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Sample GSM1020017 Query DataSets for GSM1020017
Status Public on Dec 31, 2012
Title RR_DH_P0_Cy5_ch1_B0_Cy3_ch2_7DE1412
Sample type RNA
 
Channel 1
Source name ATCC4931_DTAC_sensitive_T0
Organism Salmonella enterica subsp. enterica serovar Enteritidis
Characteristics strain: wild type
Growth protocol ATCC4931 parental strain at midlog phase, grown in TSB, time zero
Extracted molecule total RNA
Extraction protocol RNEasy Midi Kit (Qiagen) after immediate protection of RNA integrity during harvest of cells in RNAProtect reagent
Label Cy5
Label protocol incorporation of Cy5-dUTP with Reverse Transcriptase
 
Channel 2
Source name ATCC4931_SRSB_DTAC_resistant_T0
Organism Salmonella enterica subsp. enterica serovar Enteritidis
Characteristics strain: SRS DTAC resistant strain B
Growth protocol ATCC4931 SRS strain with elevated resistance to DTAC, at midlog phase, grown in TSB, time zero
Extracted molecule total RNA
Extraction protocol RNEasy Midi Kit (Qiagen) after immediate protection of RNA integrity during harvest of cells in RNAProtect reagent
Label Cy3
Label protocol incorporation of Cy3-dUTP 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 STv5_SP040504_adapforsmallpins_040817.pro
Description time course, Date of Scan Thu Jun 19 10:52:35 2008
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 Oct 15, 2012
Last update date Dec 31, 2012
Contact name Michael McClelland
E-mail(s) [email protected]
Phone 858-336-9554
Organization name University of California, Irvine
Department Microbiology & Molecular Genetics
Street address 132 Med Surge I
City Irvine
State/province CA
ZIP/Postal code 92697
Country USA
 
Platform ID GPL11279
Series (1)
GSE41606 Transcriptome of DTAC-resistant Salmonella Enteritidis

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 1110 1880 460 157 90.927216 57.514576 96.408768 6200 0.847811 0.963834 0.997292 0.998322 7.997973 0.89998 293 82 125.261581 22.438263 96.408768 7600 0.847811 0.963834 0.996864 0.999382 13.058052 0.93359 1 1 1 1 1 1 1 1 1 1 1 1 1 303 211 0.003241607 0.00502042 0.645684466 -0.189979662
2 1350 1880 1377 161 369.763367 62.409393 93.048538 7600 5.845382 0.956099 0.988052 0.99752 22.063986 0.958444 1091 92 285.630127 31.228867 97.066856 8100 5.845382 0.97046 0.990623 0.998848 34.935626 0.972926 1 1 1 1 1 1 1 1 1 1 1 1 1 1216 999 0.013009221 0.023769664 0.547303533 -0.261771748
3 1570 1860 632 151 149.986603 59.259987 90.622276 7500 21.93276 0.914965 0.994576 0.998344 10.664869 0.921041 238 92 65.190704 26.373957 75.693985 3100 21.93276 0.876167 0.997299 0.999237 9.024054 0.838588 1 1 1 1 1 1 1 1 1 1 1 1 1 481 146 0.005145917 0.003473845 1.481331935 0.170652386
4 1810 1880 601 144 119.980392 59.04092 95.078926 7900 4.155608 0.950954 0.996185 0.998123 10.179381 0.917894 245 89 47.70417 19.640984 88.129242 5600 4.155608 0.948934 0.998581 0.999397 12.473917 0.92347 1 1 1 1 1 1 1 1 1 1 1 1 1 457 156 0.004889156 0.003711779 1.317200135 0.119651767
5 2050 1880 956 145 261.090393 65.356041 95.078926 8000 0.847811 0.950954 0.991104 0.99781 14.627569 0.939859 232 91 25.515957 25.045923 70.014091 2900 0.847811 0.898502 0.999283 0.999283 9.262985 0.831797 1 1 1 1 1 1 1 1 1 1 1 1 1 811 141 0.00867638 0.003354878 2.586198804 0.412661906
6 2290 1880 394 158 86.151054 5359.33252 76.113342 2800 5.845382 0.909443 0.997101 0.998131 0.073517 0.019604 250 96 47.400536 22.425705 63.330132 1200 5.845382 0.785715 0.998802 0.999268 11.147922 0.774077 1 1 1 1 1 0 1 0 1 1 1 1 1 236 154 0.002524816 0.003664192 0.689051126 -0.161748553
7 2520 1880 878 160 207.17334 65.194778 95.078926 8000 0.847811 0.950954 0.992744 0.997948 13.467336 0.935348 279 87 68.727692 28.204084 92.361824 7300 0.847811 0.941146 0.997963 0.99913 9.892184 0.915911 1 1 1 1 1 1 1 1 1 1 1 1 1 718 192 0.007681432 0.004568344 1.681447766 0.22568338
8 2770 1870 1103 155 240.244064 60.862247 93.730225 7800 18.699764 0.955854 0.991425 0.998154 18.122893 0.950305 522 93 101.065384 24.950781 97.066856 8100 18.699764 0.97046 0.99556 0.999176 20.921189 0.956372 1 1 1 1 1 1 1 1 1 1 1 1 1 948 429 0.010142057 0.010207393 0.993599147 -0.00278879
9 2990 1880 1043 163 192.331467 54.881268 97.066856 8100 0.847811 0.97046 0.99279 0.998268 19.004663 0.952392 392 88 86.367317 24.43013 97.066856 8100 0.847811 0.97046 0.996826 0.999268 16.04576 0.944585 1 1 1 1 1 1 1 1 1 1 1 1 1 880 304 0.009414568 0.007233211 1.301575165 0.114469253
10 3230 1880 1111 164 235.810318 165.619949 95.078926 8000 5.845382 0.950954 0.992569 0.997108 6.708129 0.885165 564 89 116.882355 26.27037 97.066856 8100 5.845382 0.97046 0.996155 0.999138 21.469054 0.957391 1 1 1 1 1 1 1 1 1 1 1 1 1 947 475 0.010131359 0.011301892 0.896430314 -0.047483466
11 3470 1880 379 155 343.231689 52.893578 11.283792 300 10.845192 0.077793 0.995361 0.998444 7.165331 0.088906 956 91 489.317902 22.648684 0 200 10.845192 1 0.99472 0.999191 42.209959 0.5 0 0 0 1 1 1 0 0 1 1 1 1 1 224 865 0.002396435 0.020581341 0.116437286 -0.933907924
12 3700 1880 635 155 152.186523 58.572094 96.408768 7800 5.845382 0.963834 0.995377 0.998123 10.84134 0.922127 319 88 79.145874 27.042677 94.406982 7700 5.845382 0.953853 0.997337 0.999115 11.796169 0.927516 1 1 1 1 1 1 1 1 1 1 1 1 1 480 231 0.005135219 0.005496289 0.934306612 -0.029510578
13 3930 1880 598 147 126.977165 63.931267 97.066856 8100 0.847811 0.97046 0.996017 0.997978 9.353796 0.911924 335 88 64.860077 27.336246 95.078926 8000 0.847811 0.950954 0.998169 0.999214 12.254791 0.929848 1 1 1 1 1 1 1 1 1 1 1 1 1 451 247 0.004824966 0.005876984 0.820993566 -0.085660246
14 4180 1880 1074 157 245.723633 1981.840576 95.078926 8000 15.845122 0.950954 0.991692 0.998055 0.54192 0.144512 385 88 82.81163 23.161039 96.408768 8000 15.845122 0.963834 0.997185 0.99926 16.622743 0.946302 1 1 1 1 1 0 1 1 1 1 1 1 1 917 297 0.009810408 0.007066657 1.388267163 0.142473051
15 4410 1880 1210 161 237.067688 67.07016 97.066856 8100 10.845192 0.97046 0.990837 0.998245 18.04081 0.950102 578 91 115.698006 22.913357 97.066856 8100 10.845192 0.97046 0.995338 0.99926 25.225462 0.96327 1 1 1 1 1 1 1 1 1 1 1 1 1 1049 487 0.011222593 0.011587414 0.96851576 -0.013893308
16 4650 1880 1201 157 274.594604 60.784981 97.066856 8100 15.845122 0.97046 0.99041 0.998009 19.75817 0.95404 273 96 48.898956 24.390387 90.972847 5700 15.845122 0.923449 0.998917 0.999123 11.192935 0.924202 1 1 1 1 1 1 1 1 1 1 1 1 1 1044 177 0.011169101 0.004211442 2.652084744 0.423587397
17 4880 1880 680 149 197.621552 56.333511 95.746155 7900 10.845192 0.957094 0.994301 0.998398 12.070968 0.928932 780 87 255.960938 23.323732 96.408768 8000 10.845192 0.963834 0.991814 0.999306 33.442332 0.971785 1 1 1 1 1 1 1 1 1 1 1 1 1 531 693 0.005680836 0.016488866 0.344525563 -0.462778549
18 5110 1880 309 152 0 62.000935 0 100 5.845382 1 1 0.99807 4.983796 0.5 203 87 0 25.373709 0 100 5.845382 1 1 0.999245 8.000407 0.5 0 0 1 1 1 1 0 0 1 1 1 1 1 157 116 0.001679645 0.002760041 0.608557793 -0.215698172
19 5350 1890 1114 153 200.521927 65.069084 97.066856 8100 14.798815 0.97046 0.992203 0.998009 17.120266 0.947699 445 88 80.357498 23.53968 97.066856 8100 14.798815 0.97046 0.997169 0.999176 18.90425 0.952163 1 1 1 1 1 1 1 1 1 1 1 1 1 961 357 0.010281136 0.008494264 1.210362157 0.082915336
20 1120 2090 1147 149 264.938782 51.146732 97.066856 8100 27.18734 0.97046 0.988411 0.998199 22.425675 0.959059 303 90 57.431026 21.97394 96.408768 7800 27.18734 0.963834 0.998024 0.999275 13.789061 0.936665 1 1 1 1 1 1 1 1 1 1 1 1 1 998 213 0.010676976 0.005068006 2.106740784 0.323611103

Total number of rows: 17328

Table truncated, full table size 4837 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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