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Sample GSM341673 Query DataSets for GSM341673
Status Public on Nov 18, 2008
Title RDE2_X3339_FlightvsGround_G43_M9_7DS524
Sample type mixed
 
Channel 1
Source name X3339 total RNA after microgravity on ground 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 Thu Dec 14 18:40:49 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 3070 2220 11242 656 4651.124023 597.834045 97.066856 8100 62.226147 0.97046 0.8424 0.981491 18.80455 0.894933 3310 0 1365.876953 199.822815 95.078926 8000 62.226147 0.950954 0.954224 0.994095 16.564675 0.946134 1 1 1 1 1 1 1 1 1 1 1 1 1 10586 3310 0.019525557 0.003081485 6.336412167 0.801843419
2 3310 2220 6087 671 1797.190552 569.171753 97.066856 8100 65.741051 0.97046 0.940346 0.984146 10.694487 0.921226 10764 0 3506.433594 233.847733 97.066856 8100 65.741051 0.97046 0.876633 0.993126 46.029952 0.917755 1 1 1 1 1 1 1 1 1 1 1 1 1 5416 10764 0.009989648 0.010020877 0.996883688 -0.00135551
3 3540 2230 2596 880 745.194397 569.911011 76.113342 2300 55.341438 0.861135 0.978683 0.983513 4.555097 0.811426 6564 0 3258.269043 145.452576 94.406982 7700 55.341438 0.953175 0.909668 0.996407 45.128111 0.939779 1 1 1 1 1 1 1 1 1 1 1 1 1 1716 6564 0.00316511 0.006110836 0.517950474 -0.285711766
4 3780 2230 2819 991 1004.02179 645.300476 85.934807 4100 59.266071 0.897408 0.973907 0.981636 4.368508 0.842977 11373 0 4460.885742 172.836273 97.066856 8100 59.266071 0.97046 0.871048 0.994637 65.802159 0.914032 1 1 1 1 1 1 1 1 1 1 1 1 1 1828 11373 0.003371691 0.010587833 0.318449576 -0.496959324
5 4010 2240 1912 782 216.95163 1159.263672 70.014091 1000 49.53035 0.859933 0.994797 0.974991 1.649323 0.439819 2876 0 1584.876587 224.030396 94.743553 7800 49.53035 0.955337 0.953011 0.993248 12.837544 0.932603 1 0 1 1 1 0 1 1 1 1 1 1 1 1130 2876 0.002084251 0.002677447 0.778447064 -0.108770915
6 4250 2240 2754 947 434.497284 2183.187012 72.69075 2100 53.879944 0.879558 0.98983 0.972458 1.261459 0.336389 4676 0 2695.083984 177.816711 94.406982 7900 53.879944 0.943981 0.921844 0.995354 26.296741 0.947896 1 1 1 1 1 0 1 1 1 1 1 1 1 1807 4676 0.003332957 0.004353179 0.765637459 -0.115976827
7 4480 2250 2626 975 526.755615 917.226074 79.388519 3100 45.208813 0.903332 0.985611 0.973892 2.86298 0.763461 11912 0 6115.523926 181.165421 93.730225 7800 45.208813 0.955854 0.846489 0.994888 65.752062 0.897659 1 1 1 1 1 0 1 1 1 1 1 1 1 1651 11912 0.00304522 0.011089621 0.274600872 -0.561298088
8 4720 2260 2572 792 866.106323 592.417664 95.078926 6300 47.793411 0.950241 0.974495 0.984177 4.341532 0.842309 14902 0 6547.545898 183.071091 94.743553 7900 47.793411 0.955337 0.830704 0.994576 81.400072 0.887136 1 1 1 1 1 1 1 1 1 1 1 1 1 1780 14902 0.003283156 0.013873198 0.236654609 -0.625885033
9 4950 2260 3605 1037 1097.009399 617.376221 91.322075 7000 42.830105 0.940448 0.969093 0.981865 5.839227 0.872436 10514 0 3902.490234 124.118561 94.743553 7900 42.830105 0.955337 0.875763 0.996819 84.709329 0.917175 1 1 1 1 1 1 1 1 1 1 1 1 1 2568 10514 0.004736598 0.009788136 0.483912199 -0.31523343
10 5190 2270 4307 1180 1196.523071 709.988708 85.934807 6700 47.694771 0.933006 0.96492 0.974106 6.066294 0.876027 6275 0 2829.790771 236.364578 93.048538 7200 47.694771 0.95796 0.919998 0.992455 26.547971 0.946665 1 1 1 1 1 1 1 1 1 1 1 1 1 3127 6275 0.005767657 0.005841788 0.987310315 -0.005546326
11 5420 2270 3098 1138 1083.136108 822.680542 56.980362 1200 42.720005 0.675048 0.970062 0.974083 3.765739 0.771484 2965 0 1737.387329 247.000519 95.413124 7800 42.720005 0.964797 0.948456 0.991753 12.004023 0.928592 0 0 0 1 1 1 1 1 1 1 1 1 1 1960 2965 0.003615161 0.002760303 1.309697194 0.117170897
12 5660 2280 5316 866 1591.583008 720.969177 89.562332 7000 49.652515 0.94341 0.949432 0.975403 7.373408 0.893315 4488 0 2300.197021 139.07547 94.069214 7500 49.652515 0.957565 0.936134 0.994949 32.270249 0.957423 1 1 1 1 1 1 1 1 1 1 1 1 1 4450 4488 0.008207891 0.004178158 1.964475813 0.293246686
13 5890 2280 2612 969 779.363403 645.852295 60.238968 1100 44.89521 0.752537 0.980278 0.979401 4.044268 0.770682 12694 0 5315.038086 151.818359 94.743553 7900 44.89521 0.955337 0.865036 0.99514 83.613076 0.910024 1 0 1 1 1 1 1 1 1 1 1 1 1 1643 12694 0.003030464 0.011817634 0.256435763 -0.591021407
14 6130 2290 2250 770 732.016785 567.921143 87.403885 5300 53.44112 0.919147 0.977539 0.984444 3.961818 0.832266 10427 0 5218.209961 361.453064 97.066856 7800 53.44112 0.97046 0.882294 0.992165 28.847452 0.921529 1 1 1 1 1 1 1 1 1 1 1 1 1 1480 10427 0.002729815 0.009707142 0.281217191 -0.550958135
15 6360 2290 2769 911 647.099182 633.134583 84.062363 4100 49.052635 0.885935 0.979317 0.980843 4.373478 0.8431 8869 0 3745.71167 174.130859 97.066856 8100 49.052635 0.97046 0.891472 0.995613 50.932959 0.927648 1 1 1 1 1 1 1 1 1 1 1 1 1 1858 8869 0.003427025 0.008256703 0.41505971 -0.381889422
16 6600 2300 2577 897 364.376343 575.015747 77.357788 2400 58.707191 0.934333 0.990211 0.983803 4.481616 0.814821 9647 0 4643.51709 126.290848 94.406982 7800 58.707191 0.959758 0.87574 0.996872 76.387166 0.91716 1 1 1 1 1 1 1 1 1 1 1 1 1 1680 9647 0.003098709 0.008980992 0.345029737 -0.462143473
17 6830 2300 3945 1078 1068.384521 807.64856 78.986549 5500 54.742508 0.930912 0.967026 0.976944 4.88455 0.854747 3818 0 2060.927246 211.434509 94.743553 7600 54.742508 0.955337 0.936775 0.994766 18.057601 0.950144 1 1 1 1 1 1 1 1 1 1 1 1 1 2867 3818 0.005288095 0.003554414 1.487754567 0.172531292
18 7070 2310 4582 996 1588.626465 766.917786 89.562332 7100 65.093132 0.911104 0.956886 0.97403 5.974565 0.874601 4209 0 2627.643555 213.550919 94.743553 7900 65.093132 0.955337 0.926102 0.992897 19.709585 0.950734 1 1 1 1 1 1 1 1 1 1 1 1 1 3586 4209 0.006614269 0.00391842 1.687993939 0.227370883
19 7300 2310 2500 924 388.498505 582.844543 81.75885 2500 61.541229 0.851281 0.98996 0.980911 4.289308 0.818216 9824 0 2621.66626 173.26326 97.066856 8100 61.541229 0.97046 0.90329 0.995628 56.699845 0.935527 1 1 1 1 1 1 1 1 1 1 1 1 1 1576 9824 0.002906884 0.009145772 0.317839144 -0.497792617
20 3070 2450 2697 967 585.789795 643.458374 66.277275 800 65.968201 0.815955 0.988106 0.980804 4.191413 0.760496 14458 0 5291.270508 281.351532 97.066856 8000 65.968201 0.97046 0.858284 0.991776 51.387671 0.905523 1 0 1 1 1 1 1 1 1 1 1 1 1 1730 14458 0.003190933 0.013459851 0.23707044 -0.625122594

Total number of rows: 17328

Table truncated, full table size 5049 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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