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Sample GSM289186 Query DataSets for GSM289186
Status Public on Dec 13, 2008
Title FH_RDE2_14028s_smpB_LBlog_2_7DS597
Sample type mixed
 
Channel 1
Source name 14028s smpB RNA LBlog 061019
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics Salmonella typhimurium 14028s smpB mutant RNA harvested from LB log culture
Extracted molecule total RNA
Extraction protocol RNeasy kit (QIAGEN)
Label Cy3
Label protocol incorporation of Cy3-dCTP with Superscript RT and random hexamers
 
Channel 2
Source name 14028s gDNA
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics Salmonella typhimurium 14028s genomic DNA from stationary culture grown in LB at 37C with aeration
Extracted molecule genomic DNA
Extraction protocol SIGMA GenElute bacterial genomic DNA extraction
Label Cy5
Label protocol incorporation of Cy5-dCTP using Klenow enzyme and random hexamers
 
 
Hybridization protocol overnight hyb on Corning UltraGAPS slides at 42°C in 25% formamide / 5xSSC / 0.1% BSA
Scan protocol Perkin Elmer ScanArray 5000 scanner, image acquisition with ScanArray Express 3.0.1 software, spot quantification using Quantarray 3.0 software, adaptive quantification, protocol STv7S_01_051201
Description biological replicate, Date of Scan Tue Feb 27 13:46:46 2007
Data processing normalized based on total signal for each channel, background subtracted VALUE data obtained from log of normalized background subtracted ch1/ch2 signal.
 
Submission date May 16, 2008
Last update date Dec 13, 2008
Contact name Michael McClelland
E-mail(s) mcclelland.michael@gmail.com
Phone 858-336-9554
Organization name University of California, Irvine
Department Microbiology & Molecular Genetics
Street address 132 Med Surge I
City Irvine
State/province CA
ZIP/Postal code 92697
Country USA
 
Platform ID GPL6868
Series (1)
GSE11486 Transcriptional profiles of Salmonella typhimurium wt, hfq and smpB mutants in four different growth conditions

Data table header descriptions
ID_REF Number
X_LOCATION X-coordinate of spot
Y_LOCATION Y-coordinate of spot
CH1_MEAN Channel 1 mean
CH1_BKD_MEAN Channel 1 mean background
CH1_SD Channel 1 standard deviation
CH1_BKD_SD Channel 1 background standard deviation
CH1_DIAMETER Channel 1 diameter
CH1_AREA Channel 1 area
CH1_FOOTPRINT Channel 1 footprint
CH1_CIRCULARITY Channel 1 circularity
CH1_SPOT_UNIFORMITY Channel 1 spot uniformity
CH1_BKD_UNIFORMITY Channel 1 background uniformity
CH1_SIGNAL_NOISE_RATIO Channel 1 signal to noise ratio
CH1_CONFIDENCE Channel 1 confidence
CH2_MEAN Channel 2 mean
CH2_BKD_MEAN Channel 2 mean background
CH2_SD Channel 2 standard deviation
CH2_BKD_SD Channel 2 background standard deviation
CH2_DIAMETER Channel 2 diameter
CH2_AREA Channel 2 area
CH2_FOOTPRINT Channel 2 footprint
CH2_CIRCULARITY Channel 2 circularity
CH2_SPOT_UNIFORMITY Channel 2 spot uniformity
CH2_BKD_UNIFORMITY Channel 2 background uniformity
CH2_SIGNAL_NOISE_RATIO Channel 2 signal to noise ratio
CH2_CONFIDENCE Channel 2 confidence
CH1_DIAMETER_FILTER Channel 1 diameter filter
CH1_AREA_FILTER Channel 1 area filter
CH1_CIRCULARITY_FILTER Channel 1 circularity filter
CH1_SPOT_UNIFORMITY_FILTER Channel 1 spot uniformity filter
CH1_BKD_UNIFORMITY_FILTER Channel 1 background uniformity filter
CH1_SIGNAL_NOISE_RATIO_FILTER Channel 1 signal to noise ratio filter
CH2_DIAMETER_FILTER Channel 2 diameter filter
CH2_AREA_FILTER Channel 2 area filter
CH2_CIRCULARITY_FILTER Channel 2 circularity filter
CH2_SPOT_UNIFORMITY_FILTER Channel 2 spot uniformity filter
CH2_BKD_UNIFORMITY_FILTER Channel 2 background uniformity filter
CH2_SIGNAL_NOISE_RATIO_FILTER Channel 2 signal to noise ratio filter
IGNORE_FILTER Ignore filter
CH1_BKD_CORR Channel 1 background correlation
CH2_BKD_CORR Channel 2 background correlation
CH1%_OF_TOTAL Channel 1 % of total
CH2%_OF_TOTAL Channel 2 % of total
PRE-VALUE ch1 % of total / ch2 % of total
VALUE log10 of ch1 % of total / ch2 % of total

Data table
ID_REF X_LOCATION Y_LOCATION CH1_MEAN CH1_BKD_MEAN CH1_SD CH1_BKD_SD CH1_DIAMETER CH1_AREA CH1_FOOTPRINT CH1_CIRCULARITY CH1_SPOT_UNIFORMITY CH1_BKD_UNIFORMITY CH1_SIGNAL_NOISE_RATIO CH1_CONFIDENCE CH2_MEAN CH2_BKD_MEAN CH2_SD CH2_BKD_SD CH2_DIAMETER CH2_AREA CH2_FOOTPRINT CH2_CIRCULARITY CH2_SPOT_UNIFORMITY CH2_BKD_UNIFORMITY CH2_SIGNAL_NOISE_RATIO CH2_CONFIDENCE CH1_DIAMETER_FILTER CH1_AREA_FILTER CH1_CIRCULARITY_FILTER CH1_SPOT_UNIFORMITY_FILTER CH1_BKD_UNIFORMITY_FILTER CH1_SIGNAL_NOISE_RATIO_FILTER CH2_DIAMETER_FILTER CH2_AREA_FILTER CH2_CIRCULARITY_FILTER CH2_SPOT_UNIFORMITY_FILTER CH2_BKD_UNIFORMITY_FILTER CH2_SIGNAL_NOISE_RATIO_FILTER IGNORE_FILTER CH1_BKD_CORR CH2_BKD_CORR CH1%_OF_TOTAL CH2%_OF_TOTAL PRE-VALUE VALUE
1 2650 2510 2531 167 1305.7948 342.251495 95.078926 7700 60.811749 0.950954 0.963753 0.991402 7.395147 0.893562 5789 0 1964.049316 246.974167 97.066856 8100 60.811749 0.97046 0.934204 0.992783 23.439698 0.956136 1 1 1 1 1 1 1 1 1 1 1 1 1 2364 5789 0.028665511 0.004347948 6.592883101 0.819075375
2 2880 2510 739 148 441.485321 292.713806 90.972847 5700 56.887829 0.917003 0.987457 0.99173 2.52465 0.67324 18910 0 6242.258301 163.291641 96.408768 8000 56.887829 0.963834 0.815422 0.99472 115.80507 0.876948 1 1 1 1 1 0 1 1 1 1 1 1 1 591 18910 0.007166378 0.014202745 0.504576947 -0.297072595
3 3120 2510 702 175 351.759857 294.256958 88.129242 3100 60.811749 0.918959 0.99054 0.991806 2.38567 0.636179 7933 0 2258.634033 193.610626 97.066856 8100 60.811749 0.97046 0.917046 0.996529 40.973991 0.944697 1 1 1 1 1 0 1 1 1 1 1 1 1 527 7933 0.006390323 0.005958243 1.072518059 0.030404614
4 3350 2520 472 50 296.170654 253.109253 92.361824 6500 51.06287 0.923048 0.991035 0.993904 1.864807 0.497282 11690 0 2805.365967 181.595657 97.066856 8100 51.06287 0.97046 0.899918 0.994675 64.373786 0.933278 1 1 1 1 1 0 1 1 1 1 1 1 1 422 11690 0.005117109 0.008780015 0.582813218 -0.234470608
5 3590 2520 625 209 198.893204 287.440033 84.44017 1900 55.400902 0.881283 0.99411 0.992195 2.174367 0.579831 4073 0 1994.483032 216.029785 95.078926 8000 55.400902 0.950954 0.924141 0.993202 18.853882 0.949427 1 0 1 1 1 0 1 1 1 1 1 1 1 416 4073 0.005044354 0.003059111 1.648960959 0.217210373
6 3820 2530 733 172 335.471497 417.442505 90.27034 4100 46.675564 0.927562 0.990562 0.987587 1.75593 0.468248 6282 0 2410.462402 139.498413 97.066856 8100 46.675564 0.97046 0.920395 0.996468 45.03277 0.94693 1 1 1 1 1 0 1 1 1 1 1 1 1 561 6282 0.006802602 0.004718226 1.441771319 0.158896382
7 4060 2530 1150 312 356.025543 384.487579 77.768173 2700 51.385323 0.838364 0.990211 0.990128 2.990994 0.797598 20915 0 6284.242676 141.803543 97.066856 8100 51.385323 0.97046 0.811905 0.996346 147.492789 0.874603 1 1 1 1 1 0 1 1 1 1 1 1 1 838 20915 0.010161463 0.015708642 0.646870882 -0.189182398
8 4290 2550 760 180 417.237091 340.246552 88.129242 4400 43.829109 0.886543 0.987404 0.989311 2.233674 0.595647 18815 0 4869.346191 101.602745 97.066856 8100 43.829109 0.97046 0.831741 0.997688 185.182005 0.887828 1 1 1 1 1 0 1 1 1 1 1 1 1 580 18815 0.007032993 0.014131394 0.49768577 -0.303044776
9 4530 2540 5959 360 1804.623901 378.148773 91.669968 7200 49.108479 0.931648 0.9356 0.990501 15.758348 0.943688 14195 0 4455.18457 223.352264 95.078926 8000 49.108479 0.950954 0.858704 0.994125 63.554314 0.905802 1 1 1 1 1 1 1 1 1 1 1 1 1 5599 14195 0.067892639 0.010661447 6.36805086 0.804006523
10 4760 2550 1168 337 427.057892 349.170624 89.562332 4800 43.829109 0.910896 0.982819 0.990189 3.345069 0.812912 14890 0 2800.851318 195.756546 97.066856 8100 43.829109 0.97046 0.896255 0.995453 76.063868 0.930837 1 1 1 1 1 1 1 1 1 1 1 1 1 831 14890 0.010076582 0.011183441 0.901026945 -0.045262221
11 5000 2550 1121 327 285.121063 379.806458 85.190765 2700 48.814281 0.892549 0.991623 0.990105 2.951503 0.787068 2543 0 1107.50415 260.420593 97.066856 8100 48.814281 0.97046 0.963348 0.992943 9.764973 0.915002 1 1 1 1 1 0 1 1 1 1 1 1 1 794 2543 0.009627926 0.001909973 5.040871131 0.702505595
12 5230 2550 1287 444 510.147644 423.989777 81.75885 2300 43.829109 0.861403 0.983192 0.987198 3.035451 0.801408 5115 0 1877.882324 202.817978 97.066856 8100 43.829109 0.97046 0.945747 0.994118 25.219658 0.963262 1 1 1 1 1 1 1 1 1 1 1 1 1 843 5115 0.010222092 0.003841726 2.660807091 0.425013389
13 5470 2560 969 178 505.146637 318.287659 93.048538 6100 50.537369 0.930384 0.98587 0.99128 3.044416 0.801761 18932 0 2719.151855 211.688889 97.066856 8100 50.537369 0.97046 0.882523 0.994858 89.433131 0.921682 1 1 1 1 1 1 1 1 1 1 1 1 1 791 18932 0.009591548 0.014219269 0.674545797 -0.17098856
14 5700 2560 895 251 224.799423 288.843811 84.816299 3700 45.740379 0.875413 0.994171 0.992004 3.09856 0.803866 24258 0 3222.315918 154.502136 97.066856 8100 45.740379 0.97046 0.887756 0.995262 157.007538 0.925171 1 1 1 1 1 1 1 1 1 1 1 1 1 644 24258 0.007809048 0.018219471 0.428610029 -0.367937672
15 5940 2570 863 237 305.441223 370.154694 94.406982 5100 54.085274 0.943981 0.991631 0.989647 2.331458 0.621722 19640 0 3170.390869 123.972916 97.066856 8100 54.085274 0.97046 0.863571 0.996407 158.4217 0.909047 1 1 1 1 1 0 1 1 1 1 1 1 1 626 19640 0.007590783 0.014751027 0.514593507 -0.288535698
16 6170 2570 760 216 327.590485 360.659149 87.767311 3400 49.632385 0.8973 0.990417 0.989136 2.107253 0.561934 18524 0 3817.34375 147.314911 97.066856 8100 49.632385 0.97046 0.865845 0.995728 125.74423 0.910563 1 1 1 1 1 0 1 1 1 1 1 1 1 544 18524 0.006596463 0.013912832 0.474127974 -0.32410442
17 6410 2580 834 155 441.533569 313.793213 85.934807 5400 59.130436 0.891524 0.987556 0.991112 2.657801 0.708747 10810 0 3254.420898 280.147644 97.066856 8100 59.130436 0.97046 0.876343 0.992485 38.586796 0.917562 1 1 1 1 1 0 1 1 1 1 1 1 1 679 10810 0.008233453 0.008119073 1.014087742 0.006075533
18 6640 2580 826 225 226.662491 281.476135 76.113342 2000 55.086887 0.880974 0.993446 0.992928 2.934529 0.782541 8536 0 2691.338867 160.906586 97.066856 8100 55.086887 0.97046 0.910614 0.995346 53.049414 0.940409 1 1 1 1 1 0 1 1 1 1 1 1 1 601 8536 0.007287636 0.006411139 1.13671481 0.055651518
19 6880 2590 830 134 521.70697 289.433594 93.048538 6200 65.326866 0.929679 0.985443 0.991684 2.86767 0.764712 25133 0 4690.764648 198.134674 97.066856 8100 65.326866 0.97046 0.803818 0.994675 126.848065 0.869212 1 1 1 1 1 0 1 1 1 1 1 1 1 696 25133 0.008439592 0.018876658 0.447091446 -0.349603639
20 2640 2740 749 178 335.536987 265.083435 90.972847 3400 56.690266 0.909127 0.990761 0.992584 2.825525 0.753473 21269 0 3986.310547 183.70874 97.066856 8100 56.690266 0.97046 0.795715 0.995323 115.775656 0.86381 1 1 1 1 1 0 1 1 1 1 1 1 1 571 21269 0.006923861 0.015974521 0.433431519 -0.36307951

Total number of rows: 17328

Table truncated, full table size 5014 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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