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Sample GSM807658 Query DataSets for GSM807658
Status Public on Nov 21, 2012
Title RR2_nsrR_Cy3_ch1_wt_Cy5_ch2_7DS13322031_rep3
Sample type RNA
 
Channel 1
Source name 14028s nsrR mutant
Organism Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Characteristics genotype/variation: nsrR mutant
Growth protocol aerobically in LB to mid-log phase (OD600~0.5) at 37°C
Extracted molecule total RNA
Extraction protocol 1Vol culture was mixed with 2Vol RNAprotect reagent (Qiagen, Valencia, CA, USA) and RNA immediately purified using the Qiagen RNeasy midi kit (Qiagen).
Label Cy3
Label protocol Standard labeling using Cy3-dUTP with reverse transcriptase and random hexamers
 
Channel 2
Source name 14028s wild type
Organism Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Characteristics genotype/variation: wild type
Growth protocol aerobically in LB to mid-log phase (OD600~0.5) at 37°C
Extracted molecule total RNA
Extraction protocol 1Vol culture was mixed with 2Vol RNAprotect reagent (Qiagen, Valencia, CA, USA) and RNA immediately purified using the Qiagen RNeasy midi kit (Qiagen).
Label Cy5
Label protocol Standard labeling using Cy5-dUTP with reverse transcriptase 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 at 10?m resolution, 95% laser power, PMT for low scan set to where maximal intensity of spots was 75% of saturation; PMT for high scan was 20% higher than low scan PMT. Image acquisition with ScanArray Express 3.0.1 software, spot quantification using MolecularWare AnalyzerDG Pro version 2.50.
Description biological replicate
Data processing used values for median measurements for spot and background in high PMT setting; 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 03, 2011
Last update date Nov 21, 2012
Contact name Michael McClelland
E-mail(s) mcclelland.michael@gmail.com
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 GPL6868
Series (1)
GSE32585 The nsrR regulon in Salmonella Typhimurium 14028s

Data table header descriptions
ID_REF Number
Spot_Confidence_(Cy3H) Spot Confidence Cy3 high scan
Spot_Confidence_(Cy3L) Spot Confidence Cy3 low scan
Spot_Confidence_(Cy5H) Spot Confidence Cy5 high scan
Spot_Confidence_(Cy5L) Spot Confidence Cy5 low scan
Spot_Mean_Intensity_(Cy3H) Spot Mean Intensity Cy3 high scan
Spot_Mean_Intensity_(Cy3L) Spot Mean Intensity Cy3 low scan
Spot_Mean_Intensity_(Cy5H) Spot Mean Intensity Cy5 high scan
Spot_Mean_Intensity_(Cy5L) Spot Mean Intensity Cy5 low scan
Spot_Median_Intensity_(Cy3H) Spot Median Intensity Cy3 high scan
Spot_Median_Intensity_(Cy3L) Spot Median Intensity Cy3 low scan
Spot_Median_Intensity_(Cy5H) Spot Median Intensity Cy5 high scan
Spot_Median_Intensity_(Cy5L) Spot Median Intensity Cy5 low scan
Spot_Standard_Deviation_(Cy3H) Spot Standard Deviation Cy3 high scan
Spot_Standard_Deviation_(Cy3L) Spot Standard Deviation Cy3 low scan
Spot_Standard_Deviation_(Cy5H) Spot Standard Deviation Cy5 high scan
Spot_Standard_Deviation_(Cy5L) Spot Standard Deviation Cy5 low scan
Spot_Number_of_Pixels_(Cy3H) Spot Number of Pixels Cy3 high scan
Spot_Number_of_Pixels_(Cy3L) Spot Number of Pixels Cy3 low scan
Spot_Number_of_Pixels_(Cy5H) Spot Number of Pixels Cy5 high scan
Spot_Number_of_Pixels_(Cy5L) Spot Number of Pixels Cy5 low scan
Spot_Total_Intensity_(Cy3H) Spot Total Intensity Cy3 high scan
Spot_Total_Intensity_(Cy3L) Spot Total Intensity Cy3 low scan
Spot_Total_Intensity_(Cy5H) Spot Total Intensity Cy5 high scan
Spot_Total_Intensity_(Cy5L) Spot Total Intensity Cy5 low scan
Spot_Peak_Intensity_(Cy3H) Spot Peak Intensity Cy3 high scan
Spot_Peak_Intensity_(Cy3L) Spot Peak Intensity Cy3 low scan
Spot_Peak_Intensity_(Cy5H) Spot Peak Intensity Cy5 high scan
Spot_Peak_Intensity_(Cy5L) Spot Peak Intensity Cy5 low scan
Background_Mean_Intensity_(Cy3H) Background Mean Intensity Cy3 high scan
Background_Mean_Intensity_(Cy3L) Background Mean Intensity Cy3 low scan
Background_Mean_Intensity_(Cy5H) Background Mean Intensity Cy5 high scan
Background_Mean_Intensity_(Cy5L) Background Mean Intensity Cy5 low scan
Background_Median_Intensity_(Cy3H) Background Median Intensity Cy3 high scan
Background_Median_Intensity_(Cy3L) Background Median Intensity Cy3 low scan
Background_Median_Intensity_(Cy5H) Background Median Intensity Cy5 high scan
Background_Median_Intensity_(Cy5L) Background Median Intensity Cy5 low scan
Background_Standard_Deviation_(Cy3H) Background Standard Deviation Cy3 high scan
Background_Standard_Deviation_(Cy3L) Background Standard Deviation Cy3 low scan
Background_Standard_Deviation_(Cy5H) Background Standard Deviation Cy5 high scan
Background_Standard_Deviation_(Cy5L) Background Standard Deviation Cy5 low scan
Background_Number_of_Pixels_(Cy3H) Background Number of Pixels Cy3 high scan
Background_Number_of_Pixels_(Cy3L) Background Number of Pixels Cy3 low scan
Background_Number_of_Pixels_(Cy5H) Background Number of Pixels Cy5 high scan
Background_Number_of_Pixels_(Cy5L) Background Number of Pixels Cy5 low scan
CH1_BKD_CORR Channel 1 median values of high scan background corrected
CH2_BKD_CORR Channel 2 median values of high scan background corrected
CH1%_OF_TOTAL Channel 1 median values of high scan % of total
CH2%_OF_TOTAL Channel 2 median values of high scan % of total
PRE-VALUE ch1 median values of high scan % of total / ch2 median values of high scan % of total
VALUE log of ch1 median values of high scan % of total / ch2 median values of high scan % of total

Data table
ID_REF Spot_Confidence_(Cy3H) Spot_Confidence_(Cy3L) Spot_Confidence_(Cy5H) Spot_Confidence_(Cy5L) Spot_Mean_Intensity_(Cy3H) Spot_Mean_Intensity_(Cy3L) Spot_Mean_Intensity_(Cy5H) Spot_Mean_Intensity_(Cy5L) Spot_Median_Intensity_(Cy3H) Spot_Median_Intensity_(Cy3L) Spot_Median_Intensity_(Cy5H) Spot_Median_Intensity_(Cy5L) Spot_Standard_Deviation_(Cy3H) Spot_Standard_Deviation_(Cy3L) Spot_Standard_Deviation_(Cy5H) Spot_Standard_Deviation_(Cy5L) Spot_Number_of_Pixels_(Cy3H) Spot_Number_of_Pixels_(Cy3L) Spot_Number_of_Pixels_(Cy5H) Spot_Number_of_Pixels_(Cy5L) Spot_Total_Intensity_(Cy3H) Spot_Total_Intensity_(Cy3L) Spot_Total_Intensity_(Cy5H) Spot_Total_Intensity_(Cy5L) Spot_Peak_Intensity_(Cy3H) Spot_Peak_Intensity_(Cy3L) Spot_Peak_Intensity_(Cy5H) Spot_Peak_Intensity_(Cy5L) Background_Mean_Intensity_(Cy3H) Background_Mean_Intensity_(Cy3L) Background_Mean_Intensity_(Cy5H) Background_Mean_Intensity_(Cy5L) Background_Median_Intensity_(Cy3H) Background_Median_Intensity_(Cy3L) Background_Median_Intensity_(Cy5H) Background_Median_Intensity_(Cy5L) Background_Standard_Deviation_(Cy3H) Background_Standard_Deviation_(Cy3L) Background_Standard_Deviation_(Cy5H) Background_Standard_Deviation_(Cy5L) Background_Number_of_Pixels_(Cy3H) Background_Number_of_Pixels_(Cy3L) Background_Number_of_Pixels_(Cy5H) Background_Number_of_Pixels_(Cy5L) CH1_BKD_CORR CH2_BKD_CORR CH1%_OF_TOTAL CH2%_OF_TOTAL PRE-VALUE VALUE
1 100 100 100 100 5189.05 818.091 2735.929 276.6364 4164 786 2263 181 3501.14 551.513 2137.655 320.555 99 99 99 99 513716 80991 270857 27387 21816 2573 9416 1761 266.6573 25.56471 796.434 83.3985 0 0 356.5 0 634.049 88.2704 1076.051 158.6288 680 680 680 680 4164 1906.5 0.088366284 0.011881729 7.437157195 0.871406961
2 100 100 100 100 2211.39 277.4416 2496.701 315.3117 2103 158 2330 267 1773.684 406.255 2007.948 292.9761 77 77 77 77 170277 21363 192246 24279 8051 2480 10260 1270 273.7832 26.01355 810.451 97.0867 0 0 409 0 628.127 82.4474 1124.576 181.6293 738 738 738 738 2103 1921 0.044628793 0.011972096 3.727734367 0.571444958
3 100 100 100 100 259.8348 28.25217 985.913 117.0522 0 0 615 0 602.585 82.2891 1080.96 213.6771 115 115 115 115 29881 3249 113380 13461 3385 427 4217 1033 239.6685 25.61528 872.593 94.2101 0 0 380 0 580.008 89.8676 1331.774 184.1515 733 733 733 733 0 235 2.12E-05 0.001464572 0.014489893 -1.838934822
4 100 100 100 100 355.23 33.9734 863.77 96.8761 0 0 365 0 727.789 93.3299 1088.822 158.129 113 113 113 113 40141 3839 97606 10947 3899 474 5336 832 219.9602 25.68706 982.209 82.7184 0 0 447 0 612.308 89.4426 1428.258 172.8055 703 703 703 703 0 -82 2.12E-05 6.23E-06 3.405124926 0.53213305
5 100 100 100 100 222.2069 24.78448 675.966 71.9655 0 0 267.5 0 457.47 76.7221 889.15 127.8704 116 116 116 116 25776 2875 78412 8348 2127 548 3756 553 224.8545 20.89777 910.152 81.962 0 0 434 0 556.132 76.6082 1194.752 171.5446 763 763 763 763 0 -166.5 2.12E-05 6.23E-06 3.405124926 0.53213305
6 100 100 100 100 367.655 45.3186 965.212 108.5664 0 0 577 0 901.813 111.1709 1148.724 194.9916 113 113 113 113 41545 5121 109069 12268 6737 635 5265 1190 281.4139 19.48506 897.489 87.6088 0 0 391 0 727.743 81.4026 1150.697 169.9616 703 703 703 703 0 186 2.12E-05 0.001159193 0.018307123 -1.737379901
7 100 100 100 100 569.045 71.9643 1626.089 191.6607 72 0 1077.5 58.5 920.065 155.1447 1581.825 279.5939 112 112 112 112 63733 8060 182122 21466 4311 710 7151 1348 290.4604 22.5888 888.952 84.582 0 0 463 0 674.727 80.4864 1144.249 157.2011 732 732 732 732 72 614.5 0.001527947 0.0038297 0.39897314 -0.399056341
8 100 100 100 100 473.723 46.5804 1495.902 123.9464 0 0 955.5 0 966.639 133.2759 1674.046 238.0512 112 112 112 112 53057 5217 167541 13882 5932 927 9673 1219 264.3741 24.04268 926.724 73.6401 0 0 455 0 641.579 84.3517 1184.61 146.5758 703 703 703 703 0 500.5 2.12E-05 0.003119226 0.006803446 -2.167271058
9 100 100 100 100 1358.736 200.7033 4110.69 572.473 971 69 3407 511 1453.474 280.3087 2288.505 427.407 91 91 91 91 123645 18264 374073 52095 6450 1319 10577 2140 235.4652 24.90668 887.481 90.1811 0 0 430 0 587.534 87.9865 1173.025 190.9116 718 718 718 718 971 2977 0.020606067 0.018553321 1.110640344 0.045573445
10 100 100 100 100 409 59.5804 1532.982 125.4018 0 0 1098.5 8 738.769 142.482 1440.057 190.4334 112 112 112 112 45808 6673 171694 14045 4375 687 7882 935 264.3684 20.69701 902.502 90.9531 0 0 451 0 578.128 75.9793 1136.131 166.7095 703 703 703 703 0 647.5 2.12E-05 0.004035363 0.00525888 -2.279106739
11 100 100 100 100 345.589 25.25893 1171.563 130.0089 0 0 731 0 695.185 71.6958 1226.565 219.2124 112 112 112 112 38706 2829 131215 14561 3318 492 6135 983 232.8101 22.5888 955.51 82.3238 0 0 505.5 0 601.333 75.6893 1152.289 158.088 732 732 732 732 0 225.5 2.12E-05 0.001405366 0.015100332 -1.821013504
12 100 100 100 100 373.991 35.9737 1189.772 109.7368 0 0 734 0 752.068 100.9235 1238.175 176.4504 114 114 114 114 42635 4101 135634 12510 4405 513 5836 1074 278.404 26.75533 903.017 82.2034 0 0 478 0 688.493 88.6251 1126.882 164.7162 703 703 703 703 0 256 2.12E-05 0.001595448 0.013301269 -1.876106923
13 100 100 100 100 333.793 32.3017 1262.716 102.4483 0 0 719.5 0 632.716 115.5429 1397.875 185.9875 116 116 116 116 38720 3747 146475 11884 3037 1005 5686 849 331.764 22.45219 959.209 79.9768 0 0 469 0 713.809 79.2541 1273.378 158.171 732 732 732 732 0 250.5 2.12E-05 0.001561171 0.013593313 -1.866674683
14 100 100 100 100 431.195 48.5841 1339.292 173.7257 0 0 942 19 875.967 114.1157 1532.859 281.7979 113 113 113 113 48725 5490 151340 19631 4932 584 7321 1510 264.8199 23.76398 934.076 82.884 0 0 483 0 615.976 85.773 1224.059 165.2418 733 733 733 733 0 459 2.12E-05 0.002860589 0.007418573 -2.129679625
15 100 100 100 100 225.6435 40.5478 881.826 97.1826 0 0 446 0 577.611 141.9259 1069.745 168.003 115 115 115 115 25949 4663 101410 11176 4200 925 5647 962 271.388 25.21858 886.698 74.5137 0 0 487 0 609.816 88.5005 1110.089 149.8367 732 732 732 732 0 -41 2.12E-05 6.23E-06 3.405124926 0.53213305
16 100 100 100 100 304.114 19.91228 1028.263 89.1842 0 0 538.5 0 620.509 70.9072 1175.032 163.5676 114 114 114 114 34669 2270 117222 10167 3502 376 5117 854 252.7838 18.54338 999.518 74.4808 0 0 550 0 633.35 76.2515 1249.782 154.1015 703 703 703 703 0 -11.5 2.12E-05 6.23E-06 3.405124926 0.53213305
17 100 100 100 100 194.6306 36.045 710.495 80.1081 0 0 359 0 511.652 108.9422 932.785 165.0259 111 111 111 111 21604 4001 78865 8892 2756 662 4319 763 287.7336 22.34153 801.877 78.8429 0 0 359 0 670.774 85.408 1161.904 181.0267 732 732 732 732 0 0 2.12E-05 6.23E-06 3.405124926 0.53213305
18 100 100 100 100 245.9375 22.38393 945.866 96.9732 0 0 494.5 0 742.728 102.2834 1196.598 201.0112 112 112 112 112 27545 2507 105937 10861 5885 659 6217 1062 262.1451 20.0825 914.122 96.8933 0 0 441 0 621.878 73.1648 1137.938 199.8851 703 703 703 703 0 53.5 2.12E-05 0.000333424 0.063647195 -1.196220731
19 100 100 100 100 227.687 30.98261 1175.974 123.8435 0 0 711 0 532.326 87.4838 1329.103 211.3551 115 115 115 115 26184 3563 135237 14242 2849 555 5190 1100 262.7276 21.74232 979.033 96.0788 0 0 523 0 708.464 83.5346 1307.371 184.6062 749 749 749 749 0 188 2.12E-05 0.001171657 0.018112367 -1.742024791
20 100 100 100 100 386.165 19.73913 999.757 101.6261 0 0 501 0 802.072 62.1358 1235.62 162.7892 115 115 115 115 44409 2270 114972 11687 4383 442 6281 766 274.0909 26.94228 825.589 95.3579 0 0 371 0 638.812 102.8535 1124.88 177.644 693 693 693 693 0 130 2.12E-05 0.000810189 0.026193269 -1.581810297

Total number of rows: 17328

Table truncated, full table size 5188 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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