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Sample GSM98723 Query DataSets for GSM98723
Status Public on Mar 06, 2006
Title EC18n168 RpoH 2.5 min Time course 2
Sample type RNA
 
Channel 1
Source name Wild type control (2.5 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 2.5 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 (2.5 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 2.5 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) 2.5 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 2630 18270 100 572 694 383 83 86 19 100 100 0 605 744 395 121 122 14 100 100 0 1.010 0.981 0.982 1.013 1.443 0.970 0.927 80 524 973 1234 0.015 489 484 611 623 0
1_1_2 null null null 2830 18260 150 120 159 100 89 95 31 49 33 0 152 235 168 129 132 22 50 41 0 1.348 0.660 0.843 1.049 3.234 0.594 0.565 156 1044 54 176 0.431 31 23 70 106 -50
1_1_3 null null null 3060 18260 90 198 226 107 90 94 23 88 80 0 270 314 141 129 131 20 98 94 0 0.766 0.735 0.779 0.709 2.057 0.656 0.710 52 412 249 321 -0.385 108 141 136 185 0
1_1_4 null null null 3250 18260 90 329 484 307 76 77 15 100 100 0 385 566 333 119 119 15 100 100 0 0.951 0.913 0.906 0.897 1.327 0.881 0.929 52 406 519 855 -0.072 253 266 408 447 0
1_1_5 null null null 3480 18270 90 118 131 61 71 72 12 82 73 0 167 197 82 110 110 13 100 80 0 0.825 0.690 0.732 0.633 2.265 0.673 0.718 52 384 104 147 -0.278 47 57 60 87 0
1_1_6 null null null 3670 18260 150 78 82 20 73 75 14 29 15 0 116 123 26 111 112 14 31 19 0 1.000 0.750 0.778 0.761 3.308 0.759 0.112 156 1017 10 21 0.000 5 5 9 12 -50
1_1_7 null null null 3890 18270 100 921 1103 553 75 76 14 100 100 0 1180 1265 544 114 114 14 100 100 0 0.794 0.893 0.909 0.863 1.431 0.919 0.910 80 534 1912 2179 -0.333 846 1066 1028 1151 0
1_1_8 null null null 4100 18270 100 790 927 555 74 76 14 100 100 0 923 1051 573 111 113 13 100 100 0 0.882 0.907 0.928 0.891 1.443 0.922 0.919 80 542 1528 1793 -0.182 716 812 853 940 0
1_1_9 null null null 4310 18270 100 775 1029 671 75 77 14 100 100 0 925 1170 720 110 112 14 98 98 0 0.859 0.900 0.883 0.906 1.465 0.907 0.919 80 548 1515 2014 -0.219 700 815 954 1060 0
1_1_10 null null null 4520 18270 100 1024 1130 635 75 77 14 100 100 0 1030 1269 723 111 112 14 100 100 0 1.033 0.911 0.946 0.948 1.455 0.892 0.900 80 512 1868 2213 0.046 949 919 1055 1158 0
1_1_11 null null null 4720 18270 150 86 105 50 77 79 15 41 33 0 129 159 66 116 118 16 44 33 0 0.692 0.651 0.947 0.875 2.871 0.679 0.560 156 965 22 71 -0.531 9 13 28 43 -50
1_1_12 null null null 4930 18270 150 80 84 22 75 77 14 32 15 0 128 133 24 114 115 16 42 21 0 0.357 0.474 0.875 0.908 2.889 0.644 0.110 156 974 19 28 -1.485 5 14 9 19 -50
1_1_13 null null null 5150 18260 100 463 551 356 76 77 14 100 98 0 532 652 445 112 114 15 100 97 0 0.921 0.880 0.905 0.938 1.681 0.834 0.910 80 538 807 1015 -0.118 387 420 475 540 0
1_1_14 null null null 5360 18270 90 530 689 437 81 82 16 100 100 0 587 767 479 119 119 15 100 100 0 0.959 0.938 0.902 0.942 1.257 0.917 0.936 52 420 917 1256 -0.060 449 468 608 648 0
1_1_15 null null null 5570 18260 90 591 654 265 81 84 17 100 100 0 674 742 326 121 122 19 100 100 0 0.922 0.923 0.939 0.960 1.402 0.879 0.907 52 412 1063 1194 -0.117 510 553 573 621 0
1_1_16 null null null 5780 18270 100 492 567 296 79 80 15 100 100 0 579 662 349 119 120 14 100 100 0 0.898 0.899 0.929 0.908 1.602 0.875 0.917 80 524 873 1031 -0.155 413 460 488 543 0
1_1_17 null null null 5980 18270 150 81 86 24 77 78 15 28 12 0 120 126 27 116 117 22 17 10 0 1.000 0.900 0.925 0.933 3.287 0.399 0.183 156 964 8 19 0.000 4 4 9 10 -50
1_1_18 null null null 6190 18270 150 82 84 20 76 78 16 26 10 0 116 122 26 114 115 23 17 7 0 3.000 1.000 1.043 0.940 3.478 0.902 0.157 156 912 8 16 1.585 6 2 8 8 -50
1_1_19 null null null 6400 18270 150 111 199 199 76 78 16 63 51 0 147 265 237 113 115 16 65 50 0 1.029 0.809 0.780 0.806 2.314 0.824 0.902 156 912 69 275 0.042 35 34 123 152 -50
1_1_20 null null null 6610 18270 150 94 171 189 75 76 14 55 41 0 144 235 214 112 113 14 60 51 0 0.594 0.780 0.762 0.780 2.681 0.856 0.891 156 1062 51 219 -0.752 19 32 96 123 -50

Total number of rows: 6400

Table truncated, full table size 1263 Kbytes.




Supplementary data files not provided
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