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Sample GSM289174 Query DataSets for GSM289174
Status Public on Dec 13, 2008
Title FH_RDE2_14028s_hfq_LBlog_1_7DS505
Sample type mixed
 
Channel 1
Source Name 14028s hfq RNA LBlog 061018
Organism(s) Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics Salmonella typhimurium 14028s hfq 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(s) 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 Nov 07 12:02:47 2006
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
Contact name Michael McClelland
E-mail(s) mcclelland.michael@gmail.com
Phone 858-450-5990
Fax 858-550-3998
Organization name Sidney Kimmel Cancer Center
Department
Street address 10835 Road to the Cure
City San Diego
State/province CA
ZIP/Postal code 92121
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 2080 1520 3925 0 1952.643677 128.232758 95.413124 7900 5.418524 0.964797 0.941101 0.996391 30.608404 0.960734 13257 0 5391.910156 227.975906 97.066856 8100 5.418524 0.97046 0.815674 0.994469 58.150882 0.877116 1 1 1 1 1 1 1 1 1 1 1 1 1 3925 13257 0.044964729 0.004243884 10.59518437 1.025108518
2 2310 1520 1156 0 701.72937 158.894333 95.078926 8000 7.494142 0.950954 0.978416 0.994537 7.275275 0.892186 35269 0 11040.11035 88.751579 97.066856 8100 7.494142 0.97046 0.62748 0.996704 397.390112 0.71712 1 1 1 1 1 1 1 1 1 0 1 1 1 1156 35269 0.013243115 0.011290453 1.172948115 0.069278802
3 2550 1520 206 0 207.81308 127.325577 89.206215 3300 5.418524 0.920439 0.99337 0.996216 1.6179 0.43144 22178 0 10554.53027 123.130798 97.066856 8100 5.418524 0.97046 0.718819 0.995972 180.117406 0.812546 1 1 1 1 1 0 1 1 1 1 1 1 1 206 22178 0.002359932 0.00709971 0.332398423 -0.478341045
4 2780 1520 155 0 244.884537 158.48465 90.622276 5500 7.494142 0.912519 0.995018 0.995369 0.978013 0.260803 22953 0 10170.81152 41.979897 97.066856 8100 7.494142 0.97046 0.716339 0.998589 546.76171 0.810893 1 1 1 1 1 0 1 1 1 1 1 1 1 155 22953 0.001775677 0.007347806 0.241660881 -0.616793645
5 3020 1520 179 0 154.23912 108.660065 80.582397 2900 5.418524 0.881908 0.996063 0.996719 1.647339 0.43929 14748 0 7514.479492 83.561371 95.078926 8000 5.418524 0.950954 0.812378 0.99762 176.493036 0.874919 1 1 1 1 1 0 1 1 1 1 1 1 1 179 14748 0.002050621 0.004721188 0.434344189 -0.362165984
6 3250 1520 325 0 377.661774 147.765259 88.848671 5800 7.494142 0.903024 0.990807 0.99649 2.199434 0.586516 10508 0 6989.102051 145.038483 94.743553 7900 7.494142 0.955337 0.819679 0.995186 72.449738 0.879786 1 1 1 1 1 0 1 1 1 1 1 1 1 325 10508 0.003723194 0.003363863 1.106821051 0.044077411
7 3490 1520 243 0 295.916382 177.319305 87.403885 4100 5.418524 0.890832 0.991089 0.994637 1.370409 0.365442 41027 0 17324.51758 82.635582 94.406982 7900 5.418524 0.943981 0.602219 0.997353 496.481044 0.68825 1 1 1 1 1 0 1 1 1 0 1 1 1 243 41027 0.002783804 0.013133727 0.211958397 -0.673749374
8 3720 1520 292 0 330.026764 302.552856 89.91703 5900 7.494142 0.922739 0.990936 0.996422 0.965121 0.257365 35790 0 11888.83398 14.827861 97.066856 8100 7.494142 0.97046 0.683632 0.999458 2413.699481 0.781294 1 1 1 1 1 0 1 1 1 0 1 1 1 292 35790 0.003345147 0.011457237 0.291968008 -0.534664733
9 3960 1530 494 0 370.308716 165.564575 91.669968 7300 4.588012 0.950327 0.990944 0.994354 2.98373 0.795661 33470 0 13677.50391 116.001961 97.066856 8100 4.588012 0.97046 0.666054 0.99688 288.529606 0.761204 1 1 1 1 1 0 1 1 1 0 1 1 1 494 33470 0.005659255 0.01071455 0.528184133 -0.27721465
10 4190 1530 552 0 505.787598 212.251099 93.048538 7300 6.917486 0.956099 0.98333 0.995956 2.600693 0.693518 29412 0 12206.11621 103.098061 97.066856 8100 6.917486 0.97046 0.705154 0.996643 285.281797 0.803436 1 1 1 1 1 0 1 1 1 1 1 1 1 552 29412 0.006323702 0.009415487 0.671627754 -0.172871366
11 4430 1530 194 0 248.522675 92.243958 86.30442 3500 4.588012 0.907422 0.993004 0.997627 2.103119 0.560832 13415 0 6940.319824 85.49485 92.016548 7700 4.588012 0.946082 0.84581 0.997322 156.910036 0.897207 1 1 1 1 1 0 1 1 1 1 1 1 1 194 13415 0.002222461 0.004294463 0.517517651 -0.286074833
12 4660 1530 287 0 311.441345 91.473579 87.03894 5600 6.917486 0.930958 0.991417 0.997246 3.137518 0.805353 15042 0 6974.641113 101.397026 97.066856 8100 6.917486 0.97046 0.806992 0.996925 148.347546 0.871328 1 1 1 1 1 1 1 1 1 1 1 1 1 287 15042 0.003287867 0.004815305 0.682795148 -0.165709574
13 4900 1530 188 0 270.412537 88.307846 82.147255 3900 4.588012 0.888863 0.991592 0.997139 2.128916 0.567711 34382 0 14172.10059 81.289146 96.408768 7900 4.588012 0.963834 0.644028 0.996956 422.959294 0.736032 1 1 1 1 1 0 1 1 1 0 1 1 1 188 34382 0.002153725 0.011006503 0.195677471 -0.708459173
14 5130 1530 192 0 248.371017 70.850777 87.767311 5100 6.917486 0.934946 0.993576 0.997803 2.709921 0.722646 41167 0 15347.10156 132.78717 97.066856 8100 6.917486 0.97046 0.561768 0.996971 310.022421 0.64202 1 1 1 1 1 0 1 1 1 0 1 1 1 192 41167 0.002199549 0.013178544 0.166903761 -0.777533877
15 5370 1530 505 0 429.440399 112.413231 90.622276 7100 4.588012 0.931196 0.988197 0.996735 4.492354 0.845973 34636 0 13458.84375 119.06916 96.408768 8000 4.588012 0.963834 0.627769 0.997414 290.889764 0.717451 1 1 1 1 1 1 1 1 1 0 1 1 1 505 34636 0.005785271 0.011087814 0.521768385 -0.282522239
16 5600 1530 162 0 152.501968 107.44207 86.30442 1800 6.917486 0.894426 0.996269 0.997963 1.507789 0.402077 35229 0 13689.80176 285.15274 96.408768 8000 6.917486 0.963834 0.631302 0.996994 123.544315 0.721488 1 0 1 1 1 0 1 1 1 0 1 1 1 162 35229 0.001855869 0.011277648 0.164561718 -0.783671187
17 5840 1530 1447 0 999.522339 55.150143 87.403885 6700 4.588012 0.958749 0.968361 0.998253 26.237466 0.937019 20226 0 9937.28125 87.500351 94.743553 7900 4.588012 0.955337 0.772545 0.998138 231.153359 0.848363 1 1 1 1 1 1 1 1 1 1 1 1 1 1447 20226 0.016576806 0.006474828 2.560192623 0.408272642
18 6070 1530 186 0 175.324173 95.730629 84.44017 2700 6.917486 0.909737 0.995255 0.99646 1.942952 0.51812 21856 0 10247.80371 219.585999 96.408768 7900 6.917486 0.963834 0.738457 0.99427 99.532758 0.825638 1 1 1 1 1 0 1 1 1 1 1 1 1 186 21856 0.002130813 0.00699663 0.304548438 -0.516343624
19 6310 1530 625 0 539.233154 144.984146 93.389999 7400 4.588012 0.951752 0.983452 0.995842 4.310816 0.841542 42316 0 13303.04004 107.343773 97.066856 8100 4.588012 0.97046 0.590919 0.996597 394.210105 0.675337 1 1 1 1 1 1 1 1 1 0 1 1 1 625 42316 0.007159989 0.013546366 0.528554193 -0.276910477
20 2080 1760 269 0 450.834198 160.86937 91.669968 5200 0.452909 0.933603 0.988113 0.995438 1.672164 0.44591 37816 0 10820.19727 204.105621 95.078926 8000 0.452909 0.950954 0.649628 0.993698 185.276622 0.742432 1 1 1 1 1 0 1 1 1 0 1 1 1 269 37816 0.003081659 0.012105808 0.254560376 -0.594209196

Total number of rows: 17328

Table truncated, full table size 4981 Kbytes.




Supplementary data files not provided
Raw data included within Sample table
Processed data included within Sample table
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