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Sample GSM96657 Query DataSets for GSM96657
Status Public on Dec 18, 2008
Title TT_CRL1803_2118_082103
Sample type RNA
 
Channel 1
Source name TT_CRL1803_CY3_2118_082103
Organism Homo sapiens
Characteristics The TT cell line (ATCC nr; CRL1803) was established from a specimen obtained by
needle biopsy from a 77 year old female with thyroid medullary carcinoma.
Extracted molecule total RNA
Label CY3
 
Channel 2
Source name Human_Reference_Stratagene_CY5_2118_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.
Stratagene also supplies a QPCR Human Reference Total RNA, suitable for QRT-PCR, which has undergone further DNase treatment.
(http://www.stratagene.com/manuals/740000.pdf)
Extracted molecule total RNA
Label CY5
 
 
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 2470 90 65535 64996 2725 850 1393 3563 100 100 96 51188 45902 19941 1669 1920 1128 100 100 26 1.306 1.450 1.306 1.720 1.953 1.462 0.664 52 388 114204 108379 0.385 64685 49519 64146 44233 3379783 2386926 17.851 38.991 0 0 0.385
NMC-2 1480 2450 90 65535 64938 4304 893 1389 1573 100 100 98 50493 46776 18537 1730 1959 1139 100 100 30 1.326 1.422 1.331 1.619 1.760 1.384 0.761 52 352 113405 109091 0.407 64642 48763 64045 45046 3376782 2432328 40.400 39.348 0 0 0.407
NMC-3 1610 2440 90 65535 63670 7077 992 1354 1503 100 100 92 42908 40487 21429 1909 2055 1135 100 98 23 1.574 1.625 1.575 2.163 2.379 1.407 0.728 52 331 105542 101256 0.655 64543 40999 62678 38578 3310827 2105344 41.461 33.861 0 0 0.655
NMC-4 1820 2450 90 65535 63239 8819 736 1085 1046 100 100 90 19203 18191 9815 1701 1883 1146 94 90 0 3.702 3.790 3.650 4.538 2.026 3.912 0.658 52 358 82301 78993 1.888 64799 17502 62503 16490 3288439 945922 59.421 14.230 0 0 1.888
NMC-5 1990 2450 90 65535 64760 4200 739 1121 1381 100 100 92 23808 23646 11569 1461 1668 1162 98 98 0 2.900 2.886 2.900 3.598 2.212 3.029 0.680 52 388 87143 86206 1.536 64796 22347 64021 22185 3367536 1229593 46.082 18.914 0 0 1.536
NMC-6 2170 2450 90 65535 65535 0 702 1153 1613 100 100 100 25106 25583 10652 1387 1601 1021 100 100 0 2.733 2.679 2.733 2.992 1.650 2.871 0.693 52 379 88552 89029 1.451 64833 23719 64833 24196 3407820 1330325 39.914 23.489 0 0 1.451
NMC-7 2330 2450 80 54969 48821 18077 579 979 1404 100 100 34 65535 64025 6756 1500 1751 1581 100 100 86 0.849 0.772 0.849 0.703 1.551 0.816 0.829 52 290 118425 110767 -0.236 54390 64035 48242 62525 2538710 3329312 34.075 39.389 0 0 -0.236
NMC-8 2520 2430 90 64162 52309 19614 639 892 881 100 100 48 65535 61996 10548 1330 1514 939 100 100 86 0.989 0.852 0.989 0.746 1.697 0.865 0.865 52 401 127728 112336 -0.015 63523 64205 51670 60666 2720052 3223782 58.362 64.411 0 0 -0.015
NMC-9 2690 2460 80 65535 58613 12973 646 968 1786 100 100 71 65535 64104 7006 1334 1546 1029 100 100 94 1.011 0.923 1.011 0.898 1.313 0.927 0.911 52 318 129090 120737 0.015 64889 64201 57967 62770 3047899 3333383 32.276 60.795 0 0 0.015
NMC-10 2860 2430 90 28119 32445 22513 530 751 787 100 100 17 21571 26889 19938 1363 1553 1026 98 94 3 1.365 1.250 1.311 1.437 1.807 1.198 0.907 52 379 47797 57441 0.449 27589 20208 31915 25526 1687152 1398243 40.272 24.694 0 0 0.449
NMC-11 3020 2440 80 54394 51455 15176 478 747 836 100 100 25 41662 42828 15925 1293 1520 1002 100 100 15 1.336 1.227 1.252 1.249 1.362 1.200 0.902 52 327 94285 92512 0.417 53916 40369 50977 41535 2675671 2227045 60.656 41.226 0 0 0.417
NMC-12 3220 2440 90 61037 57130 10867 602 896 1025 100 100 38 48626 48051 13025 1232 1464 1028 100 100 11 1.275 1.207 1.244 1.235 1.278 1.179 0.930 52 383 107829 103347 0.351 60435 47394 56528 46819 2970735 2498677 54.862 45.318 0 0 0.351
NMC-13 3370 2450 80 9845 12573 11394 608 864 1544 90 84 0 8218 11894 9937 1340 1567 1806 90 78 0 1.343 1.134 1.069 1.041 2.144 1.157 0.786 52 283 16115 22519 0.425 9237 6878 11965 10554 653797 618464 7.584 5.718 0 0 0.425
NMC-14 3580 2440 80 13583 14953 8935 661 869 787 100 98 0 14323 16129 8190 1330 1408 819 98 98 0 0.995 0.966 0.907 0.936 1.896 0.995 0.741 52 334 25915 29091 -0.008 12922 12993 14292 14799 777550 838721 17.896 17.974 0 0 -0.008
NMC-15 3750 2430 80 16542 18325 10355 593 831 971 100 96 0 16226 18264 11752 1216 1391 861 100 98 1 1.063 1.040 1.029 1.053 1.918 0.972 0.675 52 294 30959 34780 0.088 15949 15010 17732 17048 952908 949724 18.016 19.597 0 0 0.088
NMC-16 3890 2440 90 54992 53432 12674 705 1034 1686 100 100 28 65535 62444 8176 1305 1458 928 100 100 80 0.845 0.862 0.895 0.837 1.224 0.857 0.934 52 372 118517 113866 -0.243 54287 64230 52727 61139 2778442 3247083 31.078 65.718 0 0 -0.243
NMC-17 4080 2460 90 57865 55629 10736 563 858 1229 100 100 34 65535 63987 6002 1309 1454 993 100 100 86 0.892 0.879 0.927 0.864 1.203 0.877 0.941 52 398 121528 117744 -0.165 57302 64226 55066 62678 2892721 3327345 44.566 62.974 0 0 -0.165
NMC-18 4270 2440 90 65535 63887 5129 553 880 1255 100 100 84 65535 65535 0 1410 1501 886 100 100 100 1.013 0.988 1.013 0.984 1.103 0.975 0.975 52 402 129107 127459 0.019 64982 64125 63334 64125 3322128 3407820 50.205 72.273 0 0 0.019
NMC-19 4440 2460 90 33247 33665 9174 562 723 694 100 100 0 30639 30418 8905 1246 1386 840 100 100 0 1.112 1.135 1.108 1.145 1.425 1.115 0.821 52 319 62078 62275 0.153 32685 29393 33103 29172 1750558 1581743 47.467 34.562 0 0 0.153
NMC-20 4620 2450 100 30404 30195 13498 576 784 866 98 98 0 27838 27550 12884 1308 1441 846 97 97 1 1.124 1.129 1.083 1.110 1.767 1.119 0.768 80 395 56358 55861 0.169 29828 26530 29619 26242 2415577 2204025 33.962 30.862 0 0 0.169

Total number of rows: 30000

Table truncated, full table size 6362 Kbytes.




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