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Sample GSM116025 Query DataSets for GSM116025
Status Public on Sep 01, 2006
Title Aerobic NO exposed Chemostat Comparison of Wt & norR mutant, Run 1 dye swap
Sample type RNA
 
Channel 1
Source Name aerobic norR::Tn5 mutant experiment samples in presence of 10 uM each of NOC-5 and NOC-7 for 5 minutes
Organism(s) Escherichia coli
Characteristics Strain MG1655, norR::Tn5
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source Name aerobic wild type experiment samples in presence of 10 uM each of NOC-5 and NOC-7 for 5 minutes
Organism(s) Escherichia coli
Characteristics Wild Type Strain MG1655
Extracted molecule total RNA
Label Cy5
 
 
Description Escherichia coli strains MG1655 and an isogenic norR::Tn5 mutant were grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions.. Cells were grown in defined media containing 8 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.1 h-1. For aerobic growth, the air-flow rate was 1 l/min, and the dissolved oxygen tension was maintained at 40% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbe® electrode and automated adjustment of stirring rate. Cells were grown as above to steady-state, At steady-state, NOC-5 and NOC-7 was added to the chemostat culture and to the nutrient feed at a final concentration of 10 uM of each unless stated otherwise. Samples were taken after a period of 5 min exposure to NOC for subsequent analysis using microarrays. Cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.
Data processing background correction, log2 transformation and Loess normalisation were performed using Genesight 4.1 software, copyright BioDiscovery
 
Submission date Jun 23, 2006
Contact name Robert Poole
E-mail(s) R.poole@shef.ac.uk
Phone 01142224447
Organization name University of Sheffield
Department Molecular Biology & Biotechnology
Street address Firth Court, Western Bank
City Sheffield
State/province South Yorkshire
ZIP/Postal code S10 2TN
Country United Kingdom
 
Platform ID GPL534
Series (2)
GSE5098 Aerobic and anaerobic transcriptional responses of wild type, hmp and norR to strains to NO in a chemostat
GSE5137 Aerobic NO-exposed Chemostat Comparison of Wt & norR mutant Responses

Data table header descriptions
ID_REF
VALUE test:reference ratio following background correction, log2 transformation, Loess normalisation
CH1_MEAN Mean data in Cy3 Channel
CH1_BKD_MEAN Background Mean in Cy3 Channel
CH1_AREA Spot Area in Cy3 Channel
CH1_BKD_AREA Background Area in Cy3 Channel
CH1_RAW Raw signal output data obtained from image analysis algorithm Cy3 Channel
CH1_BKD_RAW Raw background output data obtained from image analysis algorithm in Cy3 Channel
CH1_SD Standard Deviation obtained in Cy3 Channel
CH1_BKD_SD Background Standard Deviation in Cy3 Channel
CH2_MEAN Mean data in Cy5 Channel
CH2_BKD_MEAN Background Mean in Cy5 Channel
CH2_AREA Spot Area in Cy5 Channel
CH2_BKD_AREA Background Area in Cy5 Channel
CH2_RAW Raw signal output data obtained from image analysis algorithm in Cy5 Channel
CH2_BKD_RAW Raw background output data obtained from image analysis algorithm in Cy5 Channel
CH2_SD Standard Deviation obtained in Cy5 Channel
CH2_BKD_SD Background Standard Deviation in Cy5 Channel

Data table
ID_REF VALUE CH1_MEAN CH1_BKD_MEAN CH1_AREA CH1_BKD_AREA CH1_RAW CH1_BKD_RAW CH1_SD CH1_BKD_SD CH2_MEAN CH2_BKD_MEAN CH2_AREA CH2_BKD_AREA CH2_RAW CH2_BKD_RAW CH2_SD CH2_BKD_SD
1.1.1.1 1.145672191 1705.541176 490.0373134 85 536 144971 262660 561.9168361 339.1213715 646.6136364 464.1471136 88 537 56902 249247 420.9291787 322.2445703
1.1.1.2 938.3239437 419.7113402 71 582 66621 244272 332.9323314 261.153993 425.9545455 334.6388416 88 587 37484 196433 341.8324918 260.9892576
1.1.1.3 1.137995649 1441.776119 477.3453947 67 608 96599 290226 462.0997121 325.8355592 577.8103448 432.375 58 616 33513 266343 352.7231237 339.3673267
1.1.1.4 0.982775798 1529.634921 401.2916667 63 600 96367 240775 497.2857216 278.5496244 711.0833333 521.9577236 60 615 42665 321004 321.8879873 354.7291854
1.1.1.5 1537.795918 486.4824121 49 597 75352 290430 536.3671443 350.8689072 805.9333333 418.153719 45 605 36267 252983 502.5553988 316.121236
1.1.1.6 2293.4 394.7737643 70 526 160538 207651 869.3315724 289.6816861 1130.016393 400.0879541 61 523 68931 209246 465.1419488 296.8220458
1.1.1.7 -0.750558086 5760.348315 418.5172956 89 636 512671 266177 2357.752086 288.8497978 7169.817073 437.1679627 82 643 587925 281099 2949.67508 340.9129219
1.1.1.8 0.14943069 684.9266055 393.1608133 109 541 74657 212700 455.4233983 265.663613 532.5636364 400.3740741 110 540 58582 216202 318.416609 277.8800715
1.1.1.9 2105.260274 423.0534224 73 599 153684 253409 692.9677299 343.7225176 2804.232877 400.0367279 73 599 204709 239622 880.6915639 299.9419176
1.1.1.10 0.369698463 4337.369565 427.3196721 92 610 399038 260665 1586.818657 314.2885556 2565.170455 409.1074919 88 614 225735 251192 740.8509576 332.9451318
1.1.1.11 0.639449536 4120.405405 468.3971223 74 695 304910 325536 1174.687399 328.3584381 2059.594595 411.3660969 74 702 152410 288779 693.4936411 305.7413318
1.1.1.12 -1.606948659 1262.244444 658.5107438 45 605 56801 398399 950.3901457 850.783638 1273.733333 629.6743802 45 605 57318 380953 1098.744706 749.1622967
1.1.1.13 -1.657707555 1086.8 472.4213382 45 553 48906 261249 564.8661434 423.0806053 1164.911111 461.5804702 45 553 52421 255254 812.2207369 395.1817095
1.1.1.14 -0.378918695 5052.333333 451.960452 93 531 469867 239991 2309.73743 289.9882138 4954.426829 435.8265683 82 542 406263 236218 1854.662885 345.2899677
1.1.1.15 -0.429411622 10977.53704 513.3625731 162 513 1778361 263355 5517.682786 368.9056007 10982.41611 497.2357414 149 526 1636380 261546 4422.86251 420.0349405
1.1.1.16 1104.589286 391.8732877 56 584 61857 228854 454.9446111 270.9078554 1188.888889 408.6038035 45 631 53500 257829 825.8593429 310.6044691
1.1.1.17 -0.2643221 1303.444444 516.0991736 45 605 58655 312240 930.9276032 370.3090468 747.6363636 441.6727273 44 605 32896 267212 389.7766896 357.4602173
1.1.1.18 0.020260533 1319.488889 554.1329879 45 579 59377 320843 935.0824473 555.0910003 716.3777778 468.2694301 45 579 32237 271128 529.7237137 369.6015872
1.1.2.1 -1.037065479 9590.380952 505.3141153 147 503 1409786 254173 4921.735257 342.5441312 14339.93985 520.2765957 133 517 1907212 268983 5693.013513 438.0418787
1.1.2.2 1913.1875 450.8392555 80 591 153055 266446 704.1879027 305.2900253 1767.014286 413.1735537 70 605 123691 249970 540.3349621 322.7609324

Total number of rows: 4608

Table truncated, full table size 689 Kbytes.




Supplementary data files not provided
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