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Sample GSM50356 Query DataSets for GSM50356
Status Public on Jan 02, 2006
Title MultiRound_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 four 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 1510 18560 100 3567 3501 1347 762 801 301 96 88 0 5995 5179 2209 6054 5804 1400 5 1 0 -47.542 -3.13 5.281 6.055 2.42 0.983 0.271 80 465 2746 1864 Error 2805 -59 2739 -875 0
Hs6-1-2-1 null 1690 18550 110 4499 4374 1989 758 791 294 97 88 0 9261 7880 4150 5302 5396 1338 67 65 0 0.945 1.403 0.894 1.049 1.671 0.673 0.703 80 504 7700 6194 -0.082 3741 3959 3616 2578 0
Hs6-1-3-1 null 1870 18550 100 1305 1329 363 748 781 259 81 55 0 3797 3299 1432 5450 5412 1281 0 0 0 -0.337 -0.27 0.039 0.039 7.386 -0.051 0.017 80 456 -1096 -1570 Error 557 -1653 581 -2151 -50
Hs6-1-4-1 null 2050 18550 120 4461 4360 1753 761 778 229 100 95 0 7495 7292 2947 5729 5690 1219 64 39 0 2.095 2.303 1.622 1.798 1.842 0.88 0.512 120 582 5466 5162 1.067 3700 1766 3599 1563 0
Hs6-1-5-1 null 2220 18560 100 2635 2571 932 758 791 234 97 88 0 5741 5121 2309 5558 5481 1184 23 5 0 10.257 -4.149 2.49 2.871 2.447 0.446 0.262 80 377 2060 1376 3.359 1877 183 1813 -437 0
Hs6-1-6-1 0.70971822 2380 18550 110 7039 6504 2734 766 894 811 92 86 0 9122 8061 3734 5384 5454 1392 73 61 0 1.678 2.143 1.584 1.666 1.497 1.147 0.8 80 488 10011 8415 0.747 6273 3738 5738 2677 0
Hs6-1-7-1 0.132765648 2570 18550 120 17243 21646 13757 774 894 757 99 96 0 20948 25338 15550 5364 5454 1358 90 87 0 1.057 1.045 1.04 1.16 1.46 0.952 0.977 120 584 32053 40846 0.08 16469 15584 20872 19974 0
Hs6-1-8-1 0.110539865 2730 18570 80 5120 5320 2062 801 981 624 100 96 0 8592 8564 2672 4465 4580 896 86 80 0 1.047 1.102 1.077 1.305 1.896 0.835 0.794 52 287 8446 8618 0.066 4319 4127 4519 4099 0
Hs6-1-9-1 -0.118219434 2910 18550 120 7628 9422 6138 763 906 518 96 93 0 12020 13985 8165 4934 5163 1294 83 75 0 0.969 0.957 0.922 1.044 1.599 0.821 0.945 120 678 13951 17710 -0.046 6865 7086 8659 9051 0
Hs6-1-10-1 null 3090 18570 80 3988 3888 1181 787 934 464 100 96 0 6862 6513 1739 4260 4439 800 80 69 0 1.23 1.376 1.221 1.405 1.919 0.778 0.615 52 282 5803 5354 0.299 3201 2602 3101 2253 0
Hs6-1-11-1 0.132501017 3260 18550 120 4732 5725 3281 769 857 406 94 90 0 7746 8360 3846 5017 5211 1308 66 51 0 1.452 1.483 1.314 1.464 1.696 1.005 0.803 120 607 6692 8299 0.538 3963 2729 4956 3343 0
Hs6-1-12-1 null 3430 18570 110 3546 4086 1888 773 911 557 97 87 0 7071 7395 2921 4920 5109 1190 70 48 0 1.289 1.339 1.197 1.222 2.174 0.806 0.689 80 486 4924 5788 0.366 2773 2151 3313 2475 0
Hs6-1-13-1 -0.157928069 3620 18560 120 8895 8721 4000 772 977 773 99 91 0 15401 14676 6672 5537 5525 1321 86 80 0 0.823 0.87 0.81 0.883 1.452 0.719 0.92 120 609 17987 17088 -0.28 8123 9864 7949 9139 0
Hs6-1-14-1 0.077612886 3790 18560 120 8455 8433 4202 735 887 704 98 93 0 12372 12476 5873 5592 5538 1265 82 78 0 1.139 1.118 1.021 1.153 2.274 0.864 0.896 120 582 14500 14582 0.187 7720 6780 7698 6884 0
Hs6-1-15-1 null 3980 18560 110 5626 5276 2237 753 880 604 93 87 0 8273 7159 3225 5269 5291 1225 70 58 0 1.622 2.393 1.563 1.607 2.46 1.052 0.661 80 484 7877 6413 0.698 4873 3004 4523 1890 0
Hs6-1-16-1 null 4160 18560 110 3443 3513 1463 743 844 514 95 85 0 6540 5919 2542 5428 5342 1235 47 13 0 2.428 5.642 1.966 2.259 1.918 0.803 0.467 80 437 3812 3261 1.28 2700 1112 2770 491 0
Hs6-1-17-1 -0.038313789 4320 18560 120 9290 8784 3961 702 726 240 100 99 0 14541 13317 5924 5575 5406 1178 81 76 0 0.958 1.044 0.95 1.176 1.985 0.822 0.914 120 491 17554 15824 -0.062 8588 8966 8082 7742 0
Hs6-1-18-1 null 4490 18570 110 3816 3689 1268 708 764 350 100 95 0 6866 6565 2405 4900 5002 1139 67 46 0 1.581 1.79 1.303 1.57 2.178 0.806 0.656 80 419 5074 4646 0.661 3108 1966 2981 1665 0
Hs6-1-19-1 0.462525758 4670 18550 130 15846 15235 7850 722 761 298 99 98 0 16658 15848 7504 5168 5149 1166 84 80 0 1.316 1.359 1.309 1.439 1.756 1.2 0.95 120 602 26614 25193 0.396 15124 11490 14513 10680 0
Hs6-1-20-1 -0.074226887 4840 18560 120 4996 6017 3545 736 808 385 97 97 0 8333 9553 4696 5021 5045 1180 78 65 0 1.286 1.165 1.114 1.308 2.153 0.855 0.875 120 533 7572 9813 0.363 4260 3312 5281 4532 0

Total number of rows: 20000

Table truncated, full table size 3890 Kbytes.




Supplementary data files not provided
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