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Sample GSM289200 Query DataSets for GSM289200
Status Public on Dec 13, 2008
Title FH_RDE2_14028s_wt_LBlog_3_7DS514
Sample type mixed
 
Channel 1
Source name 14028s wt RNA LBlog 061020
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics Salmonella typhimurium 14028s wt 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 Fri Dec 08 09:24:18 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
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 2150 2250 1711 0 856.848877 190.915665 95.078926 7900 11.378351 0.950954 0.969131 0.994446 8.962072 0.908776 13943 0 5093.176758 180.255493 96.408768 7900 11.378351 0.963834 0.855644 0.994316 77.351318 0.903763 1 1 1 1 1 1 1 1 1 1 1 1 1 1711 13943 0.014167482 0.00458145 3.092357511 0.490289697
2 2380 2250 984 0 517.037659 135.193787 97.066856 8100 16.077406 0.97046 0.98394 0.995819 7.278441 0.892223 28204 0 6234.223145 138.088287 97.066856 8100 16.077406 0.97046 0.774605 0.997818 204.246142 0.849737 1 1 1 1 1 1 1 1 1 1 1 1 1 984 28204 0.008147751 0.00926739 0.879185077 -0.055919692
3 2620 2250 369 0 266.41745 82.936211 91.322075 5800 11.378351 0.938433 0.992729 0.997459 4.449203 0.844942 25022 0 7080.400391 90.004387 97.066856 8100 11.378351 0.97046 0.74752 0.997505 278.008671 0.83168 1 1 1 1 1 1 1 1 1 1 1 1 1 369 25022 0.003055407 0.008221835 0.371621012 -0.429899738
4 2850 2250 260 0 263.204681 107.190094 88.129242 5000 16.077406 0.878816 0.991653 0.996857 2.425597 0.646826 26217 0 6908.233398 176.183212 97.066856 8100 16.077406 0.97046 0.75444 0.994843 148.805324 0.836294 1 1 1 1 1 0 1 1 1 1 1 1 1 260 26217 0.002152861 0.008614493 0.249911516 -0.602213731
5 3090 2250 180 0 228.508514 100.295219 83.682846 4800 11.378351 0.905658 0.991653 0.997467 1.794702 0.478587 15217 0 7008.006836 108.835823 97.066856 8100 11.378351 0.97046 0.795731 0.996872 139.816097 0.86382 1 1 1 1 1 0 1 1 1 1 1 1 1 180 15217 0.001490442 0.005000067 0.29808449 -0.52566062
6 3320 2250 315 0 222.607254 105.872284 90.27034 5500 16.077406 0.912243 0.994339 0.997238 2.975283 0.793409 15068 0 7360.901367 111.327049 95.078926 8000 16.077406 0.950954 0.807617 0.996216 135.348957 0.871745 1 1 1 1 1 0 1 1 1 1 1 1 1 315 15068 0.002608274 0.004951108 0.526806176 -0.278349142
7 3560 2250 940 0 562.162598 133.85083 88.848671 6900 11.378351 0.918639 0.982857 0.996651 7.022743 0.889169 48073 0 17308.59375 120.383026 97.066856 8100 11.378351 0.97046 0.569885 0.996758 399.333706 0.651297 1 1 1 1 1 1 1 1 1 0 1 1 1 940 48073 0.007783421 0.015796031 0.49274536 -0.307377456
8 3790 2250 396 0 353.534363 44.998596 89.91703 6600 16.077406 0.941545 0.989822 0.998802 8.800275 0.90741 37680 0 14075.60156 169.569763 97.066856 8100 16.077406 0.97046 0.648163 0.995369 222.209428 0.740758 1 1 1 1 1 1 1 1 1 0 1 1 1 396 37680 0.003278973 0.012381055 0.264837944 -0.577019793
9 4030 2250 25443 0 10924.96191 253.981522 96.408768 7900 11.378351 0.963834 0.749306 0.992584 100.176579 0.83287 29762 0 11401.44824 140.960419 96.408768 8000 11.378351 0.963834 0.718292 0.995766 211.137284 0.812195 1 1 1 1 1 1 1 1 1 1 1 1 1 25443 29762 0.210674018 0.009779324 21.54279858 1.333302121
10 4260 2250 1138 0 718.144409 79.124428 91.669968 7000 16.077406 0.93779 0.977135 0.997345 14.38241 0.938959 35924 0 14893.89648 210.245239 97.066856 8100 16.077406 0.97046 0.660538 0.99453 170.867127 0.7549 1 1 1 1 1 1 1 1 1 0 1 1 1 1138 35924 0.009422907 0.011804061 0.798276767 -0.09784651
11 4500 2240 216 0 345.019684 73.507484 88.129242 4900 11.714128 0.918907 0.987625 0.997734 2.938476 0.783594 12626 0 4653.762207 95.12574 97.066856 8100 11.714128 0.97046 0.865479 0.997223 132.729585 0.910319 1 1 1 1 1 0 1 1 1 1 1 1 1 216 12626 0.001788531 0.004148705 0.431105816 -0.365416119
12 4730 2240 706 0 496.772583 125.722801 91.669968 7000 16.316767 0.934491 0.985359 0.99749 5.615529 0.868689 16874 0 5990.318359 122.666183 95.078926 8000 16.316767 0.950954 0.811882 0.996864 137.560324 0.874588 1 1 1 1 1 1 1 1 1 1 1 1 1 706 16874 0.005845846 0.005544531 1.054344584 0.022982572
13 4970 2240 719 0 453.603577 129.126556 92.361824 7300 11.714128 0.932806 0.987831 0.996918 5.568181 0.867868 34293 0 10608.58203 315.33197 97.066856 8100 11.714128 0.97046 0.701477 0.995285 108.752056 0.800985 1 1 1 1 1 1 1 1 1 1 1 1 1 719 34293 0.005953489 0.01126814 0.528347098 -0.277080674
14 5200 2240 433 0 360.922089 143.207733 89.91703 6100 16.316767 0.93207 0.992142 0.99511 3.02358 0.800939 37115 0 11343.08301 113.174355 97.066856 8100 16.316767 0.97046 0.660904 0.996773 327.945321 0.755319 1 1 1 1 1 1 1 1 1 0 1 1 1 433 37115 0.003585342 0.012195404 0.293991211 -0.531665653
15 5440 2240 631 0 501.105621 85.527412 94.406982 7600 11.714128 0.943981 0.98716 0.997513 7.377752 0.893365 29582 0 6649.266602 130.322403 97.066856 8100 11.714128 0.97046 0.728226 0.996269 226.990904 0.818817 1 1 1 1 1 1 1 1 1 1 1 1 1 631 29582 0.005224828 0.009720179 0.537523854 -0.269602258
16 5670 2240 227 0 223.986237 113.777924 87.403885 3900 16.316767 0.890435 0.992767 0.996887 1.995115 0.532031 28137 0 10675.43164 74.15255 97.066856 8100 16.316767 0.97046 0.717033 0.99765 379.447505 0.811356 1 1 1 1 1 0 1 1 1 1 1 1 1 227 28137 0.001879613 0.009245375 0.203303091 -0.691856018
17 5910 2240 1383 0 891.84021 106.07309 89.562332 6800 11.714128 0.932539 0.972168 0.996696 13.03818 0.933503 16606 0 7900.472168 66.213112 94.743553 7600 11.714128 0.955337 0.793068 0.997688 250.796248 0.862045 1 1 1 1 1 1 1 1 1 1 1 1 1 1383 16606 0.011451565 0.00545647 2.098713044 0.321953062
18 6140 2240 271 0 298.62204 8530.205078 88.489685 5200 16.316767 0.932487 0.99218 0.799438 0.031769 0.008472 13954 0 7280.805176 10123.1875 95.078926 8000 16.316767 0.950954 0.822388 0.597244 1.37842 0.367579 1 1 1 1 0 0 1 1 1 1 0 0 1 271 13954 0.002243944 0.004585065 0.489402843 -0.310333513
19 6380 2240 636 0 352.843933 94.934525 93.048538 7000 11.714128 0.956099 0.990547 0.996857 6.699354 0.885049 26039 0 8343.057617 113.711136 97.066856 8100 11.714128 0.97046 0.733459 0.99691 228.992524 0.822306 1 1 1 1 1 1 1 1 1 1 1 1 1 636 26039 0.005266229 0.008556005 0.615500952 -0.210771271
20 2150 2490 348 0 287.487457 147.581924 90.622276 5500 14.162977 0.930822 0.991936 0.995796 2.358012 0.628803 28520 0 10573.3916 156.680283 97.066856 8100 14.162977 0.97046 0.700539 0.996422 182.026733 0.800359 1 1 1 1 1 0 1 1 1 1 1 1 1 348 28520 0.002881522 0.009371223 0.307486206 -0.512174362

Total number of rows: 17328

Table truncated, full table size 5002 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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