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Sample GSM634858 Query DataSets for GSM634858
Status Public on Dec 07, 2010
Title CC2_wtpPBHP92_vs_rpoNpPBHP92_7DE1400
Sample type genomic
 
Channel 1
Source name RpoN-specific pulldown from wt grown with pPBHP92
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics antibody: RpoN-specific pulldown
genotype/variation: wt
: MS1868
growth phase: late log
agent: pPBHP92
Extracted molecule genomic DNA
Extraction protocol chromatin immunoprecipitation using the ChIP assay kit (USB)
Label Cy3
Label protocol amplification of purified immunoprecipitated DNA followed by purification and labeling using Cy3-dCTP with Klenow and random hexamers
 
Channel 2
Source name RpoN-specific pulldown from rpoN mutant strain grown with pPBHP92
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics antibody: RpoN-specific pulldown
genotype/variation: rpoN mutant
: TRH134
growth phase: late log
agent: pPBHP92
Extracted molecule genomic DNA
Extraction protocol chromatin immunoprecipitation using the ChIP assay kit (USB)
Label Cy5
Label protocol amplification of purified immunoprecipitated DNA followed by purification and labeling using Cy5-dCTP with Klenow 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 STv5_SP040504_adapforsmallpins_040817
Description biological replicate, Date of Scan Mon Mar 16 09:01:56 2009
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 Dec 03, 2010
Last update date Dec 06, 2010
Contact name Michael McClelland
E-mail(s) mcclelland.michael@gmail.com
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 GPL11279
Series (1)
GSE25849 Definition of Salmonella rpoN regulon

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 1640 3720 4903 137 2367.123047 219.395554 97.066856 8100 11.488427 0.97046 0.908691 0.994637 22.347764 0.939128 6079 0 2236.670898 221.1716 97.066856 8100 11.488427 0.97046 0.914482 0.993721 27.485446 0.942988 1 1 1 1 1 1 1 1 1 1 1 1 1 4766 6079 0.002248947 0.002269738 0.990839548 -0.003996667
2 1880 3730 14620 24 6959.403809 333.782318 95.078926 7900 6.187308 0.950954 0.828766 0.990387 43.801002 0.885844 23697 0 8152.347656 694.342407 97.066856 8100 6.187308 0.97046 0.766922 0.985077 34.128695 0.844615 1 1 1 1 1 1 1 1 1 1 1 1 1 14596 23697 0.006887458 0.008847836 0.778434229 -0.108778076
3 2120 3730 14635 90 8421.479492 267.070313 94.743553 7900 3.954276 0.955337 0.799362 0.991959 54.798303 0.866241 13985 0 7245.22168 121.658569 97.066856 8100 3.954276 0.97046 0.813179 0.996727 114.952856 0.875453 1 1 1 1 1 1 1 1 1 1 1 1 1 14545 13985 0.006863393 0.005221631 1.314415564 0.118732693
4 2350 3720 11205 30 3629.897461 242.463486 97.066856 8100 7.703082 0.97046 0.886513 0.993225 46.213144 0.924342 12561 0 4247.533691 118.338478 97.066856 8100 7.703082 0.97046 0.865608 0.996536 106.144681 0.910405 1 1 1 1 1 1 1 1 1 1 1 1 1 11175 12561 0.005273181 0.004689947 1.124358362 0.050904754
5 2590 3730 2387 0 1668.42041 205.722046 97.066856 8100 3.954276 0.97046 0.954735 0.994774 11.603035 0.926487 6064 0 3566.89502 153.264023 97.066856 8100 3.954276 0.97046 0.900085 0.99585 39.565711 0.93339 1 1 1 1 1 1 1 1 1 1 1 1 1 2387 6064 0.001126361 0.002264138 0.497478899 -0.303225336
6 2830 3730 1375 23 1180.258667 274.697998 97.066856 6900 6.556662 0.97046 0.96608 0.993271 5.005497 0.857255 2263 0 1666.240845 78.380707 94.406982 7600 6.556662 0.943981 0.949028 0.997261 28.871901 0.962654 1 1 1 1 1 1 1 1 1 1 1 1 1 1352 2263 0.000637972 0.000844945 0.755046286 -0.122026424
7 3060 3740 14694 0 7694.970703 170.963348 96.408768 7800 13.949251 0.963834 0.820305 0.994919 85.948246 0.880203 16235 0 7521.463379 149.356918 97.066856 8100 13.949251 0.97046 0.79126 0.995621 108.69935 0.86084 1 1 1 1 1 1 1 1 1 1 1 1 1 14694 16235 0.006933702 0.006061721 1.143850274 0.058369181
8 3290 3730 14266 14 4482.274414 292.043732 97.066856 8100 6.187308 0.97046 0.849388 0.990227 48.848848 0.899592 20493 0 4949.97168 158.939484 97.066856 8100 6.187308 0.97046 0.828934 0.99543 128.935866 0.885956 1 1 1 1 1 1 1 1 1 1 1 1 1 14252 20493 0.006725134 0.007651546 0.878924785 -0.056048288
9 3530 3730 10696 26 3833.717041 306.57251 95.078926 8000 3.954276 0.950954 0.885971 0.990494 34.888973 0.923981 17840 0 3715.915527 124.745522 97.066856 8100 3.954276 0.97046 0.876747 0.996674 143.011146 0.917831 1 1 1 1 1 1 1 1 1 1 1 1 1 10670 17840 0.005034885 0.006660986 0.755876785 -0.121548993
10 3760 3720 17179 63 5277.329102 252.76651 97.066856 8100 7.703082 0.97046 0.829933 0.992409 67.963909 0.886622 18812 0 6522.109863 162.553726 97.066856 8100 7.703082 0.97046 0.791679 0.996773 115.727892 0.86112 1 1 1 1 1 1 1 1 1 1 1 1 1 17116 18812 0.008076578 0.007023905 1.149870006 0.060648746
11 4000 3720 2441 9 1516.697998 606.163147 95.078926 8000 6.057308 0.950954 0.95768 0.991386 4.026969 0.834079 1628 0 1369.210327 97.513573 94.406982 7500 6.057308 0.943981 0.963531 0.997437 16.695112 0.94651 1 1 1 1 1 1 1 1 1 1 1 1 1 2432 1628 0.001147595 0.000607852 1.88795052 0.275990608
12 4230 3730 2031 62 1471.534058 209.469711 95.078926 7900 6.187308 0.950954 0.957901 0.994682 9.695913 0.9145 4662 0 3380.331543 144.585831 97.066856 8100 6.187308 0.97046 0.901733 0.9963 32.243823 0.934489 1 1 1 1 1 1 1 1 1 1 1 1 1 1969 4662 0.000929118 0.001740668 0.53377089 -0.272645115
13 4470 3730 6684 73 2569.727051 213.494263 94.743553 7900 3.954276 0.955337 0.913773 0.99514 31.307633 0.942515 12390 0 2984.930908 174.6586 97.066856 8100 3.954276 0.97046 0.890945 0.994911 70.938391 0.927297 1 1 1 1 1 1 1 1 1 1 1 1 1 6611 12390 0.003119552 0.0046261 0.674337465 -0.171122711
14 4710 3730 10868 28 4673.437988 235.590134 96.408768 8000 6.556662 0.963834 0.877426 0.993744 46.130964 0.918284 13074 0 4691.197754 89.976219 97.066856 8100 6.556662 0.97046 0.868912 0.997444 145.305061 0.912608 1 1 1 1 1 1 1 1 1 1 1 1 1 10840 13074 0.005115103 0.004881487 1.047857532 0.02030224
15 4940 3730 15306 0 5459.455566 317.832123 97.066856 8100 3.954276 0.97046 0.834305 0.991928 48.157499 0.889537 18226 0 4621.82373 100.859749 97.066856 8100 3.954276 0.97046 0.848877 0.99691 180.706379 0.899251 1 1 1 1 1 1 1 1 1 1 1 1 1 15306 18226 0.007222488 0.006805108 1.061333276 0.025851781
16 5180 3720 9150 102 4014.213135 303.850189 94.743553 7900 8.002781 0.955337 0.890923 0.992348 30.113524 0.927282 15403 0 5411.548828 116.390656 97.066856 8100 8.002781 0.97046 0.841553 0.996925 132.338803 0.894368 1 1 1 1 1 1 1 1 1 1 1 1 1 9048 15403 0.004269507 0.005751074 0.74238419 -0.129371286
17 5410 3720 2091 91 1284.307373 302.233582 95.413124 7800 6.057308 0.964797 0.961433 0.991783 6.91849 0.887873 2700 0 1992.303711 195.284607 95.078926 8000 6.057308 0.950954 0.940918 0.994133 13.825975 0.936813 1 1 1 1 1 1 1 1 1 1 1 1 1 2000 2700 0.000943746 0.001008109 0.936154802 -0.028652331
18 5650 3730 3137 0 2052.733643 240.375702 97.066856 8100 6.556662 0.97046 0.917831 0.995468 13.050404 0.933557 5892 0 2982.115234 120.270172 97.066856 8100 6.556662 0.97046 0.917297 0.995934 48.989703 0.944865 1 1 1 1 1 1 1 1 1 1 1 1 1 3137 5892 0.001480266 0.002199918 0.672873181 -0.172066781
19 5880 3730 17273 68 3883.89209 237.297302 97.066856 8100 3.954276 0.97046 0.851807 0.994232 72.790545 0.901204 24563 0 4637.737793 315.85379 97.066856 8100 3.954276 0.97046 0.831139 0.995918 77.766995 0.887426 1 1 1 1 1 1 1 1 1 1 1 1 1 17205 24563 0.008118575 0.009171177 0.885227112 -0.052945293
20 1640 3960 47524 147 7266.08252 279.230438 97.066856 8100 9.821233 0.97046 0.650032 0.991432 170.196345 0.742894 40155 0 6610.979004 193.36142 97.066856 8100 9.821233 0.97046 0.693871 0.994507 207.668107 0.792995 1 1 1 0 1 1 1 1 1 0 1 1 1 47377 40155 0.022355926 0.014992819 1.491108908 0.173509365

Total number of rows: 17328

Table truncated, full table size 5061 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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