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Sample GSM289182 Query DataSets for GSM289182
Status Public on Dec 13, 2008
Title FH_RDE2_14028s_hfq_MgMDil_3_7DS547
Sample type mixed
 
Channel 1
Source Name 14028s hfq RNA MgMDil 060927
Organism(s) Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics Salmonella typhimurium 14028s hfq RNA harvested from LB stat culture that had been diluted 100fold in MgM medium and grown to log phase
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 Feb 16 14:05:47 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 1540 3200 13017 190 4296.863281 274.847809 95.078926 8000 39.071594 0.950954 0.881035 0.99205 47.360756 0.92069 16650 0 6039.394043 274.877563 97.066856 8100 39.071594 0.97046 0.802612 0.992378 60.572423 0.868408 1 1 1 1 1 1 1 1 1 1 1 1 1 12827 16650 0.20209465 0.006893663 29.31600558 1.467104796
2 1780 3200 439 115 367.298523 356.465881 84.062363 4100 35.31316 0.858233 0.990044 0.991096 1.231534 0.328409 26744 0 8906.94043 162.349442 97.066856 8100 35.31316 0.97046 0.722183 0.994987 164.731087 0.814789 1 1 1 1 1 0 1 1 1 1 1 1 1 324 26744 0.005104753 0.01107292 0.461012377 -0.336287415
3 2010 3200 1590 184 755.621948 367.38269 93.048538 7600 39.071594 0.948563 0.973343 0.989563 4.327912 0.84197 13806 0 4331.761719 187.539566 97.066856 8100 39.071594 0.97046 0.857185 0.994682 73.616466 0.90479 1 1 1 1 1 1 1 1 1 1 1 1 1 1406 13806 0.022152107 0.00571615 3.875354094 0.58831139
4 2250 3190 674 120 399.852783 251.272949 87.03894 3200 29.283895 0.901416 0.986809 0.992928 2.682342 0.715291 17060 0 6534.306152 216.773621 97.066856 8100 29.283895 0.97046 0.815918 0.992508 78.699613 0.877279 1 1 1 1 1 0 1 1 1 1 1 1 1 554 17060 0.008728497 0.007063416 1.235733091 0.091924677
5 2480 3190 655 155 219.24968 284.089111 88.848671 2300 33.721161 0.910743 0.993629 0.993279 2.305615 0.614831 7107 0 3594.957764 207.615707 97.066856 8100 33.721161 0.97046 0.884109 0.993942 34.231514 0.92274 1 1 1 1 1 0 1 1 1 1 1 1 1 500 7107 0.007877705 0.002942538 2.677180344 0.427677628
6 2720 3190 492 111 252.105713 267.195007 81.75885 3000 29.283895 0.881129 0.992744 0.99157 1.841352 0.491027 11325 0 6197.726563 141.951797 97.066856 8100 29.283895 0.97046 0.838318 0.995872 79.780603 0.892212 1 1 1 1 1 0 1 1 1 1 1 1 1 381 11325 0.006002811 0.004688933 1.280208492 0.107280704
7 2950 3180 482 88 316.809723 368.514099 87.403885 3100 30.783829 0.903188 0.988609 0.988388 1.307955 0.348788 25825 0 9493.588867 154.386719 97.066856 8100 30.783829 0.97046 0.708115 0.995415 167.274751 0.80541 1 1 1 1 1 0 1 1 1 1 1 1 1 394 25825 0.006207632 0.010692423 0.580563637 -0.23615017
8 3190 3180 605 163 286.184387 336.523651 91.322075 3800 25.847124 0.919504 0.991783 0.992142 1.797793 0.479412 24924 0 7889.295898 165.22551 97.066856 8100 25.847124 0.97046 0.730263 0.995255 150.848377 0.820175 1 1 1 1 1 0 1 1 1 1 1 1 1 442 24924 0.006963891 0.010319378 0.674836347 -0.170801534
9 3420 3180 360 50 342.117828 334.488586 93.730225 4900 30.783829 0.93689 0.986725 0.990295 1.07627 0.287005 21585 0 5133.027344 92.974144 97.066856 8100 30.783829 0.97046 0.796432 0.997231 232.16132 0.864288 1 1 1 1 1 0 1 1 1 1 1 1 1 310 21585 0.004884177 0.008936919 0.546516879 -0.26239642
10 3660 3180 644 156 478.631622 287.01059 78.176407 2300 25.847124 0.841068 0.982857 0.992012 2.24382 0.598352 14901 0 5941.653809 163.471817 96.408768 8000 25.847124 0.963834 0.829872 0.99575 91.153327 0.886581 1 1 1 1 1 0 1 1 1 1 1 1 1 488 14901 0.00768864 0.006169517 1.246230415 0.095598346
11 3890 3170 2029 56 1175.85376 294.506134 95.746155 7900 30.954346 0.957094 0.967155 0.990562 6.8895 0.887508 7155 0 3587.823486 115.166756 97.066856 8100 30.954346 0.97046 0.88961 0.997276 62.127304 0.926407 1 1 1 1 1 1 1 1 1 1 1 1 1 1973 7155 0.031085425 0.002962412 10.493283 1.020911386
12 4120 3170 749 217 461.223511 402.767731 87.03894 4500 35.88512 0.890604 0.986313 0.989731 1.859633 0.495902 10096 0 4533.965332 200.628265 97.066856 8100 35.88512 0.97046 0.865929 0.994835 50.321922 0.910619 1 1 1 1 1 0 1 1 1 1 1 1 1 532 10096 0.008381878 0.004180085 2.005193228 0.302156229
13 4360 3170 300 2 296.861725 288.738251 90.27034 4900 30.954346 0.926244 0.991997 0.992279 1.039003 0.277068 24154 0 7148.658691 156.395691 97.066856 8100 30.954346 0.97046 0.758247 0.995766 154.441595 0.838832 1 1 1 1 1 0 1 1 1 1 1 1 1 298 24154 0.004695112 0.010000572 0.469484373 -0.328378859
14 4590 3160 537 31 515.960693 310.157104 94.069214 5200 38.707481 0.948274 0.985977 0.990677 1.731381 0.461702 36852 0 7692.541992 271.743408 97.066856 8100 38.707481 0.97046 0.713272 0.990738 135.613225 0.808848 1 1 1 1 1 0 1 1 1 1 1 1 1 506 36852 0.007972238 0.015257973 0.522496509 -0.281916607
15 4830 3160 738 162 392.478394 345.108734 88.489685 3300 34.186237 0.910072 0.986023 0.989891 2.138456 0.570255 25908 0 7605.688477 293.454834 97.066856 8100 34.186237 0.97046 0.746658 0.994087 88.286159 0.831106 1 1 1 1 1 0 1 1 1 1 1 1 1 576 25908 0.009075116 0.010726787 0.846023709 -0.072617466
16 5060 3160 396 82 323.368622 265.371796 89.91703 3800 38.707481 0.943689 0.989372 0.992004 1.492246 0.397932 31855 0 10831.30566 152.261353 97.066856 8100 38.707481 0.97046 0.699844 0.995399 209.212643 0.799822 1 1 1 1 1 0 1 1 1 0 1 1 1 314 31855 0.004947199 0.013189046 0.375099061 -0.425854023
17 5300 3160 377 0 391.807831 141.53978 93.730225 6100 34.186237 0.93689 0.988739 0.99604 2.663562 0.710283 15914 0 7303.496094 90.687813 97.066856 8100 34.186237 0.97046 0.789314 0.997025 175.481131 0.859543 1 1 1 1 1 0 1 1 1 1 1 1 1 377 15914 0.00593979 0.006588934 0.901479666 -0.045044065
18 5530 3150 385 8 354.34549 209.810806 90.622276 5900 43.689777 0.912519 0.991089 0.993675 1.834987 0.48933 17442 0 7437.696289 183.905579 97.066856 8100 43.689777 0.97046 0.77169 0.994339 94.842147 0.847794 1 1 1 1 1 0 1 1 1 1 1 1 1 377 17442 0.00593979 0.007221577 0.822505871 -0.084860993
19 5770 3150 341 0 366.887115 293.288269 89.206215 5500 39.739479 0.931358 0.988762 0.990944 1.162679 0.310048 31797 0 7272.882813 558.125122 97.066856 8100 39.739479 0.97046 0.683464 0.993927 56.971096 0.781102 1 1 1 1 1 0 1 1 1 0 1 1 1 341 31797 0.005372595 0.013165032 0.408095843 -0.389237829
20 1540 3440 306 7 309.516571 185.389099 90.972847 4700 42.383083 0.917003 0.987022 0.994469 1.650582 0.440155 37456 0 7020.427734 172.313919 97.066856 8100 42.383083 0.97046 0.678528 0.995621 217.370716 0.77546 1 1 1 1 1 0 1 1 1 0 1 1 1 299 37456 0.004710868 0.01550805 0.303769195 -0.517456269

Total number of rows: 17328

Table truncated, full table size 5037 Kbytes.




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