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Sample GSM50353 Query DataSets for GSM50353
Status Public on Jan 02, 2006
Title TwoRound_PCR
Sample type RNA
 
Channel 1
Source name CPP, commercially available pooled benign prostate tissue total RNA, 25ng WTA two PCR, Cy5
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name CPP, commercially available pooled benign prostate tissue total RNA, 25ng WTA two PCR, Cy3
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description See MIAME checklist
 
Submission date May 04, 2005
Last update date May 29, 2005
Contact name Scott Tomlins
E-mail(s) tomlinss@med.umich.edu
Phone 734-615-1417
Organization name University of Michigan
Department Pathology
Lab Chinnaiyan Lab
Street address 1400 E. Medical Center Dr., 5410 CCGC
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platform ID GPL2013
Series (1)
GSE2618 Whole Transcriptome Amplification for Gene Expression Profiling and Development of Molecular Archives

Data table header descriptions
ID_REF
VALUE normalized (mean of the Median of Ratios of included features = 1), log base 2, (meanF635-B635)/(meanF532-B532)
X the X-coordinate in um of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Y the Y-coordinate in um of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Dia. the diameter in um of the feature-indicator.
F635 Median median feature pixel intensity at wavelength #1 (635 nm) (Cy5).
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).
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+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 deviation above the background pixel intensity, at wavelength #1 (635 nm).
F635 % Sat. the percentage of feature ixels at wavelength #1 that are saturated.
F532 Median median feature pixel intensity at wavelength #2 (532 nm) (Cy3).
F532 Mean mean feature pixel intensity at wavelength #2 (532 nm).
F532 SD the standard deviation of the feature pixel intensity at wavelength #2 (532 nm).
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+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 deviation above the background pixel intensity, at wavelength #2 (532 nm).
F532 % Sat. the percentage of feature ixels 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.
Ratio of Means (635/532) the ratio of the arithmetic mean 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 arithmetic mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Ratios SD (635/532) the standard deviation of pixel intensity ratios.
Rgn Ratio (635/532) the regression ratio.
Rgn R? 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 the sum of the median intensities for each wavelength, with the median background subtracted.
Sum of Means 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.
Flags the type of flag associated with a feature. Features that could not be identified by Genepix are indicated with -50. Empty spots are indicated with -75.

Data table
ID_REF VALUE 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? F Pixels B Pixels Sum of Medians Sum of Means Log Ratio (635/532) F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 Flags
Hs6-1-1-1 null 1480 17730 70 2916 3146 1015 1169 1359 768 90 65 0 3786 3623 954 2494 2614 597 78 56 0 1.352 1.751 1.447 1.437 1.593 1.252 0.629 32 224 3039 3106 0.435 1747 1292 1977 1129 0
Hs6-1-2-1 null 1630 17740 110 3370 3521 1775 980 1021 389 86 81 0 4190 3857 1913 2549 2574 500 66 63 0 1.456 1.943 1.433 1.395 3.07 1.212 0.725 80 482 4031 3849 0.542 2390 1641 2541 1308 0
Hs6-1-3-1 null 1810 17720 90 1049 1073 319 935 966 326 23 5 0 1972 1751 740 2627 2587 510 0 0 0 -0.174 -0.158 0.173 0.175 5.514 0.137 0.027 52 402 -541 -738 Error 114 -655 138 -876 -50
Hs6-1-4-1 null 2020 17730 120 3479 3632 1491 925 1004 1248 85 53 0 4320 4311 1267 2695 2620 480 77 65 0 1.572 1.675 1.553 2.031 2.348 4.333 0.202 120 576 4179 4323 0.652 2554 1625 2707 1616 0
Hs6-1-5-1 null 2160 17720 90 2383 17245 23922 986 1158 1750 40 36 13 3088 3642 2318 2712 2663 504 38 25 0 3.715 17.483 4.972 4.823 4.21 12.156 0.654 52 289 1773 17189 1.894 1397 376 16259 930 -50
Hs6-1-6-1 0.287822824 2320 17730 110 5635 5563 2966 956 1028 458 92 91 0 5644 5937 3009 2724 2688 498 81 72 0 1.602 1.434 1.304 1.327 2.663 1.212 0.888 80 451 7599 7820 0.68 4679 2920 4607 3213 0
Hs6-1-7-1 -0.053086469 2490 17730 130 12600 14839 7868 964 1016 399 100 99 0 12514 14762 7427 2534 2558 523 97 95 0 1.166 1.135 1.135 1.198 1.44 1.102 0.968 120 640 21616 26103 0.221 11636 9980 13875 12228 0
Hs6-1-8-1 null 2670 17740 80 3001 3160 1737 996 1047 437 78 73 0 3730 3886 2066 2212 2274 456 65 57 0 1.321 1.293 1.026 1.08 2.843 0.945 0.756 52 308 3523 3838 0.401 2005 1518 2164 1674 0
Hs6-1-9-1 -0.01481147 2840 17740 110 6554 7666 4382 950 1020 416 97 97 0 6762 8117 4625 2290 2404 531 90 86 0 1.253 1.153 1.132 1.152 1.643 1.049 0.938 80 535 10076 12543 0.326 5604 4472 6716 5827 0
Hs6-1-10-1 null 3030 17730 80 2371 2331 1050 1016 1047 436 78 67 0 3217 2989 1288 2238 2344 505 63 50 0 1.384 1.751 1.222 1.154 2.155 1.099 0.604 52 298 2334 2066 0.469 1355 979 1315 751 0
Hs6-1-11-1 0.181576209 3190 17730 120 3516 4101 2393 1035 1127 645 93 79 0 4124 4696 2406 2482 2536 660 74 58 0 1.511 1.385 1.317 1.511 2.564 1.129 0.835 120 655 4123 5280 0.595 2481 1642 3066 2214 0
Hs6-1-12-1 null 3380 17740 70 5646 9869 11355 1102 1234 658 96 96 0 4031 4197 2293 2184 2322 606 71 65 0 2.46 4.355 1.336 1.844 3.004 26.276 0.018 32 224 6391 10780 1.299 4544 1847 8767 2013 -50
Hs6-1-13-1 0.190078531 3540 17730 120 5623 5506 2772 960 1015 415 92 90 0 6125 5966 2832 2563 2583 490 83 80 0 1.309 1.336 1.218 1.216 1.784 1.163 0.877 120 596 8225 7949 0.389 4663 3562 4546 3403 0
Hs6-1-14-1 0.390413712 3720 17730 120 4324 4624 2386 914 989 468 92 90 0 4785 4922 2296 2536 2554 508 80 75 0 1.516 1.555 1.373 1.483 2.013 1.24 0.853 120 553 5659 6096 0.6 3410 2249 3710 2386 0
Hs6-1-15-1 0.222936116 3900 17730 120 3210 3411 1645 935 987 381 90 86 0 3855 3938 1906 2539 2504 480 72 60 0 1.729 1.77 1.397 1.38 2.311 1.118 0.744 120 534 3591 3875 0.79 2275 1316 2476 1399 0
Hs6-1-16-1 null 4080 17730 100 2419 2387 1221 924 966 357 76 70 0 3433 2917 1497 2567 2503 461 56 45 0 1.726 4.18 1.47 0.993 4.401 1.061 0.555 80 388 2361 1813 0.788 1495 866 1463 350 0
Hs6-1-17-1 0.156896633 4240 17730 120 5520 5828 2818 896 977 562 95 92 0 6080 6305 2777 2518 2495 547 85 81 0 1.298 1.302 1.31 1.436 1.818 1.151 0.89 120 577 8186 8719 0.376 4624 3562 4932 3787 0
Hs6-1-18-1 null 4440 17730 80 2813 2697 1136 886 957 425 88 78 0 3331 3236 1575 2176 2222 489 73 57 0 1.668 1.708 1.345 1.071 2.538 0.986 0.484 52 281 3082 2871 0.738 1927 1155 1811 1060 0
Hs6-1-19-1 0.492396382 4590 17730 120 11768 15013 11768 869 908 329 100 100 1 10276 10930 4953 2386 2387 451 98 96 0 1.381 1.655 1.228 1.488 1.912 2.465 0.435 120 516 18789 22688 0.466 10899 7890 14144 8544 0
Hs6-1-20-1 null 4770 17730 110 3835 4770 3122 926 984 407 95 91 0 4555 5287 2880 2374 2377 465 81 77 0 1.334 1.32 1.217 1.516 2.314 1.165 0.866 80 497 5090 6757 0.416 2909 2181 3844 2913 0

Total number of rows: 20000

Table truncated, full table size 3841 Kbytes.




Supplementary data files not provided
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