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Sample GSM38547 Query DataSets for GSM38547
Status Public on Apr 06, 2005
Title Anaerobic GSNO Chemostat Run 1 Dye Swap
Sample type RNA
 
Channel 1
Source name Steady-state continuous cultured experiment samples in presence of 200uM GSNO for 5 minutes
Organism Escherichia coli
Extracted molecule total RNA
 
Channel 2
Source name Steady-state continuous cultured control samples in absence of GSNO
Organism Escherichia coli
Extracted molecule total RNA
 
 
Description Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 54 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.2 h-1. In order to establish anaerobic growth, nitrogen was sparged through the chemostat medium prior to inoculation and throughout the course of the experiment at a rate of 0.2 l/min. No dissolved oxygen was detectable using the OxyProbe. Sodium fumarate was added to anaerobic medium at a final concentration of 50 mM to act as a terminal electron acceptor. Cells were grown as above to steady-state, At steady-state, GSNO was added to the chemostat culture and to the nutrient feed at a final concentration of 200 uM unless otherwise stated. Samples were taken immediately prior to the addition of GSNO and after a period of 5 min exposure to GSNO 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.
 
Submission date Jan 06, 2005
Last update date Oct 28, 2005
Contact name Jason Barrett
E-mail(s) J.A.Barrett@sheffield.ac.uk
Phone (+44) 114 2222834
Organization name University of Sheffield
Department Department of Molecular Biology and 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 (1)
GSE2129 Transcriptional responses of Anaerobically grown Escherichia coli to GSNO under defined chemostat conditions.

Data table header descriptions
ID_REF
VALUE Cy3:Cy5 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 in 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 -0.375008143 177.4716981 185.7207792 106 462 18812 85803 61.67416014 72.25955771 203.2018349 207.261242 109 467 22149 96791 138.574246 142.6919844
1.1.1.2 -0.812090859 279.6574074 165.5386905 216 336 60406 55621 103.3917095 77.58535041 323.9444444 221.5267857 216 336 69972 74433 173.8379585 145.0689261
1.1.1.3 -0.181603517 661.025641 183.4263566 234 387 154680 70986 221.1942319 75.13276193 839.8654709 213.2910448 223 402 187290 85743 309.0038237 143.9757524
1.1.1.4 -0.255815735 530.457265 191.2244898 234 392 124127 74960 132.0564188 71.71727806 685.6680498 228.7938144 241 388 165246 88772 291.3289442 159.1161923
1.1.1.5 -1.572714487 245.4673913 156.8521303 276 399 67749 62584 85.91546035 73.09756373 390.237037 253.7057292 270 384 105364 97423 294.7542531 207.2582411
1.1.1.6 -1.079774678 453.9178082 161.6651982 146 454 66272 73396 125.2800975 79.83172156 923.8321168 213.9934641 137 459 126565 98223 326.6035247 149.8811656
1.1.1.7 0.352329223 4419.949541 167.1815789 218 380 963549 63529 1842.073954 88.19300711 4278.365979 242.7871287 194 404 830003 98086 1398.587153 191.452523
1.1.1.8 0.083748114 181.1672131 147.7847534 305 223 55256 32956 67.93585384 45.93979625 177.0622951 178.6531532 305 222 54004 39661 129.9693257 122.3609027
1.1.1.9 0.07038147 528.4466019 163.8515982 206 438 108860 71767 156.4617406 65.59651389 568.372093 177.1891304 172 460 97760 81507 248.4350576 133.1682374
1.1.1.10 -1.509834922 826.4506173 159.1564885 162 524 133885 83398 226.4485621 68.92336113 2573.891566 202.9307116 166 534 427266 108365 844.7558428 143.109361
1.1.1.11 -1.526814146 483.5177305 147.1119134 141 554 68176 81500 147.2206142 59.25057025 1328.496241 203.5273369 133 567 176690 115400 506.5751527 134.5060421
1.1.1.12 -0.688752549 341.739726 144.9293362 146 467 49894 67682 79.46387607 58.20267822 531.9174312 198.3578529 109 503 57979 99774 197.6634675 131.8721411
1.1.1.13 0.155079969 409.6153846 142.2755682 273 352 111825 50081 123.000977 49.62158707 452.5287958 194.8525346 191 434 86433 84566 184.4852126 137.0228929
1.1.1.14 -0.561078429 811.7005348 141.9487179 187 507 151788 71968 247.4914273 53.78712271 1378.649718 201.2237094 177 523 244021 105240 477.1857251 146.3539466
1.1.1.15 -0.531405595 1094.988235 143.6466667 170 450 186148 64641 389.0686767 55.94502897 1922.125 203.9957627 152 472 292163 96286 609.277779 136.5518775
1.1.1.16 0.796979173 411.3655172 130.5536842 145 475 59648 62013 122.9908218 52.96706784 325.4551724 203.0753138 145 478 47191 97070 162.650248 130.8982109
1.1.1.17 0.519705359 308.8550725 185.2120344 276 349 85244 64639 122.7704085 156.2822763 300.0144928 263.9799427 276 349 82804 92129 163.8241141 209.6217282
1.1.1.18 -0.546635031 328.0705128 142.1861386 156 505 51179 71804 92.52858963 52.0235762 421.8507463 189.3497053 134 509 56528 96379 161.9810431 113.5834577
1.1.2.1 -0.799465534 2256.924419 208.4456067 172 478 388191 99637 934.824937 83.66482849 4648.619718 290.8993135 213 437 990156 127123 3940.015679 178.9268261
1.1.2.2 0.007057588 2441.502146 175.7122302 233 417 568870 73272 925.705012 76.17513375 3042.147783 269.4787472 203 447 617556 120457 882.1199263 178.1990036

Total number of rows: 4608

Table truncated, full table size 708 Kbytes.




Supplementary data files not provided

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