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Sample GSM115776 Query DataSets for GSM115776
Status Public on Jul 14, 2006
Title Prostate_03-141C_GL4
Sample type RNA
 
Channel 1
Source name Prostate_normal_adjacent_cancer_03-141C
Organism Homo sapiens
Characteristics Prostate normal adjacent from cancer patient 03-141C
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_cancer_03-141C_LCM_GL4
Organism Homo sapiens
Characteristics Prostate Cancer patient 03-141C Gleason_Score:4+3 LCM_Gleason_Pattern:4 Gleason_Pattern:4 Age:60-69 PSA:5.7 Volume:2.3 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 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 03-141C 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) [email protected]
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 �m 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 �m 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 �m 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 R� (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).
INV_VALUE
UNF_VALUE -[INV_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 R� (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 INV_VALUE UNF_VALUE
89663 -0.881849 2290 14300 120 8089 9239 4202 113 130 98 100 99 0 3641 4213 1911 153 162 53 100 100 0 2.287 2.248 2.299 2.232 1.453 2.405 0.797 120 648 11464 13186 1.193 7976 3488 9126 4060 1108642 505578 92.949 76.434 0 0 0.881849318 -0.881849
89664 1.15385 2490 14300 120 17554 17516 4466 128 140 95 100 100 0 34600 34885 8076 181 192 89 100 100 0 0.506 0.501 0.499 0.497 1.17 0.488 0.932 120 578 51845 52092 -0.982 17426 34419 17388 34704 2101926 4186205 182.905 389.809 0 0 -1.153848536 1.15385
89665 0.828599 2680 14290 120 7011 7084 2430 111 125 88 100 100 0 9648 10077 3773 165 178 88 100 100 0 0.728 0.703 0.684 0.719 1.403 0.658 0.883 120 578 16383 16885 -0.459 6900 9483 6973 9912 850065 1209259 79.08 112.489 0 0 -0.828598724 0.828599
89666 0.65244 2880 14300 120 4602 4749 1558 111 123 86 100 99 0 5862 5897 2028 151 159 44 100 100 0 0.786 0.807 0.823 0.823 1.421 0.777 0.908 120 570 10202 10384 -0.347 4491 5711 4638 5746 569928 707619 53.791 130.409 0 0 -0.652440226 0.65244
89667 0.554621 3070 14290 120 5186 5610 1685 114 124 117 100 100 0 6128 6356 1797 151 156 40 100 100 0 0.849 0.886 0.872 0.884 1.213 0.867 0.926 120 578 11049 11701 -0.237 5072 5977 5496 6205 673199 762686 46.889 155 0 0 -0.554620689 0.554621
89668 -2.13957 3270 14290 120 22910 22246 3527 110 133 158 100 100 0 4172 4215 691 147 156 87 100 100 0 5.665 5.441 5.421 5.447 1.124 5.505 0.943 120 608 26825 26204 2.502 22800 4025 22136 4068 2669471 505777 139.956 46.655 0 0 2.139571858 -2.13957
89669 0.887925 3470 14290 120 20110 19989 4463 106 122 109 100 100 0 33275 33904 8138 144 157 147 100 100 0 0.604 0.589 0.572 0.595 1.291 0.569 0.922 120 594 53135 53643 -0.728 20004 33131 19883 33760 2398700 4068464 182.266 229.571 0 0 -0.887925039 0.887925
89670 -1.04683 3660 14290 120 2786 2766 680 104 132 465 100 100 0 1193 1175 314 144 174 527 95 49 0 2.557 2.582 2.622 2.634 1.351 2.614 0.875 120 594 3731 3693 1.354 2682 1049 2662 1031 331920 140999 5.665 1.899 0 0 1.046830922 -1.04683
89671 1.16008 3860 14290 130 19937 19895 3313 108 139 238 100 100 0 40428 40137 6296 148 169 206 100 100 0 0.492 0.495 0.496 0.494 1.119 0.488 0.938 120 679 60109 59776 -1.022 19829 40280 19787 39989 2387404 4816461 83.008 194.019 0 0 -1.16008267 1.16008
89672 0.66925 4060 14290 130 20202 20088 3209 111 143 242 100 100 0 28380 27366 4672 148 166 185 100 100 0 0.712 0.734 0.724 0.74 1.205 0.732 0.941 120 652 48323 47195 -0.491 20091 28232 19977 27218 2410569 3283905 82.417 147.027 0 0 -0.669249839 0.66925
89673 0.392823 4250 14280 130 7527 7350 1304 109 191 1411 100 98 0 7691 7362 1368 148 238 1592 99 99 0 0.983 1.004 1.01 1.01 1.235 0.984 0.937 120 665 14961 14455 -0.024 7418 7543 7241 7214 881981 883467 5.074 4.475 0 0 -0.39282293 0.392823
89674 -0.553769 4440 14280 130 2163 2172 314 110 336 1364 99 2 0 1284 1271 184 151 293 974 79 0 0 1.812 1.841 1.834 1.845 1.174 1.506 0.804 120 678 3186 3182 0.858 2053 1133 2062 1120 260660 152539 1.346 1.004 0 0 0.553769033 -0.553769
89675 -0.545426 4650 14290 130 17189 16788 4491 112 347 1388 99 98 0 9457 9173 1811 149 297 992 100 100 0 1.835 1.848 1.903 1.783 1.391 1.921 0.907 120 654 26385 25700 0.876 17077 9308 16676 9024 2014616 1100725 11.845 8.948 0 0 0.545426444 -0.545426
89676 0.408448 4840 14290 120 1027 1539 1425 106 115 51 100 100 0 1117 1408 1099 143 149 39 100 100 0 0.946 1.133 1.103 1.059 1.577 1.233 0.89 120 562 1895 2698 -0.081 921 974 1433 1265 184654 168964 27.922 32.282 0 0 -0.408447829 0.408448
89677 -1.14284 5030 14290 130 36860 35748 4992 107 120 80 100 100 0 14789 14161 2080 144 156 138 100 100 0 2.51 2.543 2.521 2.547 1.128 2.539 0.95 120 622 51398 49658 1.327 36753 14645 35641 14017 4289770 1699343 445.35 101.486 0 0 1.142837959 -1.14284
89678 0.175013 5220 14290 130 21583 20725 3632 106 130 128 100 100 0 21183 20250 4038 148 200 585 100 100 0 1.021 1.026 1.004 1.031 1.19 0.994 0.941 120 660 42512 40721 0.03 21477 21035 20619 20102 2487026 2430002 160.898 34.274 0 0 -0.175013355 0.175013
89679 0.0719646 5420 14280 130 3266 3970 2115 107 127 116 100 100 0 2881 3436 1718 147 194 565 100 100 0 1.155 1.175 1.163 1.158 1.276 1.15 0.888 120 680 5893 7152 0.208 3159 2734 3863 3289 476403 412343 33.129 5.738 0 0 -0.071964604 0.0719646
89680 1.21492 5610 14280 130 13989 14218 2532 107 118 58 100 100 0 27729 27884 4847 144 157 115 100 100 0 0.503 0.509 0.503 0.508 1.179 0.486 0.913 120 647 41467 41851 -0.991 13882 27585 14111 27740 1706133 3346046 243.103 241.104 0 0 -1.214923663 1.21492
89681 0.460427 5800 14280 130 12318 12223 2142 108 171 576 100 100 0 13532 13579 2449 145 238 719 100 100 0 0.912 0.902 0.888 0.903 1.169 0.877 0.939 120 692 25597 25549 -0.133 12210 13387 12115 13434 1466748 1629460 20.924 18.555 0 0 -0.46042738 0.460427
89682 0.296312 6010 14290 130 11033 10736 1702 112 201 682 100 100 0 10638 10601 1585 147 218 569 100 100 0 1.041 1.016 1.009 1.015 1.143 1.023 0.941 120 645 21412 21078 0.058 10921 10491 10624 10454 1288356 1272175 15.447 18.248 0 0 -0.296311976 0.296312

Total number of rows: 15488

Table truncated, full table size 3591 Kbytes.




Supplementary file Size Download File type/resource
GSM115776.gpr.gz 1.3 Mb (ftp)(http) GPR

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