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Sample GSM289198 Query DataSets for GSM289198
Status Public on Dec 13, 2008
Title FH_RDE2_14028s_wt_LBlog_1_7DS500
Sample type mixed
 
Channel 1
Source Name 14028s wt RNA LBlog 061018
Organism(s) Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics Salmonella typhimurium 14028s wt RNA harvested from LB log culture
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 14028s gDNA
Organism(s) Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics Salmonella typhimurium 14028s genomic DNA from stationary culture grown 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 biological replicate, Date of Scan Wed Nov 01 10:19:42 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 May 16, 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 GPL6868
Series (1)
GSE11486 Transcriptional profiles of Salmonella typhimurium wt, hfq and smpB mutants in four different growth conditions

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 log10 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 2870 3170 4962 0 1867.369385 167.041931 95.078926 8000 54.659565 0.950954 0.939598 0.99482 29.705116 0.959732 24737 1118 3455.432861 697.846313 95.078926 8000 54.659565 0.950954 0.870491 0.972404 35.447633 0.913661 1 1 1 1 1 1 1 1 1 1 1 1 1 4962 23619 0.062187254 0.008517861 7.300806511 0.863370839
2 3100 3170 895 0 454.877777 192.974182 95.078926 7700 51.088512 0.950954 0.985718 0.994591 4.637926 0.849351 43119 1192 10746.37207 747.749695 97.066856 8100 51.088512 0.97046 0.623642 0.977333 57.665019 0.712734 1 1 1 1 1 1 1 1 1 0 1 1 1 895 41927 0.011216766 0.015120384 0.74183075 -0.129695168
3 3340 3170 242 0 229.598206 157.774841 90.972847 5700 54.659565 0.908001 0.992973 0.996361 1.533831 0.409022 36698 1401 10643.92383 862.830322 97.066856 8100 54.659565 0.97046 0.687111 0.974007 42.532117 0.78527 1 1 1 1 1 0 1 1 1 0 1 1 1 242 35297 0.003032913 0.012729368 0.238261107 -0.622946844
4 3570 3180 315 0 358.488617 292.066589 92.705818 6300 44.39257 0.934498 0.989983 0.99305 1.078521 0.287606 35610 1252 12574.63574 1647.440918 95.078926 8000 44.39257 0.950954 0.677101 0.934662 21.615343 0.77383 1 1 1 1 1 0 1 1 1 0 1 1 1 315 34358 0.0039478 0.012390731 0.318609164 -0.496741737
5 3810 3180 282 0 420.984283 173.617004 91.669968 5700 48.459591 0.915588 0.990028 0.99456 1.624265 0.433137 30104 1273 11619.17773 1098.389893 94.743553 7800 48.459591 0.955337 0.676254 0.968628 27.40739 0.772862 1 1 1 1 1 0 1 1 1 0 1 1 1 282 28831 0.003534221 0.010397496 0.339910818 -0.468635013
6 4040 3190 425 0 367.671692 218.953201 93.389999 6500 39.132648 0.941091 0.990387 0.994576 1.941054 0.517614 23711 1731 10117.27539 1220.106812 93.730225 7800 39.132648 0.93689 0.744263 0.961304 19.433544 0.829508 1 1 1 1 1 0 1 1 1 1 1 1 1 425 21980 0.005326397 0.007926779 0.671949797 -0.172663173
7 4280 3190 635 0 474.65509 169.965134 93.730225 7600 43.692062 0.93689 0.987625 0.994926 3.73606 0.825664 44330 1336 15150.60547 733.289795 95.078926 8000 43.692062 0.950954 0.575745 0.973839 60.453589 0.657994 1 1 1 1 1 1 1 1 1 0 1 1 1 635 42994 0.007958264 0.015505183 0.513264773 -0.289658542
8 4510 3200 327 0 323.668304 233.469894 91.669968 6400 35.944798 0.924633 0.989929 0.991905 1.400609 0.373496 32800 1360 10721.12598 637.295959 95.078926 8000 35.944798 0.950954 0.704987 0.980492 51.467453 0.803324 1 1 1 1 1 0 1 1 1 1 1 1 1 327 31440 0.004098193 0.011338395 0.361443817 -0.4419592
9 4750 3200 17444 0 4977.478027 230.383301 97.066856 8100 40.861477 0.97046 0.823372 0.994904 75.717293 0.882248 29839 1539 7449.581543 1475.020508 96.408768 8000 40.861477 0.963834 0.705551 0.957169 20.229549 0.803701 1 1 1 1 1 1 1 1 1 1 1 1 1 17444 28300 0.218620408 0.010205998 21.42077737 1.330835227
10 4980 3210 920 0 660.064575 190.351135 93.389999 7400 35.393394 0.944295 0.980522 0.995155 4.833173 0.853655 34121 1674 10523.09961 1538.137085 93.048538 7600 35.393394 0.96469 0.700775 0.946144 22.183328 0.800517 1 1 1 1 1 1 1 1 1 1 1 1 1 920 32447 0.011530083 0.011701555 0.98534624 -0.006411136
11 5220 3210 310 0 277.912476 182.01561 91.322075 6700 40.377274 0.938433 0.992554 0.994095 1.703151 0.454174 22910 1354 8317.305664 802.569702 89.562332 7100 40.377274 0.927759 0.742142 0.9767 28.545807 0.828094 1 1 1 1 1 0 1 1 1 1 1 1 1 310 21556 0.003885137 0.007773869 0.499768758 -0.301230896
12 5450 3210 601 0 441.994263 159.955429 95.746155 7500 35.393394 0.957094 0.986397 0.99575 3.757297 0.826307 20747 797 8737.524414 673.653137 97.066856 8100 35.393394 0.97046 0.765312 0.98024 30.797749 0.843541 1 1 1 1 1 1 1 1 1 1 1 1 1 601 19950 0.007532152 0.007194688 1.046904718 0.019907157
13 5690 3220 473 0 309.753754 138.919937 95.078926 7200 42.320068 0.950954 0.991325 0.996025 3.404839 0.814981 29943 924 8773.651367 621.679565 94.743553 7900 42.320068 0.955337 0.740257 0.98098 48.164684 0.826838 1 1 1 1 1 1 1 1 1 1 1 1 1 473 29019 0.005927967 0.010465295 0.566440481 -0.246845717
14 5920 3220 255 0 285.418732 131.869843 88.129242 5400 37.594635 0.918411 0.993576 0.995682 1.933725 0.51566 44959 868 13605.79492 741.522949 92.705818 7800 37.594635 0.934498 0.607407 0.980019 60.630625 0.694179 1 1 1 1 1 0 1 1 1 0 1 1 1 255 44091 0.003195838 0.0159008 0.200986004 -0.696834183
15 6160 3230 297 0 280.333221 87.97541 93.730225 6000 46.385906 0.946722 0.99202 0.997391 3.375943 0.813986 29198 796 9964.608398 567.664673 94.069214 7700 46.385906 0.948812 0.720444 0.982895 51.435295 0.813629 1 1 1 1 1 1 1 1 1 1 1 1 1 297 28402 0.003722212 0.010242783 0.363398484 -0.439616889
16 6390 3230 313 0 243.595032 155.019714 91.669968 4800 42.119125 0.934491 0.992241 0.996117 2.019098 0.538426 36302 636 13162.9834 603.691589 93.389999 7700 42.119125 0.960253 0.645676 0.984688 60.133354 0.737915 1 1 1 1 1 0 1 1 1 0 1 1 1 313 35666 0.003922735 0.012862442 0.304975897 -0.515734483
17 6630 3240 986 0 659.615112 72.908447 92.361824 6900 52.079906 0.934464 0.981644 0.997978 13.52381 0.935583 24509 775 11009.32129 679.717773 90.972847 7300 52.079906 0.943127 0.723618 0.984009 36.057612 0.815745 1 1 1 1 1 1 1 1 1 1 1 1 1 986 23734 0.012357242 0.008559334 1.44371531 0.159481562
18 6860 3240 312 0 319.695099 149.061188 89.91703 6300 48.318573 0.920242 0.991447 0.995216 2.0931 0.55816 24602 767 11004.77051 545.649048 97.066856 8100 48.318573 0.97046 0.713966 0.984001 45.087589 0.809311 1 1 1 1 1 0 1 1 1 1 1 1 1 312 23835 0.003910202 0.008595758 0.454899043 -0.342084977
19 7100 3250 193 0 299.734436 152.360031 90.622276 6200 58.931999 0.912519 0.991486 0.995049 1.266736 0.337796 28357 570 7888.161621 491.651947 95.078926 8000 58.931999 0.950954 0.743599 0.983932 57.676981 0.829066 1 1 1 1 1 0 1 1 1 1 1 1 1 193 27787 0.002418811 0.010020992 0.241374414 -0.617308767
20 2860 3400 261 0 226.482544 93.978447 91.322075 4500 51.740433 0.919504 0.992783 0.99675 2.777233 0.740595 40847 691 10522.13965 523.500549 97.066856 8100 51.740433 0.97046 0.639313 0.983482 78.026661 0.730643 1 1 1 1 1 0 1 1 1 0 1 1 1 261 40156 0.003271035 0.014481698 0.22587369 -0.646134353

Total number of rows: 17328

Table truncated, full table size 5058 Kbytes.




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