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Sample GSM97593 Query DataSets for GSM97593
Status Public on Dec 18, 2008
Title A-172_CRL-1620_1940_082403
Sample type RNA
 
Channel 1
Source name A-172_CRL-1620_CY3_1940_082403
Organism Homo sapiens
Characteristics The A172 cell line (ATCC nr: CRL-1620) is derived from human brain glioblastoma.
Extracted molecule total RNA
Label CY3
 
Channel 2
Source name Human_Reference_stratagene_CY5_1940_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 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 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 1260 2500 80 65535 57723 11943 1262 1515 1218 100 100 57 34985 33672 13447 1629 1879 1576 100 100 1 1.927 1.762 1.787 1.918 1.508 1.681 0.852 52 326 97629 88504 0.946 64273 33356 56461 32043 3001603 1750966 46.148 20.173 0 0 0.946
NMC-2 1450 2500 80 65535 60832 8400 927 1272 1121 100 100 71 32826 33915 13163 1496 1696 1146 100 100 1 2.062 1.848 1.834 2.004 1.541 1.763 0.821 52 326 95938 92324 1.044 64608 31330 59905 32419 3163251 1763583 53.131 28.114 0 0 1.044
NMC-3 1610 2500 80 65535 57436 15285 1275 1426 1125 100 100 67 32100 31727 12190 1503 1735 1298 100 100 1 2.100 1.858 1.727 1.909 1.690 1.913 0.790 52 290 94857 86385 1.071 64260 30597 56161 30224 2986688 1649790 49.787 23.106 0 0 1.071
NMC-4 1790 2500 80 35110 34057 16514 1089 1250 1026 100 100 1 11746 12574 7160 1405 1606 1083 98 94 0 3.290 2.952 3.400 3.288 1.763 2.993 0.783 52 305 44362 44137 1.718 34021 10341 32968 11169 1770981 653862 31.976 10.127 0 0 1.718
NMC-5 1970 2490 80 35823 34811 14494 1032 1299 1092 100 100 3 12355 12903 6444 1415 1605 1117 94 92 0 3.180 2.940 3.138 3.219 1.670 2.962 0.805 52 334 45731 45267 1.669 34791 10940 33779 11488 1810187 670951 30.689 10.115 0 0 1.669
NMC-6 2140 2500 80 45911 44126 14548 929 1283 1103 100 100 7 16004 16300 8116 1428 1622 1106 98 98 0 3.086 2.905 3.142 3.295 1.767 2.902 0.758 52 309 59558 58069 1.626 44982 14576 43197 14872 2294574 847618 38.842 13.271 0 0 1.626
NMC-7 2310 2460 80 7024 8569 6434 805 1125 1055 94 84 0 65535 50389 20416 1429 1596 1105 100 100 55 0.097 0.159 0.147 0.137 1.979 0.159 0.595 52 331 70325 56724 -3.366 6219 64106 7764 48960 445586 2620216 7.056 44.157 0 0 -3.366
NMC-8 2490 2500 90 14744 14408 5171 755 1077 1062 100 100 0 65535 62381 9564 1422 1582 1081 100 100 84 0.218 0.224 0.221 0.209 1.437 0.213 0.822 52 341 78102 74612 -2.196 13989 64113 13653 60959 749241 3243799 12.553 56.243 0 0 -2.196
NMC-9 2660 2500 80 15921 17744 7046 723 1117 1384 100 100 0 65535 65111 2401 1418 1611 1068 100 100 96 0.237 0.267 0.237 0.246 1.502 0.262 0.778 52 328 79315 80714 -2.077 15198 64117 17021 63693 922713 3385792 12.014 59.457 0 0 -2.077
NMC-10 2830 2500 80 13648 15580 9276 755 1175 1456 100 98 0 27691 29042 16833 1411 1629 1180 98 94 3 0.491 0.537 0.482 0.603 2.080 0.490 0.721 52 314 39173 42456 -1.027 12893 26280 14825 27631 810177 1510191 9.894 23.231 0 0 -1.027
NMC-11 3000 2500 80 14941 15895 8844 806 1157 1132 96 94 0 29152 28895 15047 1200 1470 1154 100 100 0 0.506 0.545 0.502 0.526 1.890 0.517 0.782 52 321 42087 42784 -0.984 14135 27952 15089 27695 826532 1502520 13.019 23.765 0 0 -0.984
NMC-12 3190 2490 90 17679 18530 8091 757 1091 1029 100 98 0 40748 39574 16394 1265 1661 2981 98 98 1 0.429 0.464 0.478 0.467 1.487 0.432 0.790 52 376 56405 56082 -1.222 16922 39483 17773 38309 963548 2057871 16.948 12.718 0 0 -1.222
NMC-13 3370 2480 60 3071 3401 2349 810 1153 1067 78 50 0 8515 11768 10532 1236 1369 998 93 93 0 0.311 0.246 0.308 0.342 2.201 0.174 0.427 32 176 9540 13123 -1.687 2261 7279 2591 10532 108835 376582 2.107 10.420 0 0 -1.687
NMC-14 3540 2490 60 4189 5079 3607 818 1136 1257 81 59 0 8829 11787 10274 1138 1265 996 96 96 0 0.438 0.400 0.383 0.398 3.852 0.209 0.206 32 171 11062 14910 -1.190 3371 7691 4261 10649 162518 377171 3.137 10.564 0 0 -1.190
NMC-15 3720 2490 70 3989 5585 4181 1206 1418 1258 84 53 0 13652 13950 9841 1516 1641 1072 96 90 0 0.229 0.352 0.355 0.316 2.950 0.347 0.635 32 224 14919 16813 -2.125 2783 12136 4379 12434 178716 446414 3.312 11.482 0 0 -2.125
NMC-16 3890 2490 90 35710 33674 9869 1071 1416 1568 100 100 0 65535 65104 2297 1485 1694 1597 100 100 96 0.541 0.512 0.541 0.486 1.415 0.509 0.850 52 381 98689 96222 -0.887 34639 64050 32603 63619 1751040 3385392 20.573 39.706 0 0 -0.887
NMC-17 4050 2500 80 41444 39407 13136 974 1379 1616 100 100 0 65535 64068 5980 1524 1800 1305 100 100 90 0.632 0.614 0.632 0.559 1.635 0.622 0.818 52 316 104481 100977 -0.661 40470 64011 38433 62544 2049187 3331558 23.532 47.715 0 0 -0.661
NMC-18 4240 2490 90 44601 44328 12611 812 1174 1247 100 100 3 65535 65510 183 1450 1703 1152 100 100 98 0.683 0.679 0.683 0.647 1.395 0.668 0.824 52 398 107874 107576 -0.549 43789 64085 43516 64060 2305065 3406502 34.606 55.388 0 0 -0.549
NMC-19 4400 2500 80 22073 22789 6567 1061 1211 1128 100 100 0 16167 17611 6971 1389 1560 1074 100 100 0 1.422 1.339 1.407 1.407 1.652 1.298 0.692 52 251 35790 37950 0.508 21012 14778 21728 16222 1185043 915758 19.129 14.945 0 0 0.508
NMC-20 4560 2500 90 19181 19268 6130 950 1348 1902 100 100 0 17161 18300 6661 1270 1460 1082 100 100 0 1.147 1.076 1.006 1.092 1.665 1.102 0.694 52 323 34122 35348 0.198 18231 15891 18318 17030 1001939 951600 9.422 15.564 0 0 0.198

Total number of rows: 30000

Table truncated, full table size 6353 Kbytes.




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