 0.853973 1 1 1 1 1 0 1 1 1 1 1 1 1 424 24339 0.008987272 0.012194448 0.736997068 -0.13253424
10 3770 2300 445 90 338.334747 264.287903 82.147255 3000 13.185143 0.891458 0.988632 0.993065 1.68377 0.449005 19527 0 2834.924805 122.748123 97.066856 8100 13.185143 0.97046 0.881126 0.997162 159.081862 0.920751 1 1 1 1 1 0 1 1 1 1 1 1 1 355 19527 0.007524721 0.009783515 0.769122401 -0.114004539
11 4010 2300 454 110 246.558151 316.365387 85.190765 3000 18.070644 0.90197 0.993629 0.992973 1.43505 0.38268 9799 0 2477.309326 165.407669 97.066856 8100 18.070644 0.97046 0.908264 0.994896 59.24151 0.938843 1 1 1 1 1 0 1 1 1 1 1 1 1 344 9799 0.00729156 0.004909544 1.485180775 0.171779319
12 4240 2300 393 28 382.957306 269.390747 90.972847 4600 13.185143 0.926646 0.987976 0.993217 1.458847 0.389026 13385 0 2934.039307 166.787125 97.066856 8100 13.185143 0.97046 0.890877 0.995155 80.251998 0.927251 1 1 1 1 1 0 1 1 1 1 1 1 1 365 13385 0.007736685 0.00670622 1.153658109 0.062077123
13 4480 2300 374 33 265.538971 295.178497 90.972847 4700 18.070644 0.908001 0.991035 0.991043 1.26703 0.337875 23466 0 2553.172363 158.399521 97.066856 8100 18.070644 0.97046 0.913162 0.99559 148.144387 0.942108 1 1 1 1 1 0 1 1 1 1 1 1 1 341 23466 0.007227971 0.011757053 0.614777475 -0.211282053
14 4710 2300 407 81 331.043365 286.705383 89.562332 4600 13.185143 0.911104 0.986755 0.992958 1.419576 0.378554 23702 0 3745.574707 137.916168 97.066856 8100 13.185143 0.97046 0.864563 0.996468 171.858023 0.909709 1 1 1 1 1 0 1 1 1 1 1 1 1 326 23702 0.006910025 0.011875295 0.581882425 -0.23516476
15 4950 2300 289 54 247.892136 220.767609 91.322075 4200 18.070644 0.919504 0.992874 0.993797 1.309069 0.349085 21866 0 3094.65625 99.073006 97.066856 8100 18.070644 0.97046 0.861397 0.997124 220.705931 0.907598 1 1 1 1 1 0 1 1 1 1 1 1 1 235 21866 0.004981153 0.010955413 0.454675081 -0.342298848
16 5180 2300 709 209 170.158585 313.104095 83.682846 2000 13.185143 0.879903 0.994415 0.991447 2.264423 0.603846 23229 0 3829.873779 168.637909 97.066856 8100 13.185143 0.97046 0.840149 0.995499 137.744829 0.893433 1 1 1 1 1 0 1 1 1 1 1 1 1 500 23229 0.010598198 0.01163831 0.910630358 -0.040657876
17 5420 2300 630 115 430.584015 333.000641 86.30442 4900 18.070644 0.929703 0.98632 0.991257 1.891888 0.504504 10405 0 3751.389893 136.750931 96.408768 8000 18.070644 0.963834 0.877266 0.99498 76.087233 0.918177 1 1 1 1 1 0 1 1 1 1 1 1 1 515 10405 0.010916144 0.005213165 2.093957093 0.320967778
18 5650 2310 708 145 285.581268 297.536713 80.186417 2100 18.425455 0.880382 0.991867 0.992851 2.379538 0.634544 16388 0 3440.189209 155.307205 97.066856 8100 18.425455 0.97046 0.886047 0.995155 105.519895 0.924032 1 1 1 1 1 0 1 1 1 1 1 1 1 563 16388 0.011933571 0.008210798 1.453399724 0.162385074
19 5890 2310 542 102 378.139343 280.58847 88.489685 4000 22.185528 0.928403 0.990211 0.992584 1.931655 0.515108 21866 0 3103.052979 174.999405 97.066856 8100 22.185528 0.97046 0.831429 0.995598 124.948996 0.887619 1 1 1 1 1 0 1 1 1 1 1 1 1 440 21866 0.009326415 0.010955413 0.851306534 -0.069914033
20 1660 2520 773 271 182.008392 305.988037 86.672455 2100 21.285538 0.890013 0.995956 0.991264 2.526243 0.673665 33515 0 4516.199707 171.081329 97.066856 8100 21.285538 0.97046 0.763908 0.995193 195.90098 0.842606 1 1 1 1 1 0 1 1 1 1 1 1 1 502 33515 0.010640591 0.016791853 0.633675808 -0.198132873

Total number of rows: 17328

Table truncated, full table size 5014 Kbytes.




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