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Sample GSM98720 Query DataSets for GSM98720
Status Public on Mar 06, 2006
Title EC18n180 RpoH 10 min Time course 1
Sample type RNA
 
Channel 1
Source name Wild type control (10 min)
Organism Escherichia coli
Characteristics MG1655 PhtpG::lacZ delta lacX74/ptrc99A (control vector)
Treatment protocol At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 10 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 RpoH induced (10 min)
Organism Escherichia coli
Characteristics MG1655 PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)
Treatment protocol At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 10 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 vs RpoH (Sigma 32) 10 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 Mar 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)
GSE4321 Time course analysis of genes regulated by E. coli sigma 32 (rpoH) after overexpression

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))
X
Y
Dia.
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 X Y Dia. 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 2490 18460 90 1717 1756 638 242 265 171 100 98 0 1468 1545 621 156 177 71 100 100 0 1.124 1.090 1.031 1.113 1.693 1.085 0.733 52 366 2787 2903 0.169 1475 1312 1514 1389 0
1_1_2 null null null 2700 18460 90 323 343 130 249 262 119 38 11 0 275 337 178 150 169 67 69 48 0 0.592 0.503 0.683 0.666 2.995 1.216 0.251 52 321 199 281 -0.756 74 125 94 187 0
1_1_3 null null null 2870 18490 150 235 373 1248 247 271 126 14 6 0 169 221 160 161 178 65 25 12 0 -1.500 2.100 1.730 1.702 4.748 15.723 0.076 156 971 -4 186 Error -12 8 126 60 -50
1_1_4 null null null 3110 18470 80 1051 1450 1135 257 275 107 100 98 0 957 1274 888 171 184 55 100 100 0 1.010 1.082 1.065 1.019 1.798 1.210 0.813 52 283 1580 2296 0.015 794 786 1193 1103 0
1_1_5 null null null 3290 18490 150 231 239 72 239 255 99 10 0 0 165 174 47 162 174 59 12 3 0 -2.667 0.000 1.756 1.884 4.139 7.570 0.053 156 879 -5 12 Error -8 3 0 12 -50
1_1_6 null null null 3500 18490 150 250 263 85 242 255 86 20 5 0 167 183 58 163 169 39 20 14 0 2.000 1.050 1.875 1.920 4.578 5.304 0.070 156 987 12 41 1.000 8 4 21 20 -50
1_1_7 null null null 3730 18470 90 2211 2461 1329 234 241 81 100 100 0 2207 2486 1447 157 165 41 100 98 0 0.964 0.956 0.940 1.027 2.048 0.937 0.840 52 384 4027 4556 -0.052 1977 2050 2227 2329 0
1_1_8 null null null 3940 18480 80 2098 1964 890 232 240 82 100 100 0 2137 2134 911 165 169 35 100 98 0 0.946 0.880 0.932 0.893 1.605 0.905 0.822 52 320 3838 3701 -0.080 1866 1972 1732 1969 0
1_1_9 null null null 4140 18480 80 1998 2242 1023 242 253 85 98 96 0 2046 2350 1017 161 169 38 100 100 0 0.932 0.914 0.875 0.847 1.774 0.924 0.858 52 320 3641 4189 -0.102 1756 1885 2000 2189 0
1_1_10 null null null 4350 18480 80 1968 2278 1035 252 300 531 96 84 0 2097 2435 1195 170 184 58 100 100 0 0.891 0.894 0.873 0.919 1.708 0.872 0.810 52 314 3643 4291 -0.167 1716 1927 2026 2265 0
1_1_11 null null null 4550 18490 150 254 265 102 254 265 106 14 2 0 177 208 86 168 177 45 29 21 0 0.000 0.275 1.864 1.841 4.302 2.849 0.157 156 975 9 51 Error 0 9 11 40 -50
1_1_12 null null null 4760 18500 150 253 265 96 239 250 85 26 3 0 173 180 38 165 169 34 27 7 0 1.750 1.733 2.358 2.541 3.982 18.378 0.014 156 994 22 41 0.807 14 8 26 15 -50
1_1_13 null null null 4980 18480 80 1379 1365 606 236 252 83 100 96 0 1403 1374 716 166 172 32 100 100 0 0.924 0.935 0.974 0.994 1.621 0.890 0.734 52 320 2380 2337 -0.114 1143 1237 1129 1208 0
1_1_14 null null null 5190 18490 90 1336 1319 559 253 262 88 100 96 0 1404 1325 530 165 172 37 98 98 0 0.874 0.919 0.908 0.927 2.037 0.986 0.749 52 412 2322 2226 -0.194 1083 1239 1066 1160 0
1_1_15 null null null 5400 18480 80 1147 1210 475 231 248 92 100 98 0 1281 1205 559 156 161 34 100 98 0 0.814 0.933 0.966 1.004 1.966 0.897 0.798 52 320 2041 2028 -0.297 916 1125 979 1049 0
1_1_16 null null null 5610 18480 90 1370 1447 554 231 240 100 100 96 0 1310 1327 657 155 161 61 100 92 0 0.986 1.038 1.062 1.159 1.968 0.969 0.848 52 377 2294 2388 -0.020 1139 1155 1216 1172 0
1_1_17 null null null 5800 18500 150 241 241 75 230 237 84 14 3 0 163 168 34 152 157 44 16 4 0 1.000 0.688 2.257 2.099 4.150 17.101 0.018 156 958 22 27 0.000 11 11 11 16 -50
1_1_18 null null null 6010 18500 150 205 217 65 225 232 72 10 1 0 152 156 26 151 154 26 17 5 0 -20.000 -1.600 3.171 2.714 3.735 1899.092 0.000 156 918 -19 -3 Error -20 1 -8 5 -50
1_1_19 null null null 6220 18500 150 280 418 321 222 228 74 46 32 0 180 366 341 150 153 26 51 42 0 1.933 0.907 1.223 1.271 3.481 0.980 0.642 156 913 88 412 0.951 58 30 196 216 -50
1_1_20 null null null 6430 18500 150 269 364 249 223 229 71 42 30 0 174 295 230 148 150 24 50 40 0 1.769 0.959 1.494 1.772 3.668 1.204 0.557 156 1064 72 288 0.823 46 26 141 147 -50

Total number of rows: 6400

Table truncated, full table size 1279 Kbytes.




Supplementary data files not provided
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