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Sample GSM115764 Query DataSets for GSM115764
Status Public on Jul 14, 2006
Title Prostate_03-060A_GL3
Sample type RNA
 
Channel 1
Source name Prostate_cancer_03-060A_LCM_GL3
Organism Homo sapiens
Characteristics Prostate Cancer patient 03-060A Gleason_Score:4+3 LCM_Gleason_Pattern:3 Gleason_Pattern:3 Age:70-79 PSA:6.9 Volume:2.5 Margin_Status:positive 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_03-060A
Organism Homo sapiens
Characteristics Prostate normal adjacent from cancer patient 03-060A
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 03-060A with Gleason Score 4+3 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 -0.661057163 1680 14540 120 2220 2617 1054 57 94 323 100 100 0 3209 3627 1433 87 106 227 100 100 0 0.693 0.723 0.705 0.723 1.221 0.678 0.866 120 648 5285 6100 -0.529 2163 3122 2560 3540 314058 435235 7.811 15.511 0 0 -0.661057163
89664 0.142624856 1890 14540 130 8920 8680 2521 62 101 317 99 99 0 7617 7605 1494 93 111 125 100 100 0 1.177 1.147 1.186 1.077 1.447 1.202 0.937 120 631 16382 16130 0.235 8858 7524 8618 7512 1041552 912557 27.063 59.952 0 0 0.142624856
89665 -0.291897271 2080 14540 120 2231 2465 814 57 70 67 100 100 0 2528 2718 799 86 100 81 100 100 0 0.89 0.915 0.892 0.904 1.222 0.922 0.897 120 564 4616 5040 -0.168 2174 2442 2408 2632 295805 326101 35.746 32.321 0 0 -0.291897271
89666 0.169772957 2270 14530 130 4745 4751 1010 54 60 41 100 100 0 3917 3858 1060 85 87 26 100 99 0 1.224 1.245 1.21 1.337 1.557 1.191 0.922 120 632 8523 8470 0.292 4691 3832 4697 3773 570114 463001 114.415 145.038 0 0 0.169772957
89667 0.117093478 2460 14530 130 4986 5015 1148 56 66 87 100 100 0 4285 4168 1236 87 98 115 100 100 0 1.174 1.215 1.174 1.266 1.369 1.173 0.931 120 639 9128 9040 0.232 4930 4198 4959 4081 601799 500166 56.885 35.391 0 0 0.117093478
89668 -1.946221153 2660 14530 120 3144 3120 316 57 71 117 100 100 0 11253 11063 1275 92 107 141 100 100 0 0.277 0.279 0.279 0.28 1.107 0.268 0.949 120 605 14248 14034 -1.854 3087 11161 3063 10971 374418 1327507 26.06 77.702 0 0 -1.946221153
89669 -0.272266656 2860 14530 130 8842 8941 2456 56 65 80 100 100 0 9998 10025 2819 90 95 75 100 100 0 0.887 0.894 0.918 0.897 1.201 0.913 0.926 120 660 18694 18820 -0.173 8786 9908 8885 9935 1072962 1202953 110.95 132.4 0 0 -0.272266656
89670 -1.293876651 3050 14530 130 1611 1547 313 57 84 332 99 98 0 3581 3343 797 87 138 584 99 95 0 0.445 0.458 0.448 0.465 1.257 0.431 0.933 120 645 5048 4746 -1.169 1554 3494 1490 3256 185657 401108 4.407 5.488 0 0 -1.293876651
89671 0.001452126 3240 14520 130 11364 11168 1814 58 68 152 100 100 0 10497 10176 2066 89 102 222 100 100 0 1.086 1.101 1.093 1.125 1.313 1.074 0.934 120 665 21714 21197 0.119 11306 10408 11110 10087 1340129 1221171 73.026 45.378 0 0 0.001452126
89672 -0.129085541 3440 14530 120 10087 9842 1254 59 67 45 100 100 0 10273 10027 1180 90 97 70 100 100 0 0.985 0.985 0.982 0.983 1.073 0.971 0.944 120 579 20211 19720 -0.022 10028 10183 9783 9937 1181016 1203256 217.222 141.857 0 0 -0.129085541
89673 0.440055607 3630 14520 130 6062 5966 923 57 135 1085 100 99 0 4202 4163 731 88 202 1288 99 95 0 1.46 1.45 1.42 1.462 1.23 1.422 0.946 120 628 10119 9984 0.546 6005 4114 5909 4075 715932 499592 5.374 3.075 0 0 0.440055607
89674 0.192789053 3810 14520 130 1970 1971 373 56 145 1066 97 20 0 1660 1686 417 86 215 1265 83 0 0 1.216 1.197 1.196 1.213 1.196 1.144 0.93 120 658 3488 3515 0.282 1914 1574 1915 1600 236574 202378 1.713 1.163 0 0 0.192789053
89675 0.003813589 4020 14520 130 6083 5977 1242 57 88 179 100 100 0 5724 5625 1335 87 365 3240 95 22 0 1.069 1.069 1.062 1.087 1.185 1.029 0.925 120 696 11663 11458 0.096 6026 5637 5920 5538 717249 675052 32.899 1.623 0 0 0.003813589
89676 0.512500477 4220 14510 130 681 1090 839 56 69 127 100 98 0 549 1040 920 88 307 3247 0 0 0 1.356 1.086 1.207 1.213 1.347 0.973 0.892 120 651 1086 1986 0.439 625 461 1034 952 130800 124745 8.039 0.226 0 0 0.512500477
89677 -0.418667027 4410 14510 130 10117 9978 1360 59 97 236 100 100 0 12445 12120 2199 89 106 125 100 100 0 0.814 0.824 0.81 0.844 1.343 0.793 0.947 120 665 22414 21950 -0.297 10058 12356 9919 12031 1197322 1454437 41.869 96.112 0 0 -0.418667027
89678 0.539644756 4610 14520 130 14974 15172 2271 60 119 409 100 100 0 9461 9668 1490 90 138 479 100 100 0 1.592 1.578 1.574 1.579 1.068 1.598 0.953 120 663 24285 24690 0.67 14914 9371 15112 9578 1820588 1160135 36.804 19.896 0 0 0.539644756
89679 -0.100472084 4810 14520 130 2128 2554 1228 59 96 393 100 100 0 2138 2456 1100 87 160 756 100 71 0 1.009 1.053 1.033 1.039 1.244 1.068 0.902 120 660 4120 4864 0.013 2069 2051 2495 2369 306470 294706 6.254 3.037 0 0 -0.100472084
89680 0.042936634 5000 14510 130 8693 8327 1900 56 61 23 100 100 0 7948 7873 1840 87 89 25 100 100 0 1.099 1.062 1.047 1.063 1.13 1.043 0.946 120 633 16498 16057 0.136 8637 7861 8271 7786 999209 944704 359.391 311.36 0 0 0.042936634
89681 -0.126597765 5200 14510 130 4800 4773 605 57 62 24 100 100 0 4886 4852 646 87 91 33 100 100 0 0.988 0.99 0.995 0.99 1.086 0.969 0.938 120 627 9542 9481 -0.017 4743 4799 4716 4765 572809 582279 196.292 144.273 0 0 -0.126597765
89682 -0.222910825 5380 14520 130 3710 3655 495 63 85 157 100 100 0 3984 3817 810 93 143 335 99 98 0 0.937 0.965 0.94 0.998 1.316 0.935 0.948 120 639 7538 7316 -0.093 3647 3891 3592 3724 438563 457986 22.739 10.967 0 0 -0.222910825

Total number of rows: 15488

Table truncated, full table size 3389 Kbytes.




Supplementary file Size Download File type/resource
GSM115764.gpr.gz 1.3 Mb (ftp)(http) GPR

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