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Sample GSM289181 Query DataSets for GSM289181
Status Public on Dec 13, 2008
Title FH_RDE2_14028s_hfq_MgMDil_1_7DS503
Sample type mixed
 
Channel 1
Source Name 14028s hfq RNA MgMDil 060922
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 Wed Nov 01 12:37:14 2006
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 2600 3380 4095 0 2354.034668 195.408463 96.408768 8000 32.04866 0.963834 0.929825 0.994484 20.956104 0.953217 2941 671 1105.054565 408.923431 92.016548 7600 32.04866 0.946082 0.964394 0.987381 7.192055 0.89121 1 1 1 1 1 1 1 1 1 1 1 1 1 4095 2270 0.058095226 0.001383693 41.98563405 1.623100716
2 2840 3380 863 0 556.45874 173.268463 94.406982 7800 35.312775 0.943981 0.982834 0.994911 4.98071 0.856748 9476 577 2550.111084 516.477112 92.705818 7800 35.312775 0.934498 0.919426 0.98526 18.347376 0.946284 1 1 1 1 1 1 1 1 1 1 1 1 1 863 8899 0.012243267 0.005424442 2.257055593 0.353542256
3 3070 3390 2515 0 1269.477173 91.93998 94.406982 7700 24.864721 0.953175 0.959976 0.99794 27.354803 0.965934 6499 518 2140.12915 603.451172 90.972847 6900 24.864721 0.923581 0.933075 0.985558 10.76972 0.92169 1 1 1 1 1 1 1 1 1 1 1 1 1 2515 5981 0.035679974 0.003645757 9.786713036 0.990636854
4 3310 3390 256 0 267.696014 138.31282 81.75885 3600 28.950472 0.86949 0.992805 0.996117 1.850877 0.493567 7704 528 2531.55835 419.264374 94.406982 7600 28.950472 0.959758 0.915031 0.98761 18.375041 0.943354 1 1 1 1 1 0 1 1 1 1 1 1 1 256 7176 0.003631838 0.004374176 0.830290756 -0.080769797
5 3540 3390 141 0 241.744583 123.939339 84.816299 4100 24.864721 0.897919 0.990646 0.996788 1.137653 0.303374 6388 697 1753.935913 543.351868 88.129242 6800 24.864721 0.958866 0.938019 0.983101 11.756654 0.927308 1 1 1 1 1 0 1 1 1 1 1 1 1 141 5691 0.002000348 0.003468985 0.576637915 -0.239096806
6 3780 3390 398 0 414.451874 292.912262 88.848671 6200 28.950472 0.903024 0.987953 0.989517 1.358769 0.362338 6916 723 3047.210693 477.944702 90.622276 7300 28.950472 0.930653 0.915085 0.986153 14.470293 0.939285 1 1 1 1 1 0 1 1 1 1 1 1 1 398 6193 0.005646374 0.003774983 1.495735011 0.174854659
7 4010 3400 163 0 187.991302 123.76506 84.816299 4100 20.233438 0.89931 0.993797 0.996605 1.317011 0.351203 11769 652 3670.23877 494.018036 90.972847 7000 20.233438 0.944176 0.889046 0.986862 23.823017 0.92603 1 1 1 1 1 0 1 1 1 1 1 1 1 163 11117 0.00231246 0.006776438 0.341250005 -0.466927334
8 4250 3400 563 0 412.841888 148.055573 93.730225 7300 25.085205 0.955854 0.986931 0.996101 3.802626 0.827664 8880 575 2647.670898 499.349396 94.069214 7700 25.085205 0.957565 0.918434 0.984116 17.78314 0.945623 1 1 1 1 1 1 1 1 1 1 1 1 1 563 8305 0.007987207 0.005062366 1.577761758 0.198041425
9 4480 3400 250 0 219.465607 128.961517 87.767311 4500 20.233438 0.885621 0.991325 0.996323 1.938563 0.51695 8701 799 2507.279297 625.144348 92.361824 7500 20.233438 0.932136 0.925026 0.980698 13.918385 0.93718 1 1 1 1 1 0 1 1 1 1 1 1 1 250 7902 0.003546717 0.004816714 0.73633535 -0.132924349
10 4720 3410 1086 0 623.019836 124.802681 94.743553 7400 24.907936 0.957843 0.980507 0.996391 8.701736 0.906557 8705 688 2629.833984 426.648804 86.30442 6500 24.907936 0.941675 0.914619 0.987213 20.403198 0.931522 1 1 1 1 1 1 1 1 1 1 1 1 1 1086 8017 0.015406939 0.004886813 3.152757801 0.498690609
11 4950 3410 6095 0 3151.7229 164.188004 96.408768 7900 20.013239 0.963834 0.916924 0.994537 37.122079 0.944616 4694 769 1589.621338 520.263916 87.03894 6500 20.013239 0.955783 0.953583 0.984917 9.022344 0.909275 1 1 1 1 1 1 1 1 1 1 1 1 1 6095 3925 0.086468962 0.002392509 36.14154517 1.558006716
12 5190 3410 776 0 516.407471 102.107582 95.746155 7800 24.907936 0.957094 0.983635 0.997208 7.599827 0.895831 5975 703 1805.542969 489.154144 88.489685 7000 24.907936 0.944831 0.937653 0.985405 12.214963 0.929652 1 1 1 1 1 1 1 1 1 1 1 1 1 776 5272 0.01100901 0.003213581 3.425776193 0.534758987
13 5420 3410 306 0 472.542023 121.942673 89.206215 5100 20.013239 0.931173 0.987556 0.996666 2.509376 0.669167 3652 599 1367.762695 539.800293 89.206215 6800 20.013239 0.942967 0.962181 0.984528 6.765465 0.885916 1 1 1 1 1 0 1 1 1 1 1 1 1 306 3053 0.004341182 0.001860976 2.332745119 0.367867289
14 5660 3420 313 0 279.144897 54.696312 88.489685 6400 28.487593 0.915731 0.992226 0.998566 5.722506 0.870508 10955 641 3993.447021 466.40799 90.622276 7100 28.487593 0.938174 0.891014 0.985291 23.48802 0.927343 1 1 1 1 1 1 1 1 1 1 1 1 1 313 10314 0.00444049 0.006286964 0.706301092 -0.151010122
15 5890 3420 720 0 438.331329 93.682716 88.129242 6700 24.324215 0.930445 0.986801 0.99688 7.685516 0.896753 8991 606 2844.456055 405.647736 88.848671 6900 24.324215 0.938075 0.904297 0.987297 22.164551 0.936198 1 1 1 1 1 1 1 1 1 1 1 1 1 720 8385 0.010214545 0.00511113 1.99849054 0.300702097
16 6130 3420 177 0 229.250397 106.38884 89.91703 3900 28.487593 0.920242 0.991936 0.997261 1.663708 0.443656 9914 550 2806.374756 423.105804 91.322075 7400 28.487593 0.926085 0.902084 0.98793 23.431491 0.934723 1 1 1 1 1 0 1 1 1 1 1 1 1 177 9364 0.002511076 0.005707886 0.439930962 -0.356615471
17 6360 3430 782 0 540.73053 102.407417 91.669968 6900 31.349724 0.931648 0.984253 0.996674 7.636166 0.896224 7579 618 2686.822998 490.023956 82.918602 6200 31.349724 0.946333 0.916916 0.983086 15.466591 0.914593 1 1 1 1 1 1 1 1 1 1 1 1 1 782 6961 0.011094131 0.004243122 2.61461523 0.417407787
18 6600 3430 826 0 578.387878 80.951889 93.048538 7200 34.679688 0.95796 0.98111 0.997986 10.203591 0.918057 7432 532 2618.149414 459.889343 89.91703 6800 34.679688 0.919271 0.925522 0.985832 16.160409 0.944935 1 1 1 1 1 1 1 1 1 1 1 1 1 826 6900 0.011718353 0.004205939 2.786144417 0.445003624
19 6830 3430 229 0 206.5233 127.596489 88.848671 4400 31.349724 0.909475 0.994255 0.997185 1.79472 0.478592 9858 613 2815.367676 486.80423 91.669968 7600 31.349724 0.950327 0.900444 0.98629 20.25044 0.933629 1 1 1 1 1 0 1 1 1 1 1 1 1 229 9245 0.003248793 0.005635349 0.576502552 -0.239198766
20 2600 3610 157 0 127.832214 119.932854 87.03894 3600 36.146202 0.935925 0.996269 0.996803 1.309066 0.349084 9030 778 1875.666382 551.815186 92.705818 7800 36.146202 0.934498 0.91729 0.983574 16.364175 0.94486 1 1 1 1 1 0 1 1 1 1 1 1 1 157 8252 0.002227338 0.005030059 0.442805596 -0.3537869

Total number of rows: 17328

Table truncated, full table size 5028 Kbytes.




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