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Sample GSM68796 Query DataSets for GSM68796
Status Public on Jan 10, 2006
Title Comparative Genomic Hybridization between strain ISP1820 and CT18, replicate 1
Sample type genomic
 
Channel 1
Source name Salmonella typhi ISP1820 genomic DNA
Organism Salmonella enterica subsp. enterica serovar Typhi
Characteristics Genomic DNA from Salmonella typhi ISP1820
Growth protocol Salmonella typhi ISP1820 from overnight culture in LB broth.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted by standard phenol-chloroform method (Sambrook, J, Molecular Cloning, 3rd Edition)
Label Cy3
Label protocol 1.5 µg of genomic DNA was labeled with Cy3-dCTP (GE Healthcare) by random priming with Klenow (New England Biolabs) as previously described (Porwollik, S. 2001. Mutat Res 483:1-11.).
 
Channel 2
Source name Salmonella typhi CT18 genomic DNA
Organism Salmonella enterica subsp. enterica serovar Typhi
Characteristics Genomic DNA from Salmonella typhi CT18
Growth protocol Salmonella typhi from overnight culture in LB broth.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted by standard phenol-chloroform method (Sambrook, J, Molecular Cloning, 3rd Edition)
Label Cy5
Label protocol 1.5 µg of genomic DNA was labeled with Cy3-dCTP (GE Healthcare) by random priming with Klenow (New England Biolabs) as previously described (Porwollik, S. 2001. Mutat Res 483:1-11.).
 
 
Hybridization protocol Samples we hybridized as previously described (Porwolik, S. 2003.Nucleic Acids Res 31:1869-76)
Scan protocol Slide was scanned with Scan Array Lite (Perkin-Elmer) using Scan Array Express 2.1 software.
Description This sample was used to identify genes absent in ISP1820 compared to CT18
Data processing After backgroud correction and total intensity normalization, ratio to reference were calculated and log base 2 transformed.
 
Submission date Aug 09, 2005
Last update date Jan 10, 2006
Contact name Sébastien P Faucher
E-mail(s) sebastien.faucher@umontreal.ca
Phone 514-343-6111 #3135
Fax 514-343-5701
Organization name University of Montreal
Department Microbiology and Immunology
Street address C.P. 6128 Succ. Centre-Ville
City Montreal
State/province QUEBEC
ZIP/Postal code H3C 3J7
Country Canada
 
Platform ID GPL548
Series (1)
GSE3094 Analysis of genomic differences between Salmonella typhi ISP1820 and CT18

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_MEAN_SD
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
C2_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 base 2 of ch1 % of total / ch2 % of total

Data table
ID_REF X_LOCATION Y_LOCATION CH1_MEAN CH1_BKD_MEAN CH1_MEAN_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 C2_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 1300 2820 28813.81836 354.897064 30672.54492 600.140259 190.992981 27400 3.769349 0.966433 0.500351 0.987167 48.011807 0.57183 7523.932617 57.941177 7824.603516 157.502991 185.754669 22300 3.769349 0.957433 0.778679 0.99456 47.770094 0.844082 1 1 1 0 1 1 1 1 1 1 1 1 1 28458.9213 7465.99144 0.094132739 0.029059384 3.239323258 1.695692445
2 1540 2820 2980.259521 194.5 3205.816406 315.635071 190.659378 20800 1.29376 0.96514 0.92572 0.991295 9.442105 0.835165 2070.317871 87.779411 1665.71582 206.575989 179.479706 17300 1.29376 0.950508 0.956009 0.993813 10.022064 0.855491 1 1 1 1 1 1 1 1 1 1 1 1 1 2785.759521 1982.53846 0.009214375 0.007716503 1.194112775 0.255939095
3 1780 2810 799.400024 255.308823 740.845154 454.982025 186.609512 15500 11.498513 0.972353 0.978119 0.989555 1.756993 0.468531 333.529419 48.573528 330.0625 133.042175 185.411636 13600 11.498513 0.966677 0.990776 0.996414 2.506945 0.668519 1 1 1 1 1 0 1 1 1 1 1 0 1 544.091201 284.955891 0.001799675 0.001109115 1.622622169 0.698327104
4 2010 2820 647.684631 191.029419 631.188293 319.794556 190.492355 13000 1.29376 0.963444 0.982292 0.990929 2.025315 0.540084 220.319153 68.75 226.255646 176.365402 182.818344 9400 1.29376 0.950402 0.992905 0.995216 1.24922 0.333125 1 1 1 1 1 0 1 1 1 1 1 0 1 456.655212 151.569153 0.001510465 0.000589943 2.560359433 1.356346355
5 2240 2810 4621.413086 205.735291 5145.367188 414.382141 189.150833 20100 10.357807 0.964132 0.878807 0.98793 11.152539 0.837908 3288.918945 19 3376.212891 61.688915 185.411636 18500 10.357807 0.94796 0.925438 0.99839 53.314585 0.844706 1 1 1 1 1 1 1 1 1 1 1 1 1 4415.677795 3269.918945 0.014605608 0.012727289 1.147582009 0.198597256
6 2470 2810 1370.411499 256.058838 1384.507446 461.536407 184.551254 19200 13.031437 0.966454 0.956955 0.987213 2.969238 0.791797 965.539368 29.014706 795.330505 96.503418 172.977264 16500 13.031437 0.944653 0.976707 0.996574 10.005235 0.867314 1 1 1 1 1 0 1 1 1 1 1 1 1 1114.352661 936.524662 0.003685912 0.003645173 1.011176059 0.016034211
7 2720 2820 8082.76416 207.044113 9063.827148 338.881409 190.492355 21200 6.256168 0.966555 0.801849 0.991745 23.851306 0.835468 6660.356934 56.911766 6491.263672 135.807007 173.34491 18200 6.256168 0.952043 0.855247 0.995491 49.042808 0.866646 1 1 1 1 1 1 1 1 1 1 1 1 1 7875.720047 6603.445168 0.026050288 0.025702152 1.013545002 0.019410147
8 2950 2820 6203.517578 150.691177 6299.683594 276.001678 193.312149 23000 1.29376 0.975243 0.839058 0.991508 22.476376 0.830342 4566.633301 38.735294 3851.597168 116.052689 185.583237 19900 1.29376 0.9627 0.916534 0.996819 39.349655 0.844394 1 1 1 1 1 1 1 1 1 1 1 1 1 6052.826401 4527.898007 0.020020756 0.017623638 1.136017247 0.183984738
9 3190 2810 439.812073 121.338234 479.450226 255.199463 186.950348 14900 11.498513 0.965765 0.985947 0.99057 1.723405 0.459575 226.182693 65.544121 226.714813 142.484406 179.302277 10400 11.498513 0.949188 0.994568 0.996155 1.587421 0.423312 1 1 1 1 1 0 1 1 1 1 1 0 1 318.473839 160.638572 0.001053407 0.000625243 1.684795798 0.752573743
10 3420 2810 8158.407715 113.367645 8191.969727 212.030899 190.992981 23300 9.73396 0.967243 0.817108 0.99469 38.477447 0.834558 6953.65332 57.558823 5910.924316 167.009995 182.295258 20200 9.73396 0.942752 0.865753 0.994919 41.636151 0.850372 1 1 1 1 1 1 1 1 1 1 1 1 1 8045.04007 6896.094497 0.026610343 0.026841212 0.991398711 -0.012462712
11 3650 2810 12461.55273 95.411766 11787.44727 230.576706 185.411636 21900 10.357807 0.969118 0.767311 0.993301 54.04515 0.844706 9360.712891 48.529411 8169.500488 124.430702 183.686844 20900 10.357807 0.962626 0.837852 0.996422 75.228322 0.847842 1 1 1 1 1 1 1 1 1 1 1 1 1 12366.14097 9312.18348 0.040903122 0.036245195 1.128511557 0.174421193
12 3880 2820 10030.82129 211.852936 9811.243164 400.914215 186.609512 23000 8.760262 0.967239 0.790527 0.989235 25.019869 0.842528 7575.533203 99.029411 6883.736816 167.678253 180.364288 21200 8.760262 0.964306 0.850937 0.994995 45.178985 0.853883 1 1 1 1 1 1 1 1 1 1 1 1 1 9818.968353 7476.503792 0.032477914 0.029100301 1.11606797 0.158424892
13 4110 2810 8534.84668 247.632355 7762.30957 402.152649 190.157852 22200 16.803349 0.967243 0.817612 0.988121 21.222903 0.836077 6415.535645 49.10294 5427.431152 127.132103 185.239883 20900 16.803349 0.949362 0.8601 0.995911 50.463537 0.845018 1 1 1 1 1 1 1 1 1 1 1 1 1 8287.214325 6366.432705 0.027411376 0.024779644 1.106205365 0.145619244
14 4360 2810 4857.25 242.044113 4705.323242 370.642273 190.32518 20400 9.73396 0.966564 0.889709 0.989182 13.104954 0.835772 3069.195068 37.044117 3003.896973 116.603737 187.460449 20000 9.73396 0.956593 0.922508 0.995636 26.321584 0.840981 1 1 1 1 1 1 1 1 1 1 1 1 1 4615.205887 3032.150951 0.015265581 0.01180184 1.293491574 0.371270656
15 4600 2810 815.133362 361.367645 661.450195 591.173279 188.982483 13500 11.498513 0.965627 0.982552 0.983543 1.37884 0.367691 281.25 81.485291 245.339096 179.979233 188.645309 12800 11.498513 0.956195 0.99279 0.994263 1.56268 0.416715 1 1 1 1 1 0 1 1 1 1 1 0 1 453.765717 199.764709 0.001500908 0.000777531 1.930350873 0.948863105
16 4830 2810 8766.869141 260.308838 9406.90625 530.559631 191.990341 22900 9.73396 0.971901 0.786331 0.981606 16.523815 0.832745 7020.108398 51.911766 7231.794434 126.669243 187.799744 22100 9.73396 0.943458 0.850838 0.997742 55.420781 0.840364 1 1 1 1 1 1 1 1 1 1 1 1 1 8506.560303 6968.196632 0.0281369 0.02712185 1.037425527 0.053007774
17 5060 2810 6037.609863 168.338242 5791.931152 352.565216 188.476501 21800 10.357807 0.960571 0.865646 0.990402 17.124803 0.839134 4254.507324 67.941177 3793.470459 166.920471 180.364288 20700 10.357807 0.95339 0.917969 0.995201 25.48823 0.853883 1 1 1 1 1 1 1 1 1 1 1 1 1 5869.271621 4186.566147 0.019413618 0.016295094 1.191378047 0.252631281
18 5290 2810 543.084961 271.544128 624.725769 542.033691 188.813965 15300 13.031437 0.962712 0.982544 0.984245 1.001939 0.267184 249.095245 63.10294 234.740234 140.140671 183.339935 8400 13.031437 0.947913 0.994194 0.995872 1.777466 0.473991 1 1 1 1 1 0 1 1 1 1 1 0 1 271.540833 185.992305 0.000898168 0.000723926 1.240690656 0.311143451
19 5530 2830 3359.492676 105.955879 3292.302979 255.536682 192.321655 20300 11.00599 0.968689 0.921791 0.991356 13.146812 0.832142 2599.536377 47.676472 2283.052002 130.623581 182.818344 17900 11.00599 0.948988 0.944138 0.995926 19.900973 0.849421 1 1 1 1 1 1 1 1 1 1 1 1 1 3253.536797 2551.859905 0.010761628 0.009932435 1.083483338 0.115676967
20 1310 3050 1282.051147 376.088226 1024.212891 617.705994 189.319046 17600 7.78959 0.967147 0.971085 0.982475 2.075504 0.553468 764.368103 29.32353 640.12207 74.816078 182.469788 16300 7.78959 0.95134 0.982307 0.997643 10.216629 0.850055 1 1 1 1 1 0 1 1 1 1 1 1 1 905.962921 735.044573 0.002996627 0.002860965 1.047418138 0.066837493

Total number of rows: 5776

Table truncated, full table size 1941 Kbytes.




Supplementary data files not provided
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