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Sample GSM115760 Query DataSets for GSM115760
Status Public on Jul 14, 2006
Title Prostate_03-135C_GL4
Sample type RNA
 
Channel 1
Source name Prostate_cancer_03-135C_LCM_GL4
Organism Homo sapiens
Characteristics Prostate Cancer patient 03-135C Gleason_Score:4+3 LCM_Gleason_Pattern:4 Gleason_Pattern:4 Age:50-59 PSA:5.0 Volume:2.3 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_03-135C
Organism Homo sapiens
Characteristics Prostate normal adjacent from cancer patient 03-135C
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 03-135C 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 -2.10196021 2330 14410 120 2027 2510 1251 85 206 993 99 48 0 8114 9815 4389 108 174 836 100 98 0 0.243 0.25 0.227 0.246 1.461 0.222 0.79 120 675 9948 12132 -2.044 1942 8006 2425 9707 301243 1177817 2.32 11.532 0 0 -2.10196021
89664 1.220125832 2530 14400 130 26949 26019 3961 100 218 740 100 100 0 10193 9763 1620 119 143 134 100 100 0 2.665 2.688 2.701 2.706 1.179 2.724 0.953 120 664 36923 35563 1.414 26849 10074 25919 9644 3122220 1171515 34.866 71.791 0 0 1.220125832
89665 1.014950345 2710 14410 120 6400 7300 3233 118 130 64 100 100 0 3106 3617 1513 128 131 32 100 100 0 2.109 2.058 1.977 2.045 1.301 2.075 0.901 120 576 9260 10671 1.077 6282 2978 7182 3489 875944 434022 112.031 108.938 0 0 1.014950345
89666 0.309212829 2920 14410 120 8209 7984 1889 124 138 73 100 100 0 6033 5955 1043 133 140 42 100 100 0 1.37 1.35 1.368 1.325 1.265 1.395 0.924 120 592 13985 13682 0.455 8085 5900 7860 5822 958053 714605 107.479 138.452 0 0 0.309212829
89667 0.391038448 3100 14410 120 9384 9374 1698 141 166 92 100 100 0 6453 6437 1294 142 158 63 100 100 0 1.465 1.467 1.432 1.492 1.297 1.446 0.927 120 580 15554 15528 0.55 9243 6311 9233 6295 1124839 772404 100.087 99.667 0 0 0.391038448
89668 1.994592902 3300 14400 130 36175 35494 4248 137 166 98 100 100 0 8039 7796 1099 141 151 57 100 100 0 4.563 4.619 4.602 4.651 1.143 4.667 0.943 120 659 43936 43012 2.19 36038 7898 35357 7655 4259330 935557 360.49 134.123 0 0 1.994592902
89669 0.516028847 3500 14400 120 22429 21831 3339 139 162 98 100 100 0 13735 13548 1965 139 149 97 100 100 0 1.639 1.618 1.618 1.617 1.156 1.645 0.928 120 594 35886 35101 0.713 22290 13596 21692 13409 2619762 1625782 221.112 138.134 0 0 0.516028847
89670 -0.302044116 3690 14400 120 7100 7177 1091 139 189 462 100 100 0 7852 7676 1271 145 167 222 100 100 0 0.903 0.935 0.917 0.939 1.185 0.909 0.936 120 608 14668 14569 -0.147 6961 7707 7038 7531 861281 921160 15.126 33.824 0 0 -0.302044116
89671 -0.435332336 3900 14400 130 17142 16547 3032 136 200 508 100 100 0 20155 19874 3349 149 191 397 100 100 0 0.85 0.832 0.844 0.83 1.206 0.833 0.933 120 664 37012 36136 -0.234 17006 20006 16411 19725 1985658 2384909 32.179 49.579 0 0 -0.435332336
89672 0.703256848 4080 14400 120 28475 27776 3435 128 158 165 100 100 0 15208 14799 1689 139 174 322 100 100 0 1.881 1.886 1.88 1.883 1.079 1.892 0.949 120 564 43416 42308 0.912 28347 15069 27648 14660 3333082 1775898 167.382 45.419 0 0 0.703256848
89673 1.295441487 4270 14400 120 18913 18498 1974 134 190 539 100 100 0 6818 6591 1025 140 171 294 100 100 0 2.812 2.847 2.777 2.88 1.185 2.841 0.939 120 612 25457 24815 1.492 18779 6678 18364 6451 2219765 790909 33.967 21.837 0 0 1.295441487
89674 -1.301649937 4470 14400 130 2534 2530 353 122 143 78 100 100 0 5871 5937 844 143 157 67 100 100 0 0.421 0.416 0.412 0.415 1.133 0.397 0.951 120 674 8140 8202 -1.248 2412 5728 2408 5794 303563 712495 30.603 86.269 0 0 -1.301649937
89675 -0.027903987 4670 14390 130 13987 13699 2151 119 159 203 100 100 0 12506 11946 1988 140 156 89 100 100 0 1.121 1.15 1.123 1.154 1.163 1.12 0.913 120 730 26234 25386 0.165 13868 12366 13580 11806 1643870 1433570 66.7 132.472 0 0 -0.027903987
89676 1.006361414 4890 14400 100 3482 3887 2912 132 197 263 95 92 0 1737 2169 1767 146 167 102 100 98 0 2.106 1.856 2.108 1.923 1.729 1.798 0.896 80 432 4941 5778 1.074 3350 1591 3755 2023 310946 173527 14.03 19.627 0 0 1.006361414
89677 0.725421625 5050 14400 130 37397 37186 3903 156 238 630 100 100 0 19473 19054 2441 162 294 1110 100 100 0 1.928 1.96 1.963 1.968 1.117 1.943 0.943 120 640 56552 55922 0.947 37241 19311 37030 18892 4462313 2286488 58.648 16.901 0 0 0.725421625
89678 -0.083136382 5260 14400 130 24224 24403 2860 182 248 614 100 100 0 22140 22210 2295 189 304 1084 100 100 0 1.095 1.1 1.105 1.098 1.081 1.098 0.935 120 670 45993 46242 0.131 24042 21951 24221 22021 2928328 2665191 39.34 20.208 0 0 -0.083136382
89679 -0.157475322 5460 14400 120 3943 4988 2767 153 176 106 100 100 0 4233 4944 2405 173 182 66 100 100 0 0.933 1.013 0.982 0.977 1.437 1.056 0.887 120 555 7850 9606 -0.099 3790 4060 4835 4771 598597 593279 45.396 72.152 0 0 -0.157475322
89680 0.272549165 5650 14390 140 19220 18157 4096 146 260 807 99 98 0 13968 13119 3575 160 231 477 98 98 0 1.381 1.39 1.394 1.463 1.468 1.379 0.92 156 730 32882 30970 0.466 19074 13808 18011 12959 2832421 2046580 22.177 27.019 0 0 0.272549165
89681 0.309918163 5850 14380 130 14328 13723 2353 165 283 870 100 100 0 10150 9853 1704 176 228 411 100 100 0 1.42 1.401 1.401 1.4 1.105 1.409 0.945 120 618 24137 23235 0.506 14163 9974 13558 9677 1646815 1182336 15.448 23.418 0 0 0.309918163
89682 0.642902273 6030 14390 120 15529 15310 1612 198 236 217 100 100 0 8770 8647 1204 201 213 94 100 100 0 1.789 1.789 1.753 1.8 1.14 1.775 0.941 120 550 23900 23558 0.839 15331 8569 15112 8446 1837228 1037651 69.465 89.723 0 0 0.642902273

Total number of rows: 15488

Table truncated, full table size 3492 Kbytes.




Supplementary file Size Download File type/resource
GSM115760.gpr.gz 1.3 Mb (ftp)(http) GPR

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