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Sample GSM98732 Query DataSets for GSM98732
Status Public on Mar 06, 2006
Title EC18n122 RpoH 10 min Time course 4
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 2550 18650 90 1330 1497 897 77 79 20 100 100 0 1279 1627 952 101 103 17 98 98 0 1.064 0.931 0.904 0.977 1.985 0.936 0.941 52 377 2431 2946 0.089 1253 1178 1420 1526 0
1_1_2 null null null 2740 18670 150 87 103 55 78 79 17 38 24 0 111 128 55 100 101 16 37 26 0 0.818 0.893 0.927 1.032 2.834 0.986 0.423 156 900 20 53 -0.290 9 11 25 28 -50
1_1_3 null null null 2950 18670 150 82 89 36 77 78 16 32 12 0 105 113 36 99 101 16 33 16 0 0.833 0.857 1.000 0.916 3.344 1.048 0.183 156 940 11 26 -0.263 5 6 12 14 -50
1_1_4 null null null 3180 18660 90 833 984 690 79 80 16 98 98 0 819 1065 703 109 111 19 98 98 0 1.062 0.947 1.005 0.918 1.589 0.954 0.942 52 398 1464 1861 0.087 754 710 905 956 0
1_1_5 null null null 3380 18670 150 79 82 19 77 79 15 26 8 0 100 101 20 104 105 17 14 6 0 -0.500 -1.667 0.825 0.744 3.320 0.501 0.007 156 915 -2 2 Error 2 -4 5 -3 -50
1_1_6 null null null 3590 18670 150 81 81 18 77 79 16 22 6 0 105 107 18 100 102 18 19 3 0 0.800 0.571 1.188 1.120 4.375 1.775 0.001 156 1001 9 11 -0.322 4 5 4 7 -50
1_1_7 null null null 3810 18660 90 2682 2880 1519 80 81 17 100 100 0 2950 3067 1541 102 104 22 100 100 0 0.914 0.944 0.970 0.955 1.316 0.962 0.962 52 412 5450 5765 -0.130 2602 2848 2800 2965 0
1_1_8 null null null 4010 18660 80 2707 2578 1097 77 79 17 100 100 0 2775 2685 1065 101 103 16 100 100 0 0.984 0.968 0.976 0.999 1.451 0.981 0.955 52 332 5304 5085 -0.024 2630 2674 2501 2584 0
1_1_9 null null null 4220 18660 80 2545 2862 1712 81 83 19 100 100 0 2807 2909 1710 103 105 19 100 100 0 0.911 0.991 1.010 1.008 1.323 0.989 0.925 52 332 5168 5587 -0.134 2464 2704 2781 2806 0
1_1_10 null null null 4430 18660 90 2220 2139 953 78 80 17 100 100 0 2322 2265 1037 100 100 16 100 100 0 0.964 0.952 0.935 1.001 1.431 0.940 0.945 52 406 4364 4226 -0.053 2142 2222 2061 2165 0
1_1_11 null null null 4640 18670 150 95 117 67 79 80 17 47 31 0 114 140 74 99 100 16 47 33 0 1.067 0.927 1.000 1.077 2.979 0.909 0.603 156 996 31 79 0.093 16 15 38 41 -50
1_1_12 null null null 4850 18670 150 84 85 22 79 80 16 25 11 0 108 108 19 99 100 16 25 9 0 0.556 0.667 1.090 1.093 3.510 1.496 0.022 156 990 14 15 -0.848 5 9 6 9 -50
1_1_13 null null null 5070 18670 90 1150 1184 517 76 77 15 100 100 0 1131 1240 587 96 98 15 100 100 0 1.038 0.969 0.999 0.992 1.265 0.936 0.949 52 420 2109 2252 0.053 1074 1035 1108 1144 0
1_1_14 null null null 5280 18660 90 1051 1061 488 78 80 16 100 100 0 1195 1171 537 101 100 16 98 98 0 0.889 0.919 0.959 0.904 1.360 0.933 0.952 52 412 2067 2053 -0.169 973 1094 983 1070 0
1_1_15 null null null 5480 18660 90 956 900 471 79 79 16 100 100 0 1014 1029 543 97 99 15 100 100 0 0.956 0.881 0.929 0.914 1.399 0.877 0.930 52 412 1794 1753 -0.064 877 917 821 932 0
1_1_16 null null null 5700 18660 80 1010 1047 474 77 78 15 100 100 0 1163 1157 583 96 97 14 100 100 0 0.874 0.914 0.943 0.971 1.365 0.885 0.952 52 326 2000 2031 -0.194 933 1067 970 1061 0
1_1_17 null null null 5900 18670 150 84 85 20 78 79 17 21 8 0 105 107 20 96 98 36 9 0 0 0.667 0.636 1.000 1.190 3.791 0.185 0.135 156 984 15 18 -0.585 6 9 7 11 -50
1_1_18 null null null 6110 18670 150 82 84 18 79 81 18 16 5 0 104 106 21 101 103 36 5 1 0 1.000 1.000 0.909 0.950 4.035 0.206 0.138 156 988 6 10 0.000 3 3 5 5 -50
1_1_19 null null null 6340 18670 80 437 567 372 80 81 16 100 100 0 490 624 441 104 106 15 100 100 0 0.925 0.937 0.954 0.992 1.547 0.892 0.933 52 340 743 1007 -0.113 357 386 487 520 0
1_1_20 null null null 6540 18670 80 405 487 332 84 87 23 100 98 0 432 501 369 108 112 23 98 98 0 0.991 1.025 1.045 1.048 1.527 0.951 0.941 52 340 645 796 -0.013 321 324 403 393 0

Total number of rows: 6400

Table truncated, full table size 1262 Kbytes.




Supplementary data files not provided
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