NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM96659 Query DataSets for GSM96659
Status Public on Dec 18, 2008
Title A-427_HTB-53_2142_082103
Sample type RNA
 
Channel 1
Source name A-427_HTB-53_CY5_2142_082103
Organism Homo sapiens
Characteristics A-427 cell line (ATCC nr: HTB-53) was derived from lung and is an epidermoid
carcinoma.
Extracted molecule total RNA
Label CY5
 
Channel 2
Source name Human_Reference_Stratagene_CY3_2142_082103
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 14, 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 R² (635/532)
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 R² (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 1280 2500 90 65535 64317 6149 685 1028 1596 100 100 96 59029 51223 18313 1689 1905 1229 100 98 34 1.131 1.285 1.131 1.469 1.814 1.242 0.791 52 401 122190 113166 0.178 64850 57340 63632 49534 3344496 2663596 39.655 40.129 0 0 0.178
NMC-2 1460 2520 90 65535 61429 12192 685 982 1060 100 100 86 47016 42242 21480 1657 1897 1377 100 98 23 1.430 1.497 1.430 1.915 2.094 1.403 0.779 52 371 110209 101329 0.516 64850 45359 60744 40585 3194283 2196606 57.025 29.299 0 0 0.516
NMC-3 1620 2510 90 65535 65079 3017 685 1024 1125 100 100 96 64887 51880 18364 1502 1821 1408 100 100 48 1.023 1.278 1.023 1.452 1.833 1.235 0.803 52 337 128235 114772 0.033 64850 63385 64394 50378 3384128 2697773 56.938 35.553 0 0 0.033
NMC-4 1790 2500 90 65535 55131 17264 621 876 1028 100 100 67 12332 17120 12201 1699 1931 1356 98 92 0 6.105 3.535 3.899 4.480 1.995 3.410 0.632 52 372 75547 69931 2.610 64914 10633 54510 15421 2866831 890262 52.777 11.201 0 0 2.610
NMC-5 1990 2490 90 65535 60397 12362 568 813 1016 100 100 80 22388 22708 12122 1740 1930 1213 94 92 0 3.146 2.853 3.099 3.710 2.469 2.772 0.749 52 414 85615 80797 1.654 64967 20648 59829 20968 3140642 1180839 58.646 17.129 0 0 1.654
NMC-6 2170 2500 80 65535 61721 11428 616 796 856 100 100 86 30117 32592 15869 1579 1780 1196 100 98 1 2.275 1.970 2.261 2.248 1.682 1.930 0.721 52 320 93457 92118 1.186 64919 28538 61105 31013 3209511 1694803 71.174 25.763 0 0 1.186
NMC-7 2340 2500 90 40101 38756 20460 645 902 1118 100 98 13 65535 61744 11246 1667 1869 1250 100 100 86 0.618 0.634 0.626 0.503 2.119 0.679 0.763 52 353 103324 98188 -0.695 39456 63868 38111 60077 2015324 3210664 33.859 47.900 0 0 -0.695
NMC-8 2520 2500 80 51948 48196 14135 691 925 941 100 100 15 65535 64298 4403 1661 1902 1227 100 100 92 0.802 0.758 0.802 0.719 1.366 0.771 0.858 52 326 115131 110142 -0.317 51257 63874 47505 62637 2506188 3343497 50.235 50.852 0 0 -0.317
NMC-9 2680 2500 80 62432 54070 16501 642 782 674 100 100 38 65535 63943 6843 1761 2272 3021 100 100 92 0.969 0.859 0.969 0.793 1.494 0.866 0.848 52 326 125564 115610 -0.046 61790 63774 53428 62182 2811647 3325031 79.062 20.414 0 0 -0.046
NMC-10 2860 2500 80 40706 41962 17701 510 700 731 100 100 15 49047 46433 17968 1784 1979 1569 100 98 23 0.850 0.928 0.936 0.938 1.490 0.926 0.889 52 329 87459 86101 -0.234 40196 47263 41452 44649 2182043 2414507 56.446 28.333 0 0 -0.234
NMC-11 3030 2500 80 56211 49507 17671 479 629 667 100 100 28 63344 51684 18241 1589 1766 1200 100 100 44 0.902 0.979 1.017 0.993 1.378 0.981 0.932 52 328 117487 99123 -0.148 55732 61755 49028 50095 2574366 2687573 73.280 41.598 0 0 -0.148
NMC-12 3220 2500 80 61236 55351 12459 551 779 965 100 100 38 65535 56781 14071 1663 1883 1362 100 100 53 0.950 0.994 1.017 1.013 1.342 0.988 0.919 52 320 124557 109918 -0.074 60685 63872 54800 55118 2878249 2952631 56.551 40.307 0 0 -0.074
NMC-13 3390 2500 80 11862 13446 9478 510 717 894 98 94 0 19748 24872 16640 1623 1851 1262 100 98 5 0.626 0.556 0.584 0.549 1.772 0.527 0.812 52 299 29477 36185 -0.675 11352 18125 12936 23249 699207 1293341 14.238 18.242 0 0 -0.675
NMC-14 3570 2480 80 11368 13220 8408 512 781 1281 96 92 0 19356 23959 16099 1783 2057 1893 96 94 0 0.618 0.573 0.685 0.605 2.015 0.496 0.713 52 332 28429 34884 -0.695 10856 17573 12708 22176 687417 1245852 9.710 11.570 0 0 -0.695
NMC-15 3750 2480 90 12243 15789 11957 509 760 980 98 94 0 22564 25950 16343 1628 1995 1403 100 98 0 0.560 0.628 0.589 0.558 1.842 0.639 0.840 52 382 32670 39602 -0.835 11734 20936 15280 24322 821017 1349420 15.336 17.074 0 0 -0.835
NMC-16 3900 2480 90 65535 56745 15924 514 726 798 100 100 57 65535 62489 9326 1714 1945 1315 100 100 88 1.019 0.925 1.019 0.867 1.399 0.920 0.926 52 383 128842 117006 0.027 65021 63821 56231 60775 2950764 3249440 70.199 46.041 0 0 0.027
NMC-17 4080 2500 80 65535 63281 6580 483 753 1149 100 100 78 65535 65535 0 1604 1900 1301 100 100 100 1.018 0.982 1.018 0.975 1.151 0.980 0.941 52 334 128983 126729 0.025 65052 63931 62798 63931 3290608 3407820 54.419 48.912 0 0 0.025
NMC-18 4250 2500 90 65535 59907 11794 490 724 817 100 100 69 65535 65226 1690 1781 2036 1410 100 100 94 1.020 0.937 1.020 0.901 1.386 0.957 0.949 52 387 128799 122862 0.029 65045 63754 59417 63445 3115142 3391732 72.439 44.816 0 0 0.029
NMC-19 4430 2510 90 65535 60843 9382 512 774 1529 100 100 71 26923 26619 10713 1655 1950 1482 100 100 0 2.573 2.417 2.532 2.655 1.558 2.336 0.825 52 325 90291 85295 1.364 65023 25268 60331 24964 3163852 1384195 39.286 16.646 0 0 1.364
NMC-20 4600 2500 90 65535 59851 7763 565 841 1138 100 100 51 29392 28947 9792 1708 1957 1330 100 100 0 2.347 2.177 2.181 2.311 1.450 2.022 0.836 52 345 92654 86525 1.231 64970 27684 59286 27239 3112262 1505232 51.854 20.293 0 0 1.231

Total number of rows: 30000

Table truncated, full table size 6394 Kbytes.




Supplementary data files not provided
Processed data not applicable for this record
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap