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Sample GSM289193 Query DataSets for GSM289193
Status Public on Dec 13, 2008
Title FH_RDE2_14028s_smpB_MgMDil_2_7DS769
Sample type mixed
 
Channel 1
Source Name 14028s smpB RNA MgMDil 060925
Organism(s) Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics Salmonella typhimurium 14028s smpB RNA harvested from LB stat culture that had been diluted 100fold in MgM medium and grown to log phase
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 Fri May 25 13:47:40 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
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
1 750 1450 3890 1233 1418.677734 1205.937744 88.848671 5400 19.822811 0.925807 0.962433 0.961403 3.225705 0.808638 9123 68 3807.453125 249.391251 96.408768 7900 19.822811 0.963834 0.882454 0.992111 36.581075 0.921636 1 1 1 1 1 1 1 1 1 1 1 1 1 2657 9055 0.006639066 0.006250465 1.062171511 0.026194649
2 980 1460 6970 1023 1734.740723 891.600952 94.743553 7800 9.24094 0.957843 0.941475 0.97274 7.817399 0.89814 16197 0 5024.869629 131.510208 97.066856 8100 9.24094 0.97046 0.830727 0.996536 123.161542 0.887151 1 1 1 1 1 1 1 1 1 1 1 1 1 5947 16197 0.014859813 0.011180428 1.329091576 0.123554905
3 1220 1460 6839 570 1947.109497 685.350281 94.069214 7800 10.400874 0.948274 0.933304 0.982559 9.978839 0.916519 8071 0 2910.400879 184.691315 95.078926 8000 10.400874 0.950954 0.910332 0.995461 43.699943 0.940221 1 1 1 1 1 1 1 1 1 1 1 1 1 6269 8071 0.015664397 0.005571231 2.811657858 0.448962472
4 1450 1460 2337 719 949.826294 699.592773 85.190765 3000 9.24094 0.91366 0.972412 0.980537 3.340515 0.812752 10875 0 3167.379639 150.189056 97.066856 8100 9.24094 0.97046 0.880486 0.996643 72.408738 0.920324 1 1 1 1 1 1 1 1 1 1 1 1 1 1618 10875 0.004042909 0.00750677 0.538568317 -0.268759199
5 1690 1460 1838 544 869.526367 636.796997 87.03894 3400 10.400874 0.92852 0.975311 0.977112 2.88632 0.769685 5879 0 3006.617188 143.182449 95.078926 8000 10.400874 0.950954 0.897438 0.996307 41.059502 0.931625 1 1 1 1 1 0 1 1 1 1 1 1 1 1294 5879 0.003233327 0.004058143 0.796750538 -0.098677635
6 1920 1460 1806 599 1032.181641 766.168945 85.563599 3600 9.24094 0.907912 0.958977 0.975807 2.357182 0.628582 2951 0 1817.118896 146.410477 95.078926 8000 9.24094 0.950954 0.947258 0.995743 20.155661 0.954865 1 1 1 1 1 0 1 1 1 1 1 1 1 1207 2951 0.00301594 0.00203701 1.480572265 0.17042961
7 2160 1460 8324 807 15871.55859 4478.779297 97.066856 8100 10.400874 0.97046 0.522972 0.838799 1.858542 0.495611 32479 0 9880.790039 435.897491 97.066856 8100 10.400874 0.97046 0.671387 0.987328 74.510638 0.767299 1 1 1 0 0 0 1 1 1 0 1 1 1 7517 32479 0.018782784 0.02241953 0.837786678 -0.07686655
8 2390 1460 3548 588 1657.288208 803.164124 97.066856 8100 9.24094 0.97046 0.948204 0.970802 4.417528 0.844177 23195 53 5256.508301 215.346085 97.066856 8100 9.24094 0.97046 0.802322 0.992447 107.71034 0.868215 1 1 1 1 1 1 1 1 1 1 1 1 1 2960 23142 0.007396174 0.015974407 0.463001471 -0.334417629
9 2630 1460 2081 761 1279.56958 1239.833374 47.873077 800 10.400874 0.530062 0.974014 0.952759 1.678451 0.447587 23855 0 4670.191895 181.553818 97.066856 8100 10.400874 0.97046 0.779007 0.993996 131.393547 0.852671 0 0 0 1 1 0 1 1 1 1 1 1 1 1320 23855 0.003298294 0.016466575 0.200302357 -0.698313941
10 2860 1470 9255 861 2445.21875 1828.585449 92.361824 7700 0.79332 0.938643 0.920494 0.952927 5.061289 0.858383 20222 0 5505.256836 169.465088 97.066856 8100 0.79332 0.97046 0.797287 0.995621 119.328413 0.864858 1 1 1 1 1 1 1 1 1 1 1 1 1 8394 20222 0.02097415 0.013958796 1.502575862 0.176836408
11 3100 1470 9503 609 3492.655029 980.699768 97.066856 8100 4.838653 0.97046 0.886116 0.968826 9.69002 0.910932 2224 2 1193.47998 174.709793 97.066856 8100 4.838653 0.97046 0.961014 0.994232 12.729681 0.93211 1 1 1 1 1 1 1 1 1 1 1 1 1 8894 2222 0.022223504 0.001533797 14.48920708 1.16104462
12 3330 1470 4354 709 1732.950073 1227.618774 86.672455 6800 0.79332 0.92535 0.949974 0.961472 3.546704 0.819713 6557 0 3339.725342 230.197403 96.408768 8000 0.79332 0.963834 0.90493 0.994843 28.484248 0.93662 1 1 1 1 1 1 1 1 1 1 1 1 1 3645 6557 0.009107789 0.004526151 2.01225909 0.303683898
13 3570 1470 1803 601 717.34491 1471.844604 85.934807 1600 4.838653 0.865195 0.984329 0.979584 1.224993 0.326665 21514 0 6215.112793 191.098984 97.066856 8100 4.838653 0.97046 0.793663 0.994514 112.5804 0.862442 1 0 1 1 1 0 1 1 1 1 1 1 1 1202 21514 0.003003446 0.014850635 0.20224363 -0.694125148
14 3800 1470 2620 734 1395.143066 3191.721436 84.816299 5900 0.79332 0.946195 0.954987 0.882668 0.820874 0.2189 31152 23 8062.108887 230.329117 97.066856 8100 0.79332 0.97046 0.710854 0.992531 135.249943 0.807236 1 1 1 1 0 0 1 1 1 1 1 1 1 1886 31129 0.004712562 0.021487655 0.219314865 -0.658931932
15 4040 1470 16375 744 4305.910156 1917.814819 97.066856 8100 4.838653 0.97046 0.82222 0.927498 8.538363 0.797848 15551 0 3599.857666 360.557678 97.066856 8100 4.838653 0.97046 0.847397 0.989418 43.130409 0.898265 1 1 1 1 0 1 1 1 1 1 1 1 1 15631 15551 0.039057296 0.010734509 3.638479989 0.560919991
16 4270 1470 1681 551 12007.91309 857.590576 79.388519 2800 0.79332 0.826611 0.509262 0.974686 1.960143 0.522705 28849 0 9433.919922 249.805069 97.066856 8100 0.79332 0.97046 0.722313 0.992279 115.486047 0.814875 1 1 1 0 1 0 1 1 1 1 1 1 1 1130 28849 0.002823539 0.019913822 0.141787919 -0.848360771
17 4510 1470 4172 543 1681.938599 824.228821 91.669968 7200 4.838653 0.931648 0.95327 0.971809 5.061701 0.858391 6813 0 3523.421631 172.953003 97.066856 8100 4.838653 0.97046 0.883575 0.995003 39.392204 0.922384 1 1 1 1 1 1 1 1 1 1 1 1 1 3629 6813 0.009067809 0.004702862 1.928146944 0.285140128
18 4740 1480 2661 529 1308.879639 703.142334 93.048538 7200 10.764002 0.938797 0.959137 0.982735 3.78444 0.827122 8524 0 5444.279297 180.159485 97.066856 8100 10.764002 0.97046 0.851051 0.994843 47.313634 0.900701 1 1 1 1 1 1 1 1 1 1 1 1 1 2132 8524 0.005327244 0.005883927 0.905389197 -0.043164692
19 4980 1480 1609 550 1908.802734 861.406982 92.016548 5500 11.774843 0.946082 0.980125 0.970604 1.867874 0.4981 22880 0 4863.057129 234.407913 97.066856 8100 11.774843 0.97046 0.805191 0.993973 97.607626 0.870127 1 1 1 1 1 0 1 1 1 1 1 1 1 1059 22880 0.002646131 0.015793554 0.167545007 -0.775868511
20 760 1700 3147 1130 1141.519287 966.427979 0 300 15.374062 0 0.983864 0.971977 3.256321 0 29470 0 11382.13867 274.642517 97.066856 8000 15.374062 0.97046 0.716576 0.99279 107.303124 0.81105 0 0 0 1 1 1 1 1 1 1 1 1 1 2017 29470 0.005039893 0.020342484 0.247752081 -0.605982689

Total number of rows: 17328

Table truncated, full table size 5067 Kbytes.




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