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Sample GSM115783 Query DataSets for GSM115783
Status Public on Jul 14, 2006
Title Prostate_03-029B_GL3
Sample type RNA
 
Channel 1
Source name Prostate_cancer_03-029B_LCM_GL3
Organism Homo sapiens
Characteristics Prostate Cancer patient 03-029B Gleason_Score:3+4 LCM_Gleason_Pattern:3 Gleason_Pattern:3 Age:50-59 PSA:3.7 Volume:2.6 Margin_Status:negative Treatment:none
Extracted molecule total RNA
Extraction protocol Following LCM, captured cells were lysed in RNA extraction buffer (Arcturus). RNA was isolated using the PicoPure RNA Isolation Kit (Arcturus) and the samples were DNAse treated using RNase-Free DNase (Qiagen). Each slide capture session lasted no longer than 20 minutes to minimize RNA degradation. The laser capture settings were: 55 mW beam, 1.5 ms pulse, 15 µm spot size. Subsequently, RNA was amplified through two rounds of linear amplification using the MessageAmp aRNA Kit (Ambion, Inc). Sample quality and quantification was assessed by agarose gel electrophoresis and absorbance at A260.
Label Cy5
Label protocol The protocol used for indirect labeling of cDNAs was a modification of a protocol described elsewhere (http://cmgm.stanford.edu/pbrown/protocols/aadUTPCouplingProcedure.htm). In brief, cDNA probes were made from 2 µg of amplified RNA in a reaction volume of 30 µl containing 5 µg random hexamer primers, 0.2 mM 5-(3-aminoallyl)-2_-deoxyuridine-5_-triphosphate (amino acid-dUTP; Sigma-Aldrich), 0.3 mM dTTP, 0.5 mM each dATP, dCTP, and dGTP, and 380 units of Superscript II reverse transcriptase (Invitrogen) incubated at 42oC for 120 minutes. After RNA hydrolysis, purified cDNA was combined with either Cy3 or Cy5 monoreactive fluors (Amersham) that covalently couple to the cDNA-incorporated aminoallyl linker in the presence of 50 mM NaHCO3 (pH 9.0). Samples were randomly labeled with either Cy3 or Cy5 dye to account for dye-bias. The coupling reaction was quenched with hydroxylamine.
 
Channel 2
Source name Prostate_normal_adjacent_cancer_03-029B
Organism Homo sapiens
Characteristics Prostate normal adjacent from cancer patient 03-029B
Extracted molecule total RNA
Extraction protocol Following LCM, captured cells were lysed in RNA extraction buffer (Arcturus). RNA was isolated using the PicoPure RNA Isolation Kit (Arcturus) and the samples were DNAse treated using RNase-Free DNase (Qiagen). Each slide capture session lasted no longer than 20 minutes to minimize RNA degradation. The laser capture settings were: 55 mW beam, 1.5 ms pulse, 15 µm spot size. Subsequently, RNA was amplified through two rounds of linear amplification using the MessageAmp aRNA Kit (Ambion, Inc). Sample quality and quantification was assessed by agarose gel electrophoresis and absorbance at A260.
Label Cy3
Label protocol The protocol used for indirect labeling of cDNAs was a modification of a protocol described elsewhere (http://cmgm.stanford.edu/pbrown/protocols/aadUTPCouplingProcedure.htm). In brief, cDNA probes were made from 2 µg of amplified RNA in a reaction volume of 30 µl containing 5 µg random hexamer primers, 0.2 mM 5-(3-aminoallyl)-2_-deoxyuridine-5_-triphosphate (amino acid-dUTP; Sigma-Aldrich), 0.3 mM dTTP, 0.5 mM each dATP, dCTP, and dGTP, and 380 units of Superscript II reverse transcriptase (Invitrogen) incubated at 42oC for 120 minutes. After RNA hydrolysis, purified cDNA was combined with either Cy3 or Cy5 monoreactive fluors (Amersham) that covalently couple to the cDNA-incorporated aminoallyl linker in the presence of 50 mM NaHCO3 (pH 9.0). Samples were randomly labeled with either Cy3 or Cy5 dye to account for dye-bias. The coupling reaction was quenched with hydroxylamine.
 
 
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 using a GenePix 4000B fluorescent scanner (Axon Instruments, Foster City, CA). The image intensity data were gridded and extracted using GenePix Pro 4.1 software.
Description Human prostate cancer patient 03-029B with Gleason Score 3+4 prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).
Data processing Log-Ratios: For each spot and in each channel (Cy3 and Cy5); the median background intensity was subtracted from the median foreground intensity. Log-ratios of cancer expression to benign expression were created by first dividing the background subtracted intensities (CaP/Benign) and then taking the log base 2. If the median background intensity was greater than the median foreground intensity, the spot was considered missing. Removal of Control Genes: The array contained approximately 400 clones used only for quality control purposes (i.e. yeast sequences or blank spots). These clones were removed from the dataset. Lowess Normalization: For each array, the log-ratio data were centered using a print-tip specific Lowess curve (Y. H. Yang, S. Dudoit, P. Luu and T. P. Speed. Normalization for cDNA Microarray Data. SPIE BiOS 2001, San Jose, California, January 2001). This curve was fit to the log intensity versus log-ratio plot using the neighboring 20.0% of the data to calculate the fit at each spot. The Lowess fit at each point was subtracted from the observed log-ratio for that spot, resulting in a normalized log-ratio. Assessing Spot Quality: Spots of poor quality, as determined by both visual inspection and GenePix Pro 4.1 quality flags were considered missing. In addition, spots with background subtracted intensity levels less than 300 were considered missing due to poorly hybridized cDNAs. Clones which were missing on > 20% of arrays were removed from the analysis. Imputation: Missing values were imputed using k-nearest neighbors imputation (k = 10) (2). The dataset was split by Gleason pattern (Grades 3, 4 and 5) and imputation was performed separately for each pattern. Average Replicated Clones: Log-ratios from the replicated cDNA spots on each PEDB chip were averaged after normalization and imputation. These average expression values were used for comparative analysis.
 
Submission date Jun 21, 2006
Last update date Oct 02, 2008
Contact name Denise Mauldin
E-mail(s) dmauldin@fhcrc.org
Phone 2066673480
Fax 2066672917
URL http://www.pedb.org
Organization name Fred Hutchinson Cancer Research Center
Department Human Biology
Lab Peter Nelson
Street address 1100 Fairview Ave N D4-100
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL3834
Series (1)
GSE5132 Molecular Correlate to Gleason Grade in Prostate Adenocarcinoma

Data table header descriptions
ID_REF the unique identifier of the feature derived from the Array List
VALUE same as UNF_VALUE but with flagged values removed
X the X-coordinate in µm 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 µm 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 µm of the feature-indicator.
F635 Median median feature pixel intensity at wavelength #1 (635 nm).
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 deviations above the background pixel intensity, at wavelength #1 (635 nm).
F635 % Sat. the percentage of feature pixels at wavelength 635 that are saturated.
F532 Median median feature pixel intensity at wavelength #2 (532 nm).
F532 Mean mean feature pixel intensity at wavelength #2 (532 nm).
F532 SD the standard deviation of the feature 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 deviations above the background pixel intensity, at wavelength #2 (532 nm).
F532 % Sat. the percentage of feature pixels at wavelength 532 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 geometric mean of the 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 center of the feature.
Rgn R² (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 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 635 with the median background subtracted.
F532 Median - B532 the median feature pixel intensity at 532 with the median background subtracted.
F635 Mean - B635 the mean feature pixel intensity at 635 with the median background subtracted.
F532 Mean - B532 the mean feature pixel intensity at 532 with the median background subtracted.
F635 Total Intensity the sum of all pixel intensities in the feature at wavelenth 635.
F532 Total Intensity the sum of all pixel intensities in the feature at wavelenth 532.
SNR 635 the signal-to-noise ratio of the feature, calculated as (F635 Mean - B635 Mean)/B635 SD.
SNR 532 the signal-to-noise ratio of the feature, calculated as (F532 Mean - B532 Mean)/B532 SD.
Flags the type of flag associated with a feature; GenePix Pro 4.1 quality flags 0, -50, -75
Normalize the normalization status of the feature (included/not included).
UNF_VALUE Lowess-normalized, log2(CaP/Benign) ratios

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 R² (635/532) 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 F635 Total Intensity F532 Total Intensity SNR 635 SNR 532 Flags Normalize UNF_VALUE
89663 -0.220789844 1930 14670 130 1992 2270 1160 83 95 59 100 100 0 2181 2340 1146 88 92 32 99 98 0 0.912 0.971 0.902 1.106 2.132 0.956 0.822 120 748 4002 4439 -0.133 1909 2093 2187 2252 272398 280745 36.864 70.250 0 0 -0.220789844
89664 0.093730679 2130 14670 130 5367 5412 1276 86 98 60 100 100 0 5003 4889 1335 91 96 30 100 100 0 1.075 1.110 1.113 1.158 1.483 1.089 0.905 120 667 10193 10124 0.105 5281 4912 5326 4798 649432 586623 88.567 159.767 0 0 0.093730679
89665 0.446128729 2330 14680 120 1544 1586 657 77 87 51 100 99 0 1066 1144 433 89 93 27 100 100 0 1.502 1.430 1.397 1.373 1.598 1.526 0.791 120 595 2444 2564 0.586 1467 977 1509 1055 190353 137268 29.392 38.926 0 0 0.446128729
89666 -0.024191085 2520 14680 120 2648 2638 829 78 93 73 100 100 0 2605 2669 812 89 100 59 100 100 0 1.021 0.992 0.985 0.997 1.372 0.992 0.876 120 576 5086 5140 0.031 2570 2516 2560 2580 316563 320252 34.863 43.542 0 0 -0.024191085
89667 -0.164228985 2720 14680 120 2766 2809 910 83 110 133 100 99 0 2998 2957 864 90 106 77 100 99 0 0.923 0.951 0.957 0.943 1.335 0.960 0.885 120 560 5591 5593 -0.116 2683 2908 2726 2867 337063 354792 20.293 37.026 0 0 -0.164228985
89668 -0.111596876 2910 14680 140 4719 4565 1472 84 103 116 99 99 0 5039 4797 1582 91 98 53 100 100 0 0.937 0.952 0.971 0.985 1.540 0.942 0.883 156 712 9583 9187 -0.094 4635 4948 4481 4706 712081 748325 38.466 88.660 0 0 -0.111596876
89669 0.437039145 3110 14670 130 5784 5986 1768 82 91 55 100 100 0 4258 4219 1277 91 97 38 100 100 0 1.368 1.430 1.398 1.453 1.400 1.454 0.879 120 652 9869 10032 0.452 5702 4167 5904 4128 718267 506237 107.182 108.474 0 0 0.437039145
89670 -1.213964826 3300 14680 130 1213 1221 327 76 84 48 100 99 0 2521 2520 611 94 99 34 100 100 0 0.468 0.472 0.472 0.464 1.441 0.409 0.744 120 607 3564 3571 -1.094 1137 2427 1145 2426 146513 302405 23.688 71.206 0 0 -1.213964826
89671 0.402057178 3490 14680 140 8303 8080 2635 74 83 53 100 99 0 6316 6151 2633 93 97 26 100 100 0 1.322 1.322 1.336 1.481 1.921 1.277 0.815 156 703 14452 14064 0.403 8229 6223 8006 6058 1260479 959487 150.887 232.846 0 0 0.402057178
89672 0.120463334 3690 14680 140 5929 5890 2267 73 84 55 100 100 0 5468 5435 1945 91 95 24 100 100 0 1.089 1.089 1.111 1.096 1.776 1.104 0.872 156 715 11233 11161 0.123 5856 5377 5817 5344 918811 847793 105.564 222.500 0 0 0.120463334
89673 -0.415837524 3880 14680 130 2389 2435 610 73 83 50 100 100 0 3073 3013 647 94 97 24 100 100 0 0.777 0.809 0.816 0.803 1.275 0.790 0.863 120 622 5295 5281 -0.363 2316 2979 2362 2919 292199 361600 47.040 121.500 0 0 -0.415837524
89674 -0.039310026 4080 14680 140 645 707 318 71 81 50 100 100 0 640 683 310 91 94 25 99 98 0 1.046 1.074 1.055 1.118 1.803 1.069 0.798 156 718 1123 1228 0.064 574 549 636 592 110366 106515 12.520 23.560 0 0 -0.039310026
89675 -0.03762568 4280 14680 140 3968 3971 1583 67 77 49 100 100 0 3998 3897 1654 90 93 25 100 98 0 0.998 1.025 1.008 1.142 2.306 1.008 0.866 156 701 7809 7711 -0.003 3901 3908 3904 3807 619434 607950 79.469 152.160 0 0 -0.03762568
89676 -0.416308332 4470 14680 120 421 616 495 69 78 44 99 98 0 527 700 515 92 94 25 99 99 0 0.809 0.900 0.836 0.883 2.031 0.905 0.498 120 542 787 1155 -0.305 352 435 547 608 73862 83978 12.227 24.240 0 0 -0.416308332
89677 0.440757331 4670 14680 140 7126 6985 2187 77 92 97 100 100 0 5290 5127 1736 94 101 49 99 99 0 1.357 1.373 1.351 1.476 2.144 1.341 0.840 156 709 12245 11941 0.440 7049 5196 6908 5033 1089725 799873 71.062 102.571 0 0 0.440757331
89678 -1.028750508 4860 14680 140 4085 4369 1489 73 88 85 100 100 0 8273 8100 2859 96 103 52 100 100 0 0.491 0.537 0.532 0.557 1.617 0.510 0.888 156 722 12189 12300 -1.027 4012 8177 4296 8004 681635 1263564 50.365 153.788 0 0 -1.028750508
89679 -0.179419946 5060 14680 130 1291 1694 1071 70 79 46 100 99 0 1349 1851 1169 96 98 24 100 100 0 0.974 0.925 0.858 0.936 1.754 0.907 0.733 120 622 2474 3379 -0.037 1221 1253 1624 1755 203249 222105 35.109 73.042 0 0 -0.179419946
89680 0.283883971 5250 14680 140 5615 5833 2208 73 81 51 100 100 0 4607 4461 1872 95 100 29 98 98 0 1.228 1.319 1.277 1.495 2.222 1.303 0.871 156 731 10054 10126 0.297 5542 4512 5760 4366 909975 695993 112.784 150.379 0 0 0.283883971
89681 -0.05270315 5450 14680 130 3183 3276 829 72 82 52 100 100 0 3222 3222 772 93 97 27 100 100 0 0.994 1.024 0.999 1.021 1.362 1.012 0.878 120 642 6240 6333 -0.008 3111 3129 3204 3129 393132 386646 61.423 115.741 0 0 -0.05270315
89682 -0.068343025 5640 14680 130 2170 2195 567 72 81 48 100 100 0 2173 2220 563 91 95 25 100 100 0 1.008 0.997 0.998 0.999 1.403 0.964 0.875 120 624 4180 4252 0.011 2098 2082 2123 2129 263353 266457 44.042 85.000 0 0 -0.068343025

Total number of rows: 15488

Table truncated, full table size 3379 Kbytes.




Supplementary file Size Download File type/resource
GSM115783.gpr.gz 1.3 Mb (ftp)(http) GPR

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