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Sample GSM148001 Query DataSets for GSM148001
Status Public on Jan 01, 2007
Title EC18n019 hfq- rpoE overexpression 20 min
Sample type RNA
 
Channel 1
Source name hfq+ Wild type control (20 min)
Organism Escherichia coli
Characteristics MG1655 rpoHp3::lacZ delta lacX74 hfq2::omega(Km;KpnI) (hfq+)/ptrc99A (control vector)
Treatment protocol At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 20 min after induction
Growth protocol M9 minimal complete media, cultures grown aerobically at 30 degrees C in a gyratory water bath shaking at 240 rpm
Extracted molecule total RNA
Extraction protocol Culture samples for microarray analysis were added to ice-cold 5% water-saturated phenol in ethanol solution, centrifuged at 6,600 g and the cell pellets flash frozen in liquid N2 before storing at -80 degrees C until required. Total RNA was isolated from the stored cell pellets using the hot phenol method, and labeled Cy3 and Cy5 cDNA was prepared from 16 ug total RNA with 10 ug random hexamer (Integrated DNA Technologies, Inc., Coralville, IA, USA).
Label Cy3
Label protocol Indirect labeling method as described in Khodursky et al (2003; Methods Mol Biol 224:61-78)
 
Channel 2
Source name Hfq- RpoE overexpression (20 min)
Organism Escherichia coli
Characteristics MG1655 rpoHp3::lacZ delta lacX74 hfq1::omega(Km;BclI) (hfq-)/pLC245 (vector carrying inducible Ptrc::rpoE)
Treatment protocol At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 20 min after induction
Growth protocol M9 minimal complete media, cultures grown aerobically at 30 degrees C in a gyratory water bath shaking at 240 rpm
Extracted molecule total RNA
Extraction protocol Culture samples for microarray analysis were added to ice-cold 5% water-saturated phenol in ethanol solution, centrifuged at 6,600 g and the cell pellets flash frozen in liquid N2 before storing at -80 degrees C until required. Total RNA was isolated from the stored cell pellets using the hot phenol method, and labeled Cy3 and Cy5 cDNA was prepared from 16 ug total RNA with 10 ug random hexamer (Integrated DNA Technologies, Inc., Coralville, IA, USA).
Label Cy5
Label protocol Indirect labeling method as described in Khodursky et al (2003; Methods Mol Biol 224:61-78)
 
 
Hybridization protocol cDNA from 16 ug total RNA, 15 ug poly(dI-dC), 3xSSC, 25 mM Hepes (pH7), 0.225% SDS. Samples hybridized on array under a lifterslip for 12 hrs at 65 degrees C
Scan protocol Slides scanned using GenePix 4000B scanner (Axon). TIFF images analyzed using GENEPIX 3.0 software (Axon).
Description Wild type (hfq+) vs hfq- RpoE (SigmaE) 20 min after overexpression
Data processing Data filtered for PCR success, >3x local background and spot quality (GenePix Flag). Normalized using Lowess smoothing from MA plot
 
Submission date Dec 01, 2006
Last update date Dec 06, 2006
Contact name Virgil Arthur Rhodius
E-mail(s) [email protected]
Phone 1 415 476 1493
URL http://www.ucsf.edu/gross
Organization name UCSF
Department Microbiology and Immunology
Lab Gross
Street address Genentech Hall, 600 16th Street
City San Francisco
State/province CA
ZIP/Postal code 94158-2517
Country USA
 
Platform ID GPL3500
Series (1)
GSE6444 Steady-state analysis of genes regulated by the E. coli RNA chaperone, Hfq

Data table header descriptions
ID_REF
VALUE Spot R/G Expression ratio (log2-transformed and Lowess-normalized using a Lowess fit to a MA plot)
M Spot R/G Expression ratio (unnormalized). M = log2 ((F635 Median - B635)/(F532 Median - B532))
A Spot Intensity. A = log2 (sqrt(F635 Median - B635)*(F532 Median - B532))
F635 Median
F635 Mean
F635 SD
B635 Median
B635 Mean
B635 SD
% > B635+1SD
% > B635+2SD
F635 % Sat.
F532 Median
F532 Mean
F532 SD
B532 Median
B532 Mean
B532 SD
% > B532+1SD
% > B532+2SD
F532 % Sat.
Ratio of Medians
Ratio of Means
Median of Ratios
Mean of Ratios
Ratios SD
Rgn Ratio
Rgn R?
F Pixels
B Pixels
Sum of Medians
Sum of Means
Log Ratio
F635 Median - B635
F532 Median - B532
F635 Mean - B635
F532 Mean - B532
Flags

Data table
ID_REF VALUE M A F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD % > B532+1SD % > B532+2SD F532 % Sat. Ratio of Medians Ratio of Means Median of Ratios Mean of Ratios Ratios SD Rgn Ratio Rgn R? F Pixels B Pixels Sum of Medians Sum of Means Log Ratio F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 Flags
1_1_1 null null null 173 173 58 116 120 37 65 33 0 217 241 81 170 184 64 38 13 0 1.213 0.803 1.002 1.018 3.559 0.371 0.178 80 538 104 128 0.278 57 47 57 71 -50
1_1_2 null null null 141 147 44 114 116 33 40 17 0 174 178 43 171 178 44 17 5 0 9 4.714 1.035 1.149 4.896 0.788 0.032 80 540 30 40 3.17 27 3 33 7 -50
1_1_3 null null null 132 144 56 117 120 34 36 13 0 198 194 52 186 192 47 13 5 0 1.25 3.375 0.892 0.777 3.731 0.587 0.096 80 536 27 35 0.322 15 12 27 8 -50
1_1_4 null null null 210 228 102 131 135 42 75 44 0 350 365 126 215 226 61 80 53 0 0.585 0.647 0.715 0.642 2.341 0.602 0.394 52 334 214 247 -0.773 79 135 97 150 0
1_1_5 null null null 154 180 91 139 156 67 25 11 0 225 254 91 207 253 115 18 7 0 0.833 0.872 0.846 0.689 2.758 0.533 0.387 80 552 33 88 -0.263 15 18 41 47 -50
1_1_6 null null null 171 185 60 130 141 57 43 18 0 344 337 93 195 216 69 71 53 0 0.275 0.387 0.454 0.409 3.374 0.438 0.471 32 128 190 197 -1.862 41 149 55 142 0
1_1_7 null null null 504 615 411 122 143 101 87 66 0 610 706 373 177 221 172 85 57 0 0.882 0.932 0.855 0.824 1.644 1.011 0.899 80 554 815 1022 -0.181 382 433 493 529 0
1_1_8 null null null 326 347 158 112 117 31 98 90 0 446 440 165 166 166 26 94 94 0 0.764 0.858 0.916 0.836 1.773 0.88 0.754 52 332 494 509 -0.388 214 280 235 274 0
1_1_9 null null null 331 381 179 114 116 31 98 95 0 448 490 229 164 166 31 97 95 0 0.764 0.819 0.823 0.832 1.681 0.805 0.822 80 544 501 593 -0.388 217 284 267 326 0
1_1_10 null null null 363 403 169 113 115 30 97 96 0 483 505 207 163 167 36 96 95 0 0.781 0.848 0.845 0.881 1.855 0.822 0.796 80 636 570 632 -0.356 250 320 290 342 0
1_1_11 null null null 151 155 33 117 119 28 59 21 0 185 191 36 159 163 29 46 21 0 1.308 1.188 1.01 0.883 3.438 1.256 0.088 32 170 60 70 0.387 34 26 38 32 0
1_1_12 null null null 123 124 31 114 117 31 23 5 0 172 174 34 169 171 30 22 5 0 3 2 1.085 1.132 2.897 0.683 0.008 80 540 12 15 1.585 9 3 10 5 -50
1_1_13 null null null 357 405 182 116 119 30 96 92 0 404 469 235 162 163 28 96 92 0 0.996 0.941 0.996 1.035 1.733 0.86 0.856 52 420 483 596 -0.006 241 242 289 307 0
1_1_14 null null null 235 297 163 123 128 41 81 68 0 308 386 192 171 188 71 78 48 0 0.818 0.809 0.782 0.844 2.128 0.773 0.745 80 554 249 389 -0.291 112 137 174 215 0
1_1_15 null null null 437 531 347 123 123 32 96 90 0 490 563 291 165 168 28 98 98 0 0.966 1.025 1.052 0.966 1.729 1.12 0.879 52 340 639 806 -0.05 314 325 408 398 0
1_1_16 null null null 414 514 272 130 147 71 98 86 0 458 552 242 183 224 154 78 46 0 1.033 1.041 1.03 1.014 1.473 0.922 0.678 52 420 559 753 0.046 284 275 384 369 0
1_1_17 null null null 123 142 70 126 141 64 16 6 0 187 234 129 190 226 133 13 8 0 1 0.364 0.781 0.927 3.43 0.472 0.548 80 546 -6 60 0 -3 -3 16 44 -50
1_1_18 null null null 136 190 151 126 151 124 17 8 0 196 295 212 179 228 198 23 15 0 0.588 0.552 0.749 0.66 2.709 0.723 0.653 80 546 27 180 -0.766 10 17 64 116 -50
1_1_19 null null null 420 668 772 122 124 31 98 94 0 462 694 671 171 174 41 96 88 0 1.024 1.044 1.114 1.08 1.903 1.125 0.879 52 340 589 1069 0.034 298 291 546 523 0
1_1_20 null null null 274 340 196 126 152 205 37 15 0 340 412 214 178 184 39 90 71 0 0.914 0.915 0.951 1.043 2.789 0.928 0.806 32 176 310 448 -0.13 148 162 214 234 0

Total number of rows: 6400

Table truncated, full table size 1126 Kbytes.




Supplementary data files not provided
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