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Sample GSM322708 Query DataSets for GSM322708
Status Public on Sep 23, 2008
Title RRE2_14028s(wt)pBAD18preA_14028s(delpreA)pBAD18_LB10mMAra_OD0.74_6D070_2
Sample type RNA
 
Channel 1
Source Name RNA_14028s(wt)pBAD18preA
Organism(s) Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics Salmonella enterica subsp. enterica serovar Typhimurium 14028s
Salmonella typhimurium 14028s complemented with pBAD18+preA grown in LB+10mM Ara at OD0.74
Extracted molecule total RNA
Extraction protocol Promega SV RNA isolation kit
Label Cy3
Label protocol incorporation of Cy3-dCTP with SuperscriptII and random hexamers
 
Channel 2
Source Name RNA_14028s(delpreA)pBAD18
Organism(s) Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics Salmonella enterica subsp. enterica serovar Typhimurium 14028s
Salmonella typhimurium 14028s-preA mutant complemented with pBAD18 (vector control) grown in LB+10mM Ara at OD0.74
Extracted molecule total RNA
Extraction protocol Promega SV RNA isolation kit
Label Cy5
Label protocol incorporation of Cy5-dCTP with SuperscriptII 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 STv6_01_050607
Description biological replicate, Date_of_Scan = Fri Nov 04 11:17:45 2005
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 Sep 19, 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 GPL3788
Series (1)
GSE12866 PreA overexpression in Salmonella typhimurium

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 2250 22610 23870 912 3111.507813 208.544067 97.066856 8100 29.1952 0.97046 0.85994 0.991745 114.460221 0.906626 6944 202 1683.182739 124.368973 97.066856 8100 29.1952 0.97046 0.946564 0.99649 55.833861 0.964376 1 1 1 1 1 1 1 1 1 1 1 1 1 22958 6742 0.13212842 0.086041277 1.535639923 0.186289394
2 2480 22610 9056 806 1702.634155 203.414444 97.066856 8100 28.38089 0.97046 0.931152 0.991409 44.519946 0.954102 3366 178 742.190613 114.357513 97.066856 8100 28.38089 0.97046 0.9711 0.996643 29.434008 0.968187 1 1 1 1 1 1 1 1 1 1 1 1 1 8250 3188 0.047480593 0.040685196 1.167023837 0.067079727
3 2720 22610 1218 744 0 678.130127 0 100 29.1952 1 1 0.991699 1.796115 0.478964 510 184 136.349884 635.734558 67.702759 1000 29.1952 0.754514 0.996872 0.992111 0.802222 0.213926 0 0 1 1 1 0 1 0 1 1 1 0 1 474 326 0.002727976 0.004160406 0.65569947 -0.183295168
4 2950 22610 1340 810 0 222.208313 0 100 28.38089 1 1 0.992661 6.030377 0.5 504 190 54.084621 194.401764 70.917542 1900 28.38089 0.795414 0.998566 0.994736 2.592569 0.691352 0 0 1 1 1 1 1 0 1 1 1 0 1 530 314 0.003050268 0.004007262 0.761185159 -0.118509688
5 3190 22610 1194 892 0 182.570053 0 100 29.1952 1 1 0.994171 6.539955 0.5 464 192 95.207375 149.588242 71.364975 900 29.1952 0.770348 0.997879 0.996063 3.101848 0.763891 0 0 1 1 1 1 1 0 1 1 1 1 1 302 272 0.001738077 0.003471259 0.500705232 -0.30041787
6 3420 22610 1922 848 57.743687 176.725937 22.567585 400 28.38089 0.35015 0.999023 0.994278 10.875597 0.400171 490 162 149.939697 129.104126 86.672455 4800 28.38089 0.92253 0.996048 0.995972 3.795386 0.827449 0 0 0 1 1 1 1 1 1 1 1 1 1 1074 328 0.00618111 0.00418593 1.47663966 0.169274529
7 3660 22610 2682 832 403.459045 189.686768 86.672455 6600 29.1952 0.940013 0.987228 0.994186 14.139099 0.933362 1896 164 658.00824 164.665359 93.389999 7700 29.1952 0.960253 0.978027 0.995407 11.514261 0.926004 1 1 1 1 1 1 1 1 1 1 1 1 1 1850 1732 0.010647163 0.022103751 0.481690334 -0.317232068
8 3890 22610 8430 906 2029.031128 206.254547 97.066856 8100 28.38089 0.97046 0.931076 0.992783 40.871826 0.954051 3914 178 1049.393433 120.761887 97.066856 8100 28.38089 0.97046 0.964874 0.996857 32.410888 0.970939 1 1 1 1 1 1 1 1 1 1 1 1 1 7524 3736 0.043302301 0.047678762 0.908209437 -0.04181399
9 4130 22610 3170 872 599.16333 182.417358 88.489685 6700 29.1952 0.936069 0.983444 0.994522 17.377732 0.942448 1184 202 464.799438 147.298187 90.27034 7200 29.1952 0.93745 0.987671 0.994949 8.038117 0.90038 1 1 1 1 1 1 1 1 1 1 1 1 1 2298 982 0.013225503 0.012532265 1.055316255 0.023382627
10 4360 22610 15626 806 5552.78418 196.66214 93.730225 7800 28.38089 0.955854 0.858261 0.992905 79.456066 0.905507 7406 172 2904.112549 124.20192 94.743553 7900 28.38089 0.955337 0.9263 0.996918 59.628708 0.950867 1 1 1 1 1 1 1 1 1 1 1 1 1 14820 7234 0.085292411 0.092320172 0.923876223 -0.03438621
11 4600 22600 1730 730 51.710735 212.788574 29.854109 1000 19.657873 0.792327 0.998764 0.993195 8.130136 0.649271 700 166 407.140533 113.319534 85.190765 6300 19.657873 0.909892 0.987396 0.997208 6.177223 0.877709 0 0 1 1 1 1 1 1 1 1 1 1 1 1000 534 0.005755223 0.006814898 0.844506184 -0.073397166
12 4830 22600 2100 746 310.873932 181.496185 48.533428 2700 18.426807 0.881187 0.991104 0.994812 11.570491 0.742667 732 150 451.615234 142.891479 92.361824 7400 18.426807 0.938643 0.987076 0.996033 5.122769 0.859605 0 1 1 1 1 1 1 1 1 1 1 1 1 1354 582 0.007792573 0.007427473 1.04915528 0.020839771
13 5070 22600 2796 812 809.958862 193.66478 93.048538 7900 19.657873 0.930384 0.966782 0.993774 14.437318 0.939163 1066 186 317.894592 114.260963 94.069214 7700 19.657873 0.948274 0.990189 0.99678 9.32952 0.911735 1 1 1 1 1 1 1 1 1 1 1 1 1 1984 880 0.011418363 0.011230543 1.016724026 0.007203087
14 5300 22600 3444 882 891.75116 241.175598 88.129242 7000 18.426807 0.920811 0.975586 0.992508 14.280052 0.938575 1332 134 650.06012 133.357971 95.078926 8000 18.426807 0.950954 0.98024 0.996216 9.988154 0.916584 1 1 1 1 1 1 1 1 1 1 1 1 1 2562 1198 0.014744882 0.015288853 0.964420422 -0.015733602
15 5540 22600 2620 840 518.133484 173.350418 89.562332 7200 19.657873 0.9462 0.984772 0.993729 15.113895 0.941568 942 172 293.632019 101.471466 94.743553 7900 19.657873 0.955337 0.990463 0.996597 9.283398 0.911374 1 1 1 1 1 1 1 1 1 1 1 1 1 1780 770 0.010244298 0.009826725 1.042493529 0.018073368
16 5770 22600 1526 826 0 160.577545 0 100 18.426807 1 1 0.995377 9.503197 0.5 578 208 62.792175 121.409889 64.820457 800 18.426807 0.789073 0.998703 0.99678 4.760732 0.760496 0 0 1 1 1 1 1 0 1 1 1 1 1 700 370 0.004028656 0.004721933 0.85317949 -0.068959593
17 6010 22600 2410 906 414.201599 249.230881 53.523727 2900 19.657873 0.87745 0.989502 0.991394 9.669749 0.767619 1004 186 486.456726 148.303207 89.206215 6000 19.657873 0.917392 0.987564 0.995468 6.769914 0.885974 0 1 1 1 1 1 1 1 1 1 1 1 1 1504 818 0.008655856 0.010439301 0.829160536 -0.081361377
18 6240 22600 1306 932 0 211.09671 0 100 18.426807 1 1 0.992737 6.186738 0.5 626 176 140.748001 110.146988 26.462839 500 18.426807 0.535028 0.997467 0.997025 5.683315 0.611461 0 0 1 1 1 1 0 0 0 1 1 1 1 374 450 0.002152454 0.005742892 0.374803104 -0.426196821
19 6480 22600 3296 834 477.425232 267.656616 92.361824 7700 19.657873 0.938643 0.983704 0.991486 12.314286 0.93014 1872 148 600.694336 114.286163 94.743553 7900 19.657873 0.955337 0.980209 0.996704 16.379936 0.945593 1 1 1 1 1 1 1 1 1 1 1 1 1 2462 1724 0.01416936 0.022001655 0.644013362 -0.191105122
20 2250 22830 1880 730 214.230072 226.508652 78.176407 3800 15.115161 0.890631 0.994202 0.993042 8.299904 0.862355 664 166 218.452423 100.321205 93.389999 7500 15.115161 0.951752 0.992722 0.996658 6.61874 0.883974 1 1 1 1 1 1 1 1 1 1 1 1 1 1150 498 0.006618507 0.006355467 1.041388047 0.017612588

Total number of rows: 5776

Table truncated, full table size 1561 Kbytes.




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