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Sample GSM115777 Query DataSets for GSM115777
Status Public on Jul 14, 2006
Title Prostate_02-053C_GL4
Sample type RNA
 
Channel 1
Source name Prostate_cancer_02-053C_LCM_GL4
Organism Homo sapiens
Characteristics Prostate Cancer patient 02-053C Gleason_Score:3+4 LCM_Gleason_Pattern:4 Gleason_Pattern:4 Age:60-69 PSA:1.0 Volume:<0.1 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_02-053C
Organism Homo sapiens
Characteristics Prostate normal adjacent from cancer patient 02-053C
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 02-053C 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 -2.591087037 1980 14350 130 366 453 306 115 143 123 90 53 0 1680 2017 952 183 201 94 100 100 0 0.168 0.184 0.154 0.162 1.658 0.177 0.608 120 672 1748 2172 -2.576 251 1497 338 1834 54377 242064 2.52 19.319 0 0 -2.591087037
89664 0.690292162 2170 14350 150 27898 27384 4287 121 145 93 100 100 0 10152 9763 2100 189 201 79 100 100 0 2.788 2.848 2.789 2.945 1.364 2.812 0.95 156 728 37740 36837 1.479 27777 9963 27263 9574 4271870 1523057 292.892 121.038 0 0 0.690292162
89665 0.906759165 2370 14350 130 7153 7607 2984 119 144 112 100 100 0 3055 3076 1172 183 202 133 100 100 0 2.449 2.588 2.55 2.617 1.339 2.667 0.904 120 618 9906 10381 1.292 7034 2872 7488 2893 912791 369118 66.634 21.609 0 0 0.906759165
89666 -0.76838331 2560 14350 130 3800 4150 3910 111 132 90 100 100 0 5041 5163 2791 182 212 198 100 100 0 0.759 0.811 0.784 0.794 1.335 0.99 0.539 120 649 8548 9020 -0.397 3689 4859 4039 4981 497941 619606 44.644 25.005 0 0 -0.76838331
89667 -1.002701015 2770 14340 130 2858 2848 590 106 128 94 100 100 0 4603 4578 1160 181 211 200 100 100 0 0.622 0.624 0.632 0.635 1.275 0.585 0.903 120 638 7174 7139 -0.684 2752 4422 2742 4397 341735 549416 28.936 21.835 0 0 -1.002701015
89668 -0.181057305 2960 14350 140 21294 21193 3382 107 128 88 100 100 0 14049 14055 2376 176 194 86 100 100 0 1.527 1.519 1.515 1.524 1.144 1.523 0.963 156 679 35060 34965 0.611 21187 13873 21086 13879 3306068 2192630 239.375 161.174 0 0 -0.181057305
89669 0.485512351 3160 14340 140 34457 33714 6918 105 127 93 100 100 0 14152 13828 2952 175 195 107 100 100 0 2.458 2.462 2.482 2.5 1.278 2.506 0.942 156 675 48329 47262 1.297 34352 13977 33609 13653 5259451 2157211 361.151 127.411 0 0 0.485512351
89670 -1.117232677 3340 14340 150 2384 2402 471 103 122 85 100 100 0 4255 4192 781 176 189 93 100 100 0 0.559 0.572 0.557 0.574 1.253 0.557 0.92 156 750 6360 6315 -0.839 2281 4079 2299 4016 374649 654001 26.824 43.043 0 0 -1.117232677
89671 0.366717862 3550 14350 150 37571 36481 6944 106 130 91 100 100 0 16614 16346 2906 177 196 102 100 100 0 2.279 2.25 2.27 2.243 1.178 2.323 0.927 156 723 53902 52544 1.189 37465 16437 36375 16169 5690987 2549989 399.462 158.333 0 0 0.366717862
89672 0.18921733 3740 14350 150 18233 18155 3298 104 190 1109 100 100 0 9682 9685 1758 180 200 101 100 100 0 1.908 1.899 1.893 1.9 1.145 1.911 0.95 156 659 27631 27556 0.932 18129 9502 18051 9505 2832186 1510800 16.199 93.911 0 0 0.18921733
89673 0.326645313 3930 14340 150 4229 4279 816 103 182 1065 100 100 0 2842 2801 553 177 190 69 100 100 0 1.548 1.591 1.591 1.601 1.183 1.915 0.73 156 716 6791 6800 0.631 4126 2665 4176 2624 667552 436958 3.847 37.841 0 0 0.326645313
89674 0.138199665 4130 14340 150 974 995 272 102 164 662 82 8 0 918 931 266 175 250 753 48 0 0 1.174 1.181 1.167 1.195 1.4 1.232 0.756 156 759 1615 1649 0.231 872 743 893 756 155288 145229 1.255 0.904 0 0 0.138199665
89675 -0.033295248 4330 14340 140 10647 10533 2052 101 151 636 100 100 0 7271 7248 1419 176 215 502 100 100 0 1.486 1.475 1.476 1.476 1.163 1.491 0.93 156 715 17641 17504 0.572 10546 7095 10432 7072 1643074 1130736 16.324 14.01 0 0 -0.033295248
89676 0.326976284 4490 14340 80 3521 3454 1455 124 212 215 100 98 0 2490 2382 956 213 255 156 100 100 0 1.492 1.535 1.528 1.543 1.646 1.51 0.853 52 282 5674 5499 0.577 3397 2277 3330 2169 179618 123846 15.079 13.635 0 0 0.326976284
89677 -2.584264204 4720 14340 150 3516 3491 732 101 141 140 100 100 0 14401 14312 2379 181 206 112 100 100 0 0.24 0.24 0.241 0.237 1.142 0.24 0.95 156 839 17635 17521 -2.058 3415 14220 3390 14131 544650 2232615 23.929 125.946 0 0 -2.584264204
89678 -0.49835907 4920 14340 150 4034 4336 1403 98 109 57 100 100 0 4498 4717 1385 177 187 66 100 100 0 0.911 0.933 0.939 0.921 1.222 0.975 0.922 156 734 8257 8778 -0.135 3936 4321 4238 4540 676356 735875 74.158 68.636 0 0 -0.49835907
89679 0.119300058 5100 14330 130 1768 2499 1666 105 116 65 100 100 0 1576 2426 1883 180 193 80 100 99 0 1.191 1.066 1.188 1.18 1.52 0.984 0.885 120 610 3059 4640 0.252 1663 1396 2394 2246 299841 291094 36.662 27.913 0 0 0.119300058
89680 0.69741847 5310 14330 150 23304 23147 4642 105 127 90 100 100 0 8625 8451 1613 180 194 80 100 100 0 2.747 2.786 2.816 2.784 1.162 2.901 0.933 156 770 31644 31313 1.458 23199 8445 23042 8271 3610861 1318310 255.778 103.213 0 0 0.69741847
89681 0.238016859 5500 14340 140 2774 2837 802 107 127 83 100 100 0 2138 2220 545 175 188 65 100 100 0 1.359 1.335 1.344 1.322 1.221 1.386 0.924 156 617 4630 4775 0.442 2667 1963 2730 2045 442602 346349 32.651 31.262 0 0 0.238016859
89682 0.297213173 5700 14330 150 2168 2195 476 106 120 75 100 100 0 1690 1726 366 173 186 78 100 100 0 1.359 1.345 1.355 1.348 1.217 1.377 0.91 156 704 3579 3642 0.443 2062 1517 2089 1553 342398 269269 27.667 19.744 0 0 0.297213173

Total number of rows: 15488

Table truncated, full table size 3480 Kbytes.




Supplementary file Size Download File type/resource
GSM115777.gpr.gz 1.3 Mb (ftp)(http) GPR

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