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Sample GSM807659 Query DataSets for GSM807659
Status Public on Nov 21, 2012
Title RR2_wt_Cy3_ch1_nsrR_Cy5_ch2_7DS13322030_rep3
Sample type RNA
 
Channel 1
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 Cy3
Label protocol Standard labeling using Cy3-dUTP with reverse transcriptase and random hexamers
 
Channel 2
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 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 ch2 median values of high scan % of total / ch1 median values of high scan % of total
INV_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 INV_VALUE
1 100 100 100 100 27386.41 4667.86 6685.61 353.478 30358.5 5012.5 6489.5 339.5 16302.04 2819.291 4023.63 281.2025 138 138 138 138 3779325 644165 922614 48780 59828 14432 16091 1066 446.361 29.24127 644.22 8.0091 0 0 383 0 840.069 87.07 756.173 34.6332 659 659 659 659 30358.5 6106.5 0.110036054 0.010730286 10.25471757 -1.01092 1.010923704
2 100 100 100 100 10389.59 1533.478 5661.33 260.5739 10342 1518 5792 235 6288.58 1084.62 2884.398 209.443 115 115 115 115 1194803 176350 651053 29966 30182 4508 14976 977 436.113 36.0798 587.316 8.34049 8 0 366 0 815.077 103.9843 697.569 34.0303 652 652 652 652 10334 5426 0.037456152 0.009534518 3.928478887 -0.594224 0.594224423
3 100 100 100 100 732.375 58.7143 1100.527 12.0625 396.5 0 934.5 0 994.67 145.2768 883.692 31.7133 112 112 112 112 82026 6576 123259 1351 4739 765 3492 173 479.585 47.1257 597.685 5.72175 10 0 408.5 0 880.459 123.7963 680.5 25.67373 708 708 708 708 386.5 526 0.001400891 0.000924282 1.515652045 -0.1806 0.18059951
4 100 100 100 100 688.257 41.646 1198.283 17.0885 155 0 1005 0 1062.094 104.5275 1007.354 42.6182 113 113 113 113 77773 4706 135406 1931 4743 591 4546 194 480.114 52.7297 626.489 6.14509 39 0 439 0 864.987 132.6361 689.965 25.23387 703 703 703 703 116 566 0.000420448 0.00099457 0.422743865 0.373923 -0.373922686
5 100 100 100 100 518.388 34.6897 662.569 8.82759 53 0 337.5 0 830.055 98.9222 729.736 31.9351 116 116 116 116 60133 4024 76858 1024 4169 560 3071 217 439.616 41.526 642.952 7.51639 0 0 427 0 882.495 101.9036 717.233 30.09872 732 732 732 732 53 -89.5 0.000192101 1.76E-06 109.3230212 -2.03871 2.038711625
6 100 100 100 100 854.465 59.5 1081.167 16.35088 279.5 0 890 0 1472.503 132.2045 972.388 43.6247 114 114 114 114 97409 6783 123253 1864 11663 611 4593 195 415.906 40.1067 615.009 6.99147 0 0 367 0 833.322 103.5079 718.009 25.16951 703 703 703 703 279.5 523 0.001013063 0.000919011 1.102340793 -0.0423159 0.042315879
7 100 100 100 100 2329 204.8936 4285.39 156.8298 1566.5 81 4170.5 139.5 2519.131 265.1748 1481.46 165.5038 94 94 94 94 218926 19260 402827 14742 16873 1128 8722 1073 465.441 43.3222 601.614 7.66618 0 0 374 0 877.435 116.4039 665.04 40.3073 689 689 689 689 1566.5 3796.5 0.005677865 0.006671175 0.851104233 0.0700172 -0.070017249
8 100 100 100 100 1266.574 115.0213 2985.383 68.7872 705 0 2847 25 1574.331 178.9115 1209.062 93.7149 47 47 47 47 59529 5406 140313 3233 8218 753 5502 393 579.553 49.9374 725.042 10.53194 99 0 490 0 979.776 134.4649 813.085 47.9945 767 767 767 767 606 2357 0.00219648 0.004141699 0.530333177 0.275451 -0.275451203
9 100 100 100 100 3748.41 444.899 6042.84 287.4031 2883 194 5091 171 3353.27 549.321 4280.68 316.729 129 129 129 129 483545 57392 779527 37075 14013 2157 15535 1219 483.192 37.9669 645.256 9.26917 84 0 424 0 812.671 125.0232 704.931 45.7888 665 665 665 665 2799 4667 0.01014513 0.00820081 1.237088738 -0.0924009 0.092400853
10 100 100 100 100 1721.833 223.9259 2637.157 60.0648 1393.5 78 2359.5 0 1560.383 310.4591 1635.803 102.2977 108 108 108 108 185958 24184 284813 6487 6439 1487 10492 492 508.121 35.0897 635.415 11.55698 60 0 445 0 870.601 102.7637 679.488 48.9912 702 702 702 702 1333.5 1914.5 0.004833344 0.003364142 1.436724193 -0.157373 0.157373405
11 100 100 100 100 978.411 71.2143 1229.902 17.41964 555.5 0 873.5 0 1184.23 142.2141 1125.934 45.7103 112 112 112 112 109582 7976 137749 1951 6346 656 5528 229 505.793 50.5114 597 8.79857 34.5 0 403.5 0 888.767 195.5151 648.968 40.764 700 700 700 700 521 470 0.001888393 0.00082588 2.286523246 -0.359176 0.359175621
12 100 100 100 100 689.257 77.2478 1151.044 16.69027 156 0 781 0 1154.806 144.7379 988.253 44.108 113 113 113 113 77886 8729 130068 1886 6387 566 3751 238 517.366 47.357 583.329 6.91181 26 0 357 0 953.768 184.7418 651.868 35.3056 703 703 703 703 130 424 0.000471192 0.000745049 0.632431148 0.198987 -0.198986749
13 100 100 100 100 1552.713 233.9081 2779.621 70.8161 1177 77 2588 27 1311.697 318.167 1343.818 96.1224 87 87 87 87 135086 20350 241827 6161 5562 1509 7919 416 461.791 42.7206 592.069 6.06362 0 0 329 0 876.977 127.0919 769.291 25.52195 723 723 723 723 1177 2259 0.004266101 0.003969494 1.074721625 -0.031296 0.031295988
14 100 100 100 100 1282.66 136.4151 2085.736 57.6038 931 42 1932 0 1456.095 182.2076 1014.248 83.9737 53 53 53 53 67981 7230 110544 3053 5910 657 4421 313 487.032 40.5893 585.842 8.64295 37 0 343 0 872 120.9261 657.065 32.3325 745 745 745 745 894 1589 0.003240352 0.002792176 1.16051131 -0.0646494 0.064649377
15 100 100 100 100 555.172 58.1293 795.5 16.89655 73.5 0 456.5 0 906.931 129.3023 843.324 48.5195 116 116 116 116 64400 6743 92278 1960 4391 664 3102 268 470.772 41.3342 560.862 8.09004 18 0 318 0 837.779 126.1054 653.08 32.9939 733 733 733 733 55.5 138.5 0.000201163 0.000243371 0.826568718 0.082721 -0.082721035
16 100 100 100 100 412.434 63.2301 634.788 4.56637 0 0 377 0 738.183 141.0078 785.371 20.59901 113 113 113 113 46605 7145 71731 516 3655 718 3975 172 388.09 37.9161 523.767 7.62447 0 0 296 0 787.705 109.5466 639.251 28.64889 703 703 703 703 0 81 3.62E-06 0.000142332 0.025465414 1.59405 -1.594049259
17 100 100 100 100 1022.491 59.5 1072.436 28.72727 533.5 0 805.5 0 1263.413 133.6164 964.325 71.8179 110 110 110 110 112474 6545 117968 3160 6014 1063 5440 429 450.602 36.7008 556.4 5.60109 0 0 337 0 889.59 105.7461 653.857 23.86704 732 732 732 732 533.5 468.5 0.0019337 0.000823244 2.34887867 -0.370861 0.370860584
18 100 100 100 100 524.911 47.25 569.75 6.39286 129 0 317.5 0 915.543 124.6075 686.035 22.18406 112 112 112 112 58790 5292 63812 716 4168 653 2824 120 460.35 38.3656 567.219 3.87055 0 0 318 0 840.258 104.853 697.014 19.78824 703 703 703 703 129 -0.5 0.000467568 1.76E-06 266.0881082 -2.42503 2.425025466
19 100 100 100 100 665.096 77.0696 1157.6 21.66957 285 0 948 0 1030.117 155.8485 917.911 43.7554 115 115 115 115 76486 8863 133124 2492 5233 801 4206 184 433.316 34.9536 518.128 5.87705 0 0 283.5 0 843.26 104.3706 660.127 22.64406 732 732 732 732 285 664.5 0.001032998 0.001167653 0.884678821 0.0532144 -0.05321437
20 100 100 100 100 1757.585 199.1808 2429.66 74.5 1463 99.5 2309 25 1492.058 264.3708 1300.102 109.1492 94 94 94 94 165213 18723 228388 7003 5588 1189 7708 450 467.332 33.7039 638.685 8.75446 4.5 0 408.5 0 866.429 91.8054 722.976 31.42982 672 672 672 672 1458.5 1900.5 0.005286414 0.003339541 1.582975944 -0.199474 0.199474315

Total number of rows: 17328

Table truncated, full table size 5436 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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