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Sample GSM212798 Query DataSets for GSM212798
Status Public on Sep 13, 2007
Title RDE2_X3339_FlightvsGround_F25_LB_7DS518_2
Sample type mixed
 
Channel 1
Source Name Salmonella enterica subsp. enterica serovar Typhimurium X3339 total RNA after flight F25
Organism(s) Salmonella enterica
Characteristics Salmonella typhimurium X3339 total RNA harvested after exposure to conditions
Extracted molecule total RNA
Extraction protocol total RNA preparation
Label Cy3
Label protocol incorporation of Cy3-dCTP with Reverse Transcriptase
 
Channel 2
Source Name Salmonella enterica subsp. enterica serovar Typhimurium X3339 gDNA from overnight cultures in LB
Organism(s) Salmonella enterica
Characteristics Salmonella typhimurium X3339 grown O/N in LB at 37C with aeration
Extracted molecule genomic DNA
Extraction protocol total gDNA preparation
Label Cy5
Label protocol incorporation of Cy5-dCTP with Klenow enzyme
 
 
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 Wed Dec 13 09:12:30 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 Jul 24, 2007
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 GPL4805
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 2400 21020 2034 144 941.983704 307.208893 94.406982 7900 60.80267 0.943981 0.971413 0.992058 6.620902 0.884003 2345 0 894.315491 94.255424 97.066856 8100 60.80267 0.97046 0.971535 0.997284 24.879205 0.962797 1 1 1 1 1 1 1 1 1 1 1 1 1 1890 2345 0.027522639 0.018943693 1.452865547 0.162225425
2 2640 21030 868 175 465.022949 278.543549 92.361824 7100 57.08717 0.932136 0.985619 0.991623 3.116209 0.804543 3943 0 1409.28186 79.293579 97.066856 8100 57.08717 0.97046 0.949402 0.99781 49.726599 0.966268 1 1 1 1 1 1 1 1 1 1 1 1 1 693 3943 0.010091634 0.031852871 0.316820245 -0.499187074
3 2870 21030 1359 536 339.225555 481.05127 79.388519 1400 53.399765 0.852321 0.991997 0.986549 2.825063 0.75335 2801 0 1118.721436 152.122025 96.408768 8000 53.399765 0.963834 0.9589 0.995605 18.41285 0.951011 1 0 1 1 1 0 1 1 1 1 1 1 1 823 2801 0.011984726 0.022627414 0.529655144 -0.276006806
4 3110 21040 1259 449 190.039932 490.701599 77.357788 1200 51.122551 0.862029 0.994614 0.983833 2.565714 0.68419 3500 0 1203.368042 128.306961 97.066856 8100 51.122551 0.97046 0.957832 0.99617 27.278333 0.965845 1 0 1 1 1 0 1 1 1 1 1 1 1 810 3500 0.011795417 0.028274169 0.417179964 -0.379676557
5 3340 21040 668 177 185.405777 322.322327 86.672455 2300 46.969196 0.940013 0.994484 0.990143 2.07246 0.552656 1161 0 547.461121 76.244514 93.048538 7900 46.969196 0.930384 0.983574 0.997505 15.227325 0.941953 1 1 1 1 1 0 1 1 1 1 1 1 1 491 1161 0.007150061 0.009378946 0.762352345 -0.11784426
6 3580 21050 868 342 667.22052 363.441772 58.08688 700 46.562702 0.768497 0.985878 0.990067 2.388278 0.636874 1718 0 963.333618 97.25766 94.743553 7800 46.562702 0.955337 0.972076 0.997505 17.664418 0.949147 0 0 1 1 1 0 1 1 1 1 1 1 1 526 1718 0.00765974 0.013878578 0.551911003 -0.258130947
7 3810 21050 641 216 260.216156 296.100952 85.563599 3100 41.960407 0.894956 0.993156 0.992142 2.164802 0.577281 4723 0 1678.464478 55.271507 97.066856 8100 41.960407 0.97046 0.940231 0.998283 85.450899 0.960154 1 1 1 1 1 0 1 1 1 1 1 1 1 425 4723 0.006188953 0.038153971 0.162209936 -0.789922548
8 4050 21060 1128 225 483.74765 257.405792 94.406982 7200 43.848099 0.943981 0.985886 0.993797 4.382186 0.843314 5264 0 1465.190796 124.297707 97.066856 8100 43.848099 0.97046 0.944298 0.99585 42.349937 0.962865 1 1 1 1 1 1 1 1 1 1 1 1 1 903 5264 0.013149705 0.04252435 0.309227663 -0.509721662
9 4280 21060 2201 255 800.633484 299.096619 95.078926 7900 38.926163 0.950954 0.975311 0.991295 7.358826 0.893149 4204 0 1122.313843 94.191513 95.078926 8000 38.926163 0.950954 0.956352 0.997124 44.632471 0.967303 1 1 1 1 1 1 1 1 1 1 1 1 1 1946 4204 0.028338125 0.033961316 0.834423634 -0.078613403
10 4520 21070 1071 217 432.442932 361.760834 92.016548 6600 43.326965 0.929531 0.987732 0.988495 2.960519 0.789472 2958 0 912.727966 82.597305 97.066856 8100 43.326965 0.97046 0.972519 0.996765 35.812306 0.973554 1 1 1 1 1 0 1 1 1 1 1 1 1 854 2958 0.012436155 0.023895712 0.520434608 -0.283633831
11 4750 21070 887 316 241.235168 333.149841 78.582527 2600 38.338184 0.892458 0.993462 0.991013 2.662466 0.709991 1121 0 595.663452 115.029907 97.066856 8000 38.338184 0.97046 0.98262 0.996353 9.745292 0.914859 1 1 1 1 1 0 1 1 1 1 1 1 1 571 1121 0.008315041 0.009055812 0.918199313 -0.037063036
12 4990 21080 1931 238 722.181213 346.694946 97.066856 8100 45.075451 0.97046 0.977173 0.989487 5.569738 0.867895 1335 0 698.018738 177.449326 95.078926 8000 45.075451 0.950954 0.977928 0.99501 7.523275 0.894994 1 1 1 1 1 1 1 1 1 1 1 1 1 1693 1335 0.024653877 0.010784576 2.286031237 0.35908216
13 5220 21080 884 211 253.221237 380.817047 92.016548 3000 40.30368 0.928608 0.992142 0.988197 2.321325 0.61902 4648 0 1479.144897 111.112572 97.066856 8100 40.30368 0.97046 0.94429 0.997757 41.83145 0.96286 1 1 1 1 1 0 1 1 1 1 1 1 1 673 4648 0.00980039 0.037548096 0.261008958 -0.583344587
14 5450 21090 792 283 296.533691 288.402985 82.918602 2500 40.26844 0.902914 0.990143 0.991013 2.746157 0.732309 3471 0 1496.40564 98.431618 94.406982 7700 40.26844 0.959758 0.954514 0.997467 35.26306 0.969676 1 1 1 1 1 0 1 1 1 1 1 1 1 509 3471 0.007412182 0.028039897 0.264344109 -0.577830363
15 5690 21090 1052 272 440.332672 345.892975 84.44017 5100 44.48547 0.905532 0.987473 0.989304 3.041403 0.801643 4146 0 1473.724365 128.353592 95.746155 7900 44.48547 0.957094 0.951591 0.997116 32.301394 0.967728 1 1 1 1 1 1 1 1 1 1 1 1 1 780 4146 0.01135855 0.033492773 0.339134344 -0.469628227
16 5920 21100 721 233 198.872482 291.284241 79.788467 1900 46.648876 0.88739 0.995506 0.99218 2.475245 0.660065 3224 0 1559.814453 134.414032 92.361824 7700 46.648876 0.932136 0.95137 0.995804 23.985591 0.954757 1 0 1 1 1 0 1 1 1 1 1 1 1 488 3224 0.007106375 0.026044549 0.272854586 -0.564068743
17 6160 21100 869 204 503.588226 375.969452 88.489685 5800 50.334156 0.933826 0.988396 0.98967 2.311358 0.616362 1528 0 806.246094 93.950432 93.389999 7700 50.334156 0.960253 0.974579 0.996338 16.263895 0.945247 1 1 1 1 1 0 1 1 1 1 1 1 1 665 1528 0.009683892 0.012343694 0.784521336 -0.105395241
18 6390 21110 1781 285 922.083374 379.274628 93.730225 7100 54.13583 0.953147 0.970955 0.992493 4.695806 0.850653 1982 0 985.642517 89.296112 91.322075 7200 54.13583 0.94599 0.969246 0.998131 22.195815 0.95661 1 1 1 1 1 1 1 1 1 1 1 1 1 1496 1982 0.021785115 0.016011258 1.360612359 0.133734411
19 6630 21110 750 269 200.386826 358.777039 83.682846 1800 57.341934 0.909129 0.994263 0.989273 2.090435 0.557449 3751 0 1231.592163 82.427589 96.408768 8000 57.341934 0.963834 0.954712 0.997849 45.506608 0.969808 1 0 1 1 1 0 1 1 1 1 1 1 1 481 3751 0.007004439 0.030301831 0.231155633 -0.63609552
20 2400 21260 530 157 243.737 225.804825 83.682846 2500 57.002193 0.893492 0.993217 0.994408 2.34716 0.625909 5508 0 1331.533569 128.144608 97.066856 8100 57.002193 0.97046 0.957893 0.995667 42.98269 0.971929 1 1 1 1 1 0 1 1 1 1 1 1 1 373 5508 0.005431717 0.044495464 0.122073492 -0.913378632

Total number of rows: 5776

Table truncated, full table size 1592 Kbytes.




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