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Sample GSM97590 Query DataSets for GSM97590
Status Public on Dec 18, 2008
Title SW480_CLL-228_1857_082403
Sample type RNA
 
Channel 1
Source name SW480_CLL-228_CY5_1857_082403
Organism Homo sapiens
Characteristics SW480 (ATCC nr: CLL-228) was isolated from the tissue of a 51-year-old Caucasian
male and was established from a primary adenocarcinoma of the colon.
Extracted molecule total RNA
Label CY5
 
Channel 2
Source name Human_Reference_Stratagene_CY3_1857_082403
Organism Homo sapiens
Characteristics Stratagene’s Universal Human Reference RNA is composed of total RNA from 10 human cell lines. The reference RNA is designed to
be used as a reference for microarray gene-profiling experiments. Since RNA species differ in abundance between cell lines, an ideal
reference sample should represent these different RNAs. Equal quantities of DNase-treated total RNA from each cell line were
pooled to make the Universal Human Reference RNA. This Universal Reference RNA is suitable for microarray experiments.
(http://www.stratagene.com/manuals/740000.pdf)
Extracted molecule total RNA
Label CY3
 
 
Description The universal human reference is used as "control" to enable comparision between a group of neuroendocrine cell lines and a group of non-neuroendocrine cell lines.
Data processing Log Ratio (635/532)
 
Submission date Feb 20, 2006
Last update date Dec 18, 2008
Contact name Tom Even Wheeler
E-mail(s) tom.wheeler@ntnu.no
Phone +47 92228833
Organization name Norwegian University of Science and Technology, NTNU
Department Department of cancer research and molecular medicine
Street address Olav Kyrresgt. 3
City Trondheim
ZIP/Postal code N-7489
Country Norway
 
Platform ID GPL3313
Series (1)
GSE4328 Identification of novel neuroendocrine markers by gene expression profiling

Data table header descriptions
ID_REF
X The X-coordinate in µm of the center of the fature-indicator associated with the feature, where (0,0) is the top left of the image.
Y The Y-coordinate in µm of the center of the fature-indicator associated with the feature, where (0,0) is the top left of the image.
Dia. The diameter (µm)of the feature-indicator
F635 Median Median feature pixel intensity of the foreground of the Cy5 channel.
F635 Mean Mean feature pixel intensity of the foreground of the Cy5 channel.
F635 SD Standard deviation of feature pixel intensity of the foreground of the Cy5 channel.
B635 Median Median feature background of the Cy5 channel.
B635 Mean Mean feature background of the Cy5 channel.
B635 SD Standard deviation feature of the background of the Cy5 channel.
% > B635+1SD Percent of the feature pixels (in the Cy5 channel) expressing fluorescence greater than the background in addition with one standard deviation.
% > B635+2SD Percent of the feature pixels (in the Cy5 channel) expressing fluorescence greater than the background in addition with two standard deviations.
F635 % Sat. Percent of feature pixels of foreground that is saturated in the Cy5 channel.
F532 Median Median of feature pixels of the foreground in the Cy3 channel.
F532 Mean Mean of feature pixels of the foreground in the Cy3 channel.
F532 SD Standard deviation of feature of the foreground of the Cy3 channel.
B532 Median Background median of the Cy3 channel
B532 Mean Background mean of the Cy3 channel
B532 SD Std.deviation of the background in the Cy3 channel
% > B532+1SD Percent of the feature pixels (in the Cy3 channel) expressing fluorescence greater than the background in addition with one standard deviation.
% > B532+2SD Percent of the feature pixels (in the Cy3 channel) expressing fluorescence greater than the background in addition with two standard deviations.
F532 % Sat. Percent of feature pixels of foreground that is saturated in the Cy3 channel.
Ratio of Medians (635/532) The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
Ratio of Means (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 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 centre of the feature
Rgn R? (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:
Sum of Medians Sum of the median intensities for each wavelength, median background subtracted.
Sum of Means The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.
VALUE same as UNF_VALUE but with flagged values removed
F635 Median - B635 Median of foreground (Cy5) without Cy5 background.
F532 Median - B532 Median of foreground (Cy3) without Cy3 background
F635 Mean - B635 Mean of foreground (Cy5) without Cy5 background
F532 Mean - B532 Mean of foreground (Cy3) without Cy3 background
F635 Total Intensity The sum of feature pixel intensities of Cy5
F532 Total Intensity The sum of feature pixel intensities of Cy3
SNR 635 The signal-to-noise ratio of Cy5, defined by(Mean Foreground 1-Mean background)/(Std.dev.background)
SNR 532 The signal-to-noise ratio of Cy3, defined by(Mean Foreground 1-Mean background)/(Std.dev.background)
Flags Spot flagged as -50 (GenePix "not found") Spot flagged as -75 (Blank/empty) Spot flagged as -100 (manually flagged)
Normalize
UNF_VALUE Log (base2) ratio of the ratio of the medians Cy5/Cy3 (635/532)

Data table
ID_REF X Y Dia. F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD % > B532+1SD % > B532+2SD F532 % Sat. Ratio of Medians (635/532) Ratio of Means (635/532) Median of Ratios (635/532) Mean of Ratios (635/532) Ratios SD (635/532) Rgn Ratio (635/532) Rgn R? (635/532) F Pixels B Pixels Sum of Medians Sum of Means VALUE F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 F635 Total Intensity F532 Total Intensity SNR 635 SNR 532 Flags Normalize UNF_VALUE
NMC-1 1300 2680 90 65535 63227 8222 1856 2309 1894 100 100 90 65535 54478 18217 1339 1612 1190 100 100 63 0.992 1.155 0.992 1.289 1.637 1.152 0.813 52 414 127875 114510 -0.012 63679 64196 61371 53139 3287809 2832843 32.164 44.425 0 0 -0.012
NMC-2 1490 2680 90 65535 63935 6467 2265 2740 2335 100 100 90 65535 53999 17802 1350 1664 1412 100 100 61 0.986 1.171 0.986 1.282 1.551 1.161 0.791 52 388 127455 114319 -0.021 63270 64185 61670 52649 3324600 2807929 26.208 37.064 0 0 -0.021
NMC-3 1650 2680 100 65535 56065 18118 3706 19383 26835 82 77 76 63106 42701 26489 1946 14811 24594 67 55 48 1.011 1.285 0.972 1.954 2.812 1.084 0.769 80 408 122989 93114 0.016 61829 61160 52359 40755 4485200 3416095 1.367 1.134 0 0 0.016
NMC-4 1820 2670 100 65535 63453 6743 39186 38190 27224 0 0 88 50479 43939 21800 5343 26979 29072 66 35 35 0.584 0.629 0.556 0.796 2.395 0.663 0.552 80 452 71485 62863 26349 45136 24267 38596 5076249 3515090 0.928 0.583 -100 0 -0.777
NMC-5 2020 2680 90 65535 65321 1543 5689 16675 23090 100 100 98 42982 41703 19212 2117 9535 19133 78 53 19 1.464 1.506 1.465 1.772 1.882 1.474 0.656 52 382 100711 99218 59846 40865 59632 39586 3396696 2168568 2.107 1.681 -100 0 0.550
NMC-6 2170 2680 90 65535 64653 3925 2328 3166 2865 100 100 94 49422 47139 19019 1458 1654 1128 98 98 25 1.318 1.364 1.318 1.645 2.210 1.349 0.723 52 371 111171 108006 0.398 63207 47964 62325 45681 3361971 2451233 21.461 40.324 0 0 0.398
NMC-7 2350 2660 90 49779 46027 20244 1904 2488 2791 100 100 38 65535 65328 916 1365 1733 2551 100 100 92 0.746 0.690 0.746 0.596 1.811 0.741 0.754 52 396 112045 108086 -0.423 47875 64170 44123 63963 2393407 3397062 15.600 24.929 0 0 -0.423
NMC-8 2530 2680 80 65535 58131 17279 1851 2244 1871 100 98 78 65535 64730 4341 1366 1880 2907 100 100 92 0.992 0.888 0.992 0.793 1.802 0.938 0.884 52 310 127853 119644 -0.011 63684 64169 56280 63364 3022786 3365946 29.870 21.620 0 0 -0.011
NMC-9 2700 2680 80 65535 58614 17043 1759 2072 1758 100 100 80 65535 64073 6334 1493 1742 1379 100 100 92 0.996 0.909 0.996 0.828 1.609 0.950 0.913 52 328 127818 119435 -0.006 63776 64042 56855 62580 3047942 3331798 32.163 45.200 0 0 -0.006
NMC-10 2870 2680 80 65118 52173 16800 1651 2072 2048 100 100 46 65535 51517 18653 1212 1470 1088 100 100 53 0.987 1.004 0.993 1.036 1.329 0.991 0.941 52 334 127790 100827 -0.019 63467 64323 50522 50305 2712991 2678897 24.463 45.999 0 0 -0.019
NMC-11 3050 2670 90 65535 57459 15598 1523 2348 3538 100 100 73 65535 59950 12553 1279 1541 1329 100 100 80 0.996 0.953 0.996 0.925 1.254 0.966 0.944 52 400 128268 114607 -0.005 64012 64256 55936 58671 2987861 3117408 15.577 43.950 0 0 -0.005
NMC-12 3250 2670 80 65535 60204 11258 1602 2366 3344 100 100 75 65535 63983 5643 1272 1461 1000 100 100 92 0.995 0.934 0.995 0.915 1.223 0.945 0.957 52 326 128196 121313 -0.007 63933 64263 58602 62711 3130588 3327091 17.296 62.522 0 0 -0.007
NMC-13 3410 2670 80 14878 17827 12981 1470 1882 1831 92 80 0 22313 28526 18873 1237 1412 1309 100 98 7 0.636 0.599 0.623 0.515 2.377 0.603 0.761 52 302 34484 43646 -0.653 13408 21076 16357 27289 927003 1483335 8.708 20.714 0 0 -0.653
NMC-14 3610 2660 70 29488 31979 15972 1388 2009 1941 96 96 3 45465 43516 19283 1267 1614 3161 100 100 21 0.636 0.724 0.735 0.700 1.590 0.709 0.805 32 231 72298 72840 -0.653 28100 44198 30591 42249 1023338 1392497 15.440 13.256 0 0 -0.653
NMC-15 3760 2670 90 21314 25086 15334 1379 2155 4068 96 86 1 32820 35276 17907 1207 1467 1374 98 98 9 0.631 0.696 0.744 0.662 2.113 0.720 0.818 52 387 51548 57776 -0.665 19935 31613 23707 34069 1304453 1834365 5.637 24.606 0 0 -0.665
NMC-16 3950 2680 90 65535 61098 11302 1365 2192 3788 100 100 80 65535 64747 4897 1435 1745 1434 100 100 94 1.001 0.943 1.001 0.918 1.253 0.928 0.923 52 393 128270 123045 0.002 64170 64100 59733 63312 3177088 3366825 15.551 43.934 0 0 0.002
NMC-17 4110 2680 90 65535 64169 6066 1392 2409 4755 100 100 90 65535 65535 0 1461 1899 1568 100 100 100 1.001 0.980 1.001 0.973 1.145 0.980 0.960 52 362 128217 126851 0.002 64143 64074 62777 64074 3336788 3407820 12.988 40.584 0 0 0.002
NMC-18 4280 2680 90 65535 65535 0 1300 1783 1914 100 100 100 65535 65535 0 1309 1672 1436 100 100 100 1.000 1.000 1.000 1.000 1.000 0.985 0.952 52 386 128461 128461 0.000 64235 64226 64235 64226 3407820 3407820 33.308 44.473 0 0 0.000
NMC-19 4460 2670 90 43532 40967 14297 1439 1936 2226 100 100 3 22687 23167 10514 1156 1431 1335 100 100 0 1.955 1.796 1.811 1.867 1.684 1.811 0.730 52 366 63624 61539 0.967 42093 21531 39528 22011 2130277 1204706 17.534 16.282 0 0 0.967
NMC-20 4630 2680 80 41287 42763 13410 1439 1914 2684 100 100 9 25955 25494 8626 1236 1540 1606 100 100 0 1.612 1.704 1.659 1.729 1.663 1.812 0.676 52 298 64567 65582 0.689 39848 24719 41324 24258 2223652 1325703 15.219 14.915 0 0 0.689

Total number of rows: 30000

Table truncated, full table size 6441 Kbytes.




Supplementary data files not provided
Processed data not applicable for this record
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