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Sample GSM183697 Query DataSets for GSM183697
Status Public on Nov 10, 2008
Title SQ 037 LuxI plus VAI_2-1
Sample type mixed
 
Channel 1
Source Name pool of 100 Euprymna scolopes light organs
Organism(s) Euprymna scolopes
Characteristics Euprymna scolopes, age 18 hours, hatchling, genetic variation: pooled clutches rep2 same, source: Paiko HI, tissue: light organ
Growth protocol 6hr innoculation with V.fischeri ES114 LuxI- mutant (Cheryl Whistler)(5000 cells/ml), then transferred into OSW without V.fischeri with VAI. Dissected at 18hrs post-innoculation.
Extracted molecule total RNA
Extraction protocol Total RNA isolation was accomplished with Epicenter and Qiagen RNeasy Mini Kit reagents. Total RNA was cleaned up using Millipore Microcon 30
Label cy5
Label protocol 1 µg Total RNA was labeled with Genisphere 3DNA Array 350 RNA labeling kit.
 
Channel 2
Source Name Euprymna Scolopoes run-off reference
Organism(s) Euprymna scolopes
Characteristics RNA transcribed from equal volumes of stationary culture of E. coli cDNA clones representing each unique spot on the microarray.
Growth protocol 13,962 nonredundant E. coli clones were grown individually to stationary phase and then equal volumes were combined. A plasmid prep was performed on 50ml of the combined samples. Inserts were then amplified via PCR for 10 cycles then 1µl of the PCR product was then used for an additional 25 cycles of PCR amplification.
Extracted molecule other
Extraction protocol Trizol procedure
Label cy3
Label protocol Samples were labeled with Genisphere 3DNA Array 350 RNA labeling kit.
 
 
Hybridization protocol oligoarray control targets and hybridization buffer (Agilent in Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially with 6x SSC/0.005% Triton X-102 and 0.1x SSC/0.005 Triton X-102 before scanning. Slides were hybridized for 17 h 60 degrees c in a rotating oven, and washed.
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.1.0.0 analysis software.
Description Euprymna scolopes, age 18 hours, hatchling, genetic variation: pooled clutches rep2 same, source: Paiko HI, tissue: light organ
Data processing raw data as output from GenePix Pro 5.1.0.0 analysis software. VALUEs represent log2 (test/ref) ratios.
 
Submission date Apr 24, 2007
Contact name Bartley Joseph Brown
E-mail(s) bbrown@eng.uiowa.edu
Phone 319 335 6432
Organization name The University of Iowa
Lab CBCB
Street address 5317
City Iowa City
State/province IA
ZIP/Postal code 52242
Country USA
 
Platform ID GPL3825
Series (1)
GSE13533 Colonization, luminescence, and autoinducer effects on host transcription during development of squid-vibrio association

Data table header descriptions
ID_REF
VALUE log2 of PRE_VALUE
Dia. The diameter in µm of the feature-indicator.
F635 Median Median feature pixel intensity at wavelength #1 (635 nm).
F635 Mean Mean feature pixel intensity at wavelength #1 (635 nm).
F635 SD The standard deviation of the feature pixel intensity at wavelength #1 (635 nm).
F635 CV The coefficient of variation of feature pixel intensity.
B635 The actual background value used for the feature in GenePix Pro calculations (as opposed to B635 Median, for example, which is the local median background.) This column is required because GenePix Pro 5.0 has global and negative control background subtraction methods. If you choose a non-local method, B635 is different to B635 Median.
B635 Median The median feature background intensity at wavelength #1 (635 nm).
B635 Mean The mean feature background intensity at wavelength #1 (635 nm).
B635 SD The standard deviation of the feature background intensity at wavelength #1 (635 nm).
B635 CV The coefficient of variation of local background pixel intensity.
% > B635+1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm).
% > B635+2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm).
F635 % Sat. The percentage of feature pixels at wavelength #1 that are saturated.
F532 Median Median feature pixel intensity at wavelength #2 (532 nm).
F532 Mean Mean feature pixel intensity at wavelength #2 (532 nm).
F532 SD The standard deviation of the feature intensity at wavelength #2 (532 nm).
F532 CV The coefficient of variation of local background pixel intensity.
B532 The actual background value used for the feature in GenePix Pro calculations (as opposed to B532 Median, for example, which is the local median background.) This column is required because GenePix Pro 5.0 has global and negative control background subtraction methods. If you choose a non-local method, B532 is different to B532 Median.
B532 Median The median feature background intensity at wavelength #2 (532 nm).
B532 Mean The mean feature background intensity at wavelength #2 (532 nm).
B532 SD The standard deviation of the feature background intensity at wavelength #2 (532 nm).
B532 CV The coefficient of variation of feature pixel intensity.
% > B532+1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm).
% > B532+2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm).
F532 % Sat. The percentage of feature pixels at wavelength #2 that are saturated.
Ratio of Medians (635/532) The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
Median of Ratios (635/532) The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Mean of Ratios (635/532) The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Ratios SD (635/532) The geometric standard deviation of the pixel intensity ratios.
Rgn Ratio (635/532) The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.
Rgn R2 (635/532) The coefficient of determination for the current regression value.
F Pixels The total number of feature pixels.
B Pixels The total number of background pixels.
Circularity A measure of circularity from 0 to 100, using a metric based on the variance of the distance of each boundary pixel to the centroid of the feature: 100 is most circular, 0 is most non-circular. Circular features always have a circularity of 100, square features always have a circularity of 79 (= p/4*100).
Sum of Medians (635/532) The sum of the median intensities for each wavelength, with the median background subtracted.
Sum of Means (635/532) The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.
Log Ratio (635/532) Log (base 2) transform of the ratio of the medians.
F635 Median - B635 The median feature pixel intensity at wavelength #1 with the median background subtracted.
F532 Median - B532 The median feature pixel intensity at wavelength #2 with the median background subtracted.
F635 Mean - B635 The mean feature pixel intensity at wavelength #1 with the median background subtracted.
F532 Mean - B532 The mean feature pixel intensity at wavelength #2 with the median background subtracted.
F635 Total Intensity The sum of feature pixel intensities at wavelength #1.
F532 Total Intensity The sum of feature pixel intensities at wavelength #2.
SNR 635 The signal-to-noise ratio of the feature, calculated as (F635 Mean - B635 Mean) / B635 SD.
SNR 532 The signal-to-noise ratio of the feature, calculated as (F532 Mean - B532 Mean) / B532 SD.
Flags The type of flag associated with a feature.
Normalize The normalization status of the feature (included/not included).
Autoflag Reports whether or not a feature has been flagged from the Flag Features dialog box. It applies to good and bad flags only.
UNF_VALUE Ratio of means, the ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.
PRE_VALUE same as UNF_VALUE but with flagged values removed

Data table
ID_REF VALUE Dia. F635 Median F635 Mean F635 SD F635 CV B635 B635 Median B635 Mean B635 SD B635 CV % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD F532 CV B532 B532 Median B532 Mean B532 SD B532 CV % > B532+1SD % > B532+2SD F532 % Sat. Ratio of Medians (635/532) Median of Ratios (635/532) Mean of Ratios (635/532) Ratios SD (635/532) Rgn Ratio (635/532) Rgn R2 (635/532) F Pixels B Pixels Circularity Sum of Medians (635/532) Sum of Means (635/532) Log Ratio (635/532) F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 F635 Total Intensity F532 Total Intensity SNR 635 SNR 532 Flags Normalize Autoflag UNF_VALUE PRE_VALUE
1_1_1 90 45 70 77 110 44 44 77 205 266 3 0 0 60 84 124 147 56 56 87 188 216 3 2 0 0.250 1.370 1.398 4.346 0.148 0.009 256 1688 100 5 54 -2.000 1 4 26 28 17827 21427 -0.034 -0.016 -50 0 0 0.929
1_2_1 0.5301 90 182 213 149 69 44 44 65 84 129 68 37 0 82 172 171 99 55 55 72 80 111 37 28 0 5.111 3.043 2.710 7.813 0.312 0.027 35 1915 35 165 286 2.354 138 27 169 117 7438 6020 1.762 1.250 0 0 0 1.444 1.444
1_3_1 90 43 57 55 96 45 45 65 92 141 4 1 0 55 63 39 61 57 57 75 89 118 1 0 0 1.000 1.000 1.099 4.583 0.267 0.018 256 1809 100 -4 18 0.000 -2 -2 12 6 14655 16012 -0.087 -0.135 -50 0 0 2.000
1_4_1 90 47 64 75 117 43 43 59 64 108 10 3 0 61 82 86 104 56 56 66 60 90 8 5 0 0.800 1.012 0.871 4.781 0.014 0.000 256 1786 100 9 47 -0.322 4 5 21 26 16471 21119 0.078 0.267 -50 0 0 0.808
1_5_1 90 43 71 144 202 43 43 58 48 82 16 8 0 60 79 103 130 56 56 71 72 101 5 3 0 0.000 1.444 1.376 4.210 0.656 0.006 256 1716 100 4 51 Error 0 4 28 23 18089 20250 0.271 0.111 -50 0 0 1.217
1_6_1 -0.8520 70 60 255 558 218 43 43 60 55 91 45 30 0 388 438 345 78 55 55 69 65 94 85 85 0 0.051 0.083 0.298 24.459 0.994 0.003 20 1083 49 350 595 -4.292 17 333 212 383 5091 8759 3.545 5.677 0 0 0 0.554 0.554
1_7_1 90 45 60 46 76 43 43 57 52 91 13 3 0 56 71 63 88 55 55 72 81 112 5 3 0 2.000 1.250 1.261 4.503 0.050 0.002 256 1856 100 3 33 1.000 2 1 17 16 15415 18120 0.058 -0.012 -50 0 0 1.063
1_8_1 -0.1600 70 157 164 143 87 45 45 62 90 145 52 26 0 122 188 168 89 55 55 68 71 104 47 36 0 1.672 3.596 2.728 12.869 0.019 0.000 19 1110 35 179 252 0.741 112 67 119 133 3122 3581 1.133 1.690 0 0 0 0.895 0.895
1_9_1 -0.2951 100 897 939 482 51 44 44 59 49 83 99 98 0 1052 1153 648 56 55 55 71 89 125 98 96 0 0.856 0.796 0.844 2.454 0.720 0.509 350 2086 92 1850 1993 -0.225 853 997 895 1098 328666 403596 17.959 12.157 0 0 0 0.815 0.815
1_10_1 0.0412 105 541 639 435 68 43 43 59 55 93 97 93 0 542 634 394 62 55 55 71 74 104 96 90 0 1.023 0.990 1.033 3.181 1.080 0.327 349 1995 92 985 1175 0.032 498 487 596 579 222873 221364 10.545 7.608 0 0 0 1.029 1.029
1_11_1 90 47 59 39 66 43 43 59 57 96 13 3 0 58 70 56 80 55 55 70 69 98 5 3 0 1.333 1.417 1.398 4.665 0.017 0.000 256 1677 100 7 31 0.415 4 3 16 15 15084 17819 0.000 0.000 -50 0 0 1.067
1_12_1 0.0370 65 143 163 114 69 43 43 55 40 72 77 66 0 116 173 149 86 56 56 70 66 94 50 33 0 1.667 2.390 1.510 5.627 -0.008 0.000 18 981 86 160 237 0.737 100 60 120 117 2938 3119 2.700 1.561 0 0 0 1.026 1.026
1_13_1 -1.2076 110 1804 1883 694 36 44 44 61 74 121 99 99 0 4307 4300 1481 34 56 56 72 75 104 100 100 0 0.414 0.416 0.431 1.669 0.398 0.767 440 2404 91 6011 6083 -1.272 1760 4251 1839 4244 828578 1892076 24.622 56.373 0 0 0 0.433 0.433
1_14_1 1.3561 110 1186 1349 830 61 46 46 61 68 111 99 99 0 463 566 439 77 57 57 67 54 80 93 86 0 2.808 2.924 3.064 3.010 3.003 0.444 392 2238 94 1546 1812 1.489 1140 406 1303 509 528718 222028 18.941 9.241 0 0 0 2.560 2.560
1_15_1 90 48 70 67 95 46 46 62 67 108 15 4 0 64 79 62 78 59 59 72 66 91 8 4 0 0.400 1.667 1.486 4.469 0.303 0.002 256 1691 100 7 44 -1.322 2 5 24 20 17973 20150 0.119 0.106 -50 0 0 1.200
1_16_1 0.0426 110 11746 11375 7303 64 52 52 72 70 97 100 100 0 12187 11058 6114 55 68 68 89 92 103 100 100 0 0.965 1.011 0.964 1.484 1.085 0.942 432 2263 92 23813 22313 -0.052 11694 12119 11323 10990 4913923 4777071 161.471 119.228 0 0 0 1.030 1.030
1_17_1 -0.0174 110 2268 2389 1165 48 69 69 138 197 142 100 98 0 2325 2428 961 39 80 80 126 130 103 100 99 0 0.980 0.945 0.942 1.766 1.039 0.734 452 2437 94 4444 4668 -0.030 2199 2245 2320 2348 1079692 1097557 11.426 17.708 0 0 0 0.988 0.988
1_18_1 90 548 673 524 77 88 88 186 246 132 69 48 0 399 539 440 81 101 101 171 175 102 64 46 0 1.544 1.362 1.449 4.059 1.851 0.209 256 1527 100 758 1023 0.626 460 298 585 438 172244 137957 1.980 2.103 -50 0 0 1.336
1_19_1 0.2437 125 4386 4966 3311 66 64 64 122 206 168 99 98 0 3610 4224 2868 67 84 84 147 278 189 97 96 0 1.226 1.168 1.191 1.785 1.183 0.873 499 2770 91 7848 9042 0.294 4322 3526 4902 4140 2478037 2107656 23.515 14.665 0 0 0 1.184 1.184
1_20_1 0.1309 110 2091 2815 2061 73 58 58 93 179 192 98 97 0 1954 2593 1785 68 75 75 112 280 250 96 92 0 1.082 1.057 1.079 2.003 1.133 0.814 404 2229 82 3912 5275 0.114 2033 1879 2757 2518 1137315 1047651 15.207 8.861 0 0 0 1.095 1.095

Total number of rows: 30000

Table truncated, full table size 6162 Kbytes.




Supplementary file Size Download File type/resource
GSM183697.gpr.gz 2.6 Mb (ftp)(http) GPR
Raw data provided as supplementary file
Raw data included within Sample table
Processed data not provided for this record
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