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Sample GSM341672 Query DataSets for GSM341672
Status Public on Nov 18, 2008
Title RDE2_X3339_FlightvsGround_F423_M9_7DS525
Sample type mixed
 
Channel 1
Source name X3339 total RNA after microgravity in flight on M9 minimal media
Organism Salmonella enterica
Characteristics Salmonella typhimurium X3339 total RNA harvested after exposure to space flight, grown in M9 minimal media
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 Typhimurium X3339 gDNA from overnight cultures in LB
Organism Salmonella enterica
Characteristics Salmonella typhimurium X3339 grown O/N 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 Salmonella enterica subsp. enterica serovar Typhimurium 14028s
biological replicate, Date of Scan Fri Dec 15 11:40:18 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 Nov 12, 2008
Last update date Nov 17, 2008
Contact name Michael McClelland
E-mail(s) [email protected]
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)
GSE8573 Salmonella Typhimurium transcription profiles in space flight

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 log 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 2730 2240 7192 220 2803.873535 360.054688 97.066856 8100 39.593006 0.97046 0.903725 0.989998 19.974743 0.935816 2521 0 2007.925171 86.259094 95.078926 7700 39.593006 0.960865 0.921761 0.997612 29.225904 0.94784 1 1 1 1 1 1 1 1 1 1 1 1 1 6972 2521 0.016869506 0.001882299 8.962181898 0.952413754
2 2970 2240 1738 240 1002.333862 357.025574 89.562332 6900 43.686771 0.922802 0.9617 0.992371 4.867999 0.854397 6262 0 3010.056396 73.289223 93.730225 7700 43.686771 0.955854 0.922691 0.997696 85.442303 0.948461 1 1 1 1 1 1 1 1 1 1 1 1 1 1498 6262 0.003624573 0.004675508 0.77522536 -0.110572028
3 3200 2250 959 205 441.05304 442.984375 85.934807 4100 34.50103 0.939941 0.986465 0.988602 2.164862 0.577296 3844 0 2501.96875 101.672318 90.27034 7200 34.50103 0.935593 0.930267 0.997139 37.807735 0.951352 1 1 1 1 1 0 1 1 1 1 1 1 1 754 3844 0.001824384 0.002870114 0.635648737 -0.196782812
4 3440 2250 933 194 508.596863 324.245148 89.562332 4900 39.131172 0.894245 0.983704 0.989906 2.877452 0.767321 5184 0 3484.459961 103.855545 92.016548 7400 39.131172 0.936246 0.906914 0.996841 49.915486 0.937943 1 1 1 1 1 0 1 1 1 1 1 1 1 739 5184 0.00178809 0.003870622 0.461964568 -0.335391333
5 3670 2250 722 112 335.769409 314.045715 95.078926 5600 34.50103 0.950954 0.990845 0.992821 2.299028 0.613074 2124 0 1271.788696 110.576088 92.705818 7200 34.50103 0.953771 0.966202 0.996864 19.208493 0.952849 1 1 1 1 1 0 1 1 1 1 1 1 1 610 2124 0.001475961 0.00158588 0.930688921 -0.031195456
6 3910 2250 706 106 437.552734 345.41507 92.016548 4600 39.131172 0.932959 0.985535 0.992004 2.043918 0.545045 2294 0 2082.914307 71.840714 90.972847 7300 39.131172 0.958918 0.95285 0.997871 31.931754 0.954864 1 1 1 1 1 0 1 1 1 1 1 1 1 600 2294 0.001451765 0.00171281 0.847592408 -0.071812942
7 4140 2260 1249 135 714.570251 239.876587 89.206215 6600 31.828224 0.930687 0.977455 0.993378 5.206844 0.861243 10384 0 5510.760254 101.590286 95.078926 7700 31.828224 0.960865 0.880302 0.997398 102.214497 0.920202 1 1 1 1 1 1 1 1 1 1 1 1 1 1114 10384 0.002695443 0.00775319 0.347656003 -0.458850267
8 4380 2260 3486 91 1615.718872 257.73941 95.078926 8000 36.796246 0.950954 0.952347 0.992775 13.525289 0.935589 11567 0 5519.064453 80.449989 96.408768 7800 36.796246 0.963834 0.875359 0.997154 143.778764 0.916906 1 1 1 1 1 1 1 1 1 1 1 1 1 3395 11567 0.008214569 0.008636475 0.951148362 -0.021751736
9 4610 2260 1258 258 616.604858 338.350861 88.489685 6500 31.828224 0.932567 0.983177 0.990448 3.718034 0.825115 10355 0 4551.841797 127.943375 94.406982 7700 31.828224 0.959758 0.873489 0.995094 80.934242 0.91566 1 1 1 1 1 1 1 1 1 1 1 1 1 1000 10355 0.002419608 0.007731538 0.312952999 -0.504520882
10 4850 2270 1618 178 1505.611572 413.560272 89.562332 6700 37.103619 0.929413 0.960121 0.99099 3.912368 0.830863 5443 0 3083.638672 103.491615 93.048538 7100 37.103619 0.948563 0.922821 0.996597 52.593633 0.948547 1 1 1 1 1 1 1 1 1 1 1 1 1 1440 5443 0.003484235 0.004064004 0.857340578 -0.066846621
11 5080 2270 777 170 431.776093 304.197754 84.816299 4400 32.183079 0.888225 0.986229 0.990982 2.554259 0.681136 2902 0 1535.630737 206.62468 91.669968 6900 32.183079 0.951053 0.959259 0.993629 14.044789 0.937674 1 1 1 1 1 0 1 1 1 1 1 1 1 607 2902 0.001468702 0.002166772 0.67782956 -0.168879496
12 5320 2270 3934 112 1857.528809 312.281525 94.743553 7900 37.103619 0.955337 0.942093 0.990303 12.597607 0.931496 2789 0 1638.753662 108.532562 90.622276 7100 37.103619 0.940031 0.955627 0.997078 25.697357 0.953111 1 1 1 1 1 1 1 1 1 1 1 1 1 3822 2789 0.009247741 0.002082401 4.44090405 0.64747139
13 5550 2270 981 185 1126.287476 345.501862 90.622276 6700 32.183079 0.949552 0.970642 0.989479 2.839348 0.757159 9646 0 3902.09668 130.735657 96.408768 7900 32.183079 0.963834 0.885506 0.995399 73.782473 0.92367 1 1 1 1 1 0 1 1 1 1 1 1 1 796 9646 0.001926008 0.007202164 0.267420706 -0.572804968
14 5790 2280 937 172 532.501648 255.395538 92.016548 6100 39.992416 0.936923 0.983757 0.992699 3.668819 0.823596 7373 0 3967.634521 118.680962 95.746155 7800 39.992416 0.957094 0.898834 0.996315 62.124539 0.932556 1 1 1 1 1 1 1 1 1 1 1 1 1 765 7373 0.001851 0.005505034 0.336237713 -0.473353577
15 6020 2280 1604 334 680.125488 383.514832 88.489685 6800 35.474857 0.902569 0.979652 0.988182 4.182368 0.83825 8741 0 3854.426758 100.286018 91.669968 7400 35.474857 0.962502 0.899506 0.997772 87.160704 0.933004 1 1 1 1 1 1 1 1 1 1 1 1 1 1270 8741 0.003072902 0.006526448 0.470838342 -0.327128178
16 6260 2280 905 41 700.513062 322.207458 92.361824 7500 39.992416 0.923048 0.981628 0.991005 2.808749 0.749 7273 0 4312.67334 47.552094 94.743553 7900 39.992416 0.955337 0.895844 0.998581 152.948051 0.930562 1 1 1 1 1 0 1 1 1 1 1 1 1 864 7273 0.002090541 0.005430369 0.384972207 -0.414570624
17 6490 2290 1200 102 640.661682 406.97522 91.322075 7200 41.002201 0.938433 0.981674 0.989326 2.948582 0.786289 2934 0 2270.612305 146.342636 93.048538 7200 41.002201 0.948563 0.940269 0.99601 20.048839 0.954646 1 1 1 1 1 0 1 1 1 1 1 1 1 1098 2934 0.002656729 0.002190665 1.212750471 0.083771452
18 6730 2290 3640 190 1889.187988 306.243805 94.406982 7800 44.967857 0.943981 0.943954 0.990837 11.885955 0.927985 4089 0 2558.320068 65.180611 92.705818 7500 44.967857 0.952866 0.932556 0.99884 62.73338 0.955037 1 1 1 1 1 1 1 1 1 1 1 1 1 3450 4089 0.008347647 0.003053043 2.734205836 0.436831206
19 6960 2290 1605 124 685.929138 243.445099 95.078926 7900 41.002201 0.950954 0.977791 0.994347 6.592862 0.883624 11062 0 3786.492188 109.035477 94.743553 7900 41.002201 0.955337 0.890549 0.997192 101.453218 0.927032 1 1 1 1 1 1 1 1 1 1 1 1 1 1481 11062 0.003583439 0.008259418 0.433861013 -0.362649374
20 2730 2470 1087 281 466.207336 298.294006 92.705818 6800 42.793091 0.962363 0.986008 0.992752 3.644056 0.822822 10293 0 4104.557617 114.724815 96.408768 7700 42.793091 0.963834 0.895279 0.996948 89.719037 0.930186 1 1 1 1 1 1 1 1 1 1 1 1 1 806 10293 0.001950204 0.007685245 0.253759489 -0.59557771

Total number of rows: 17328

Table truncated, full table size 5080 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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