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Sample GSM115782 Query DataSets for GSM115782
Status Public on Jul 14, 2006
Title Prostate_03-152A_GL5
Sample type RNA
 
Channel 1
Source name Prostate_normal_adjacent_cancer_03-152A
Organism Homo sapiens
Characteristics Prostate normal adjacent from cancer patient 03-152A
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_03-152A_LCM_GL5
Organism Homo sapiens
Characteristics Prostate Cancer patient 03-152A Gleason_Score:5+4 LCM_Gleason_Pattern:5 Gleason_Pattern:5 Age:60-69 PSA:9.0 Volume:8 Margin_Status:positive Treatment:Vit E
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 03-152A with Gleason Score 5+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) [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 -0.501383 1560 14650 110 3213 3830 1805 118 148 193 100 100 0 2583 3009 1508 116 152 300 100 98 0 1.255 1.283 1.233 1.3 1.383 1.24 0.867 80 563 5562 6605 0.327 3095 2467 3712 2893 306429 240735 19.078 9.523 0 0 0.501383163 -0.501383
89664 1.50582 1760 14650 130 3689 3786 1015 127 151 177 100 100 0 11068 11166 2606 120 153 276 100 100 0 0.325 0.331 0.321 0.328 1.251 0.322 0.909 120 699 14510 14705 -1.62 3562 10948 3659 11046 454291 1339908 20.537 39.902 0 0 -1.505816312 1.50582
89665 0.47244 1960 14660 120 2004 1936 649 129 139 69 100 99 0 3138 3107 941 122 130 57 100 100 0 0.622 0.605 0.622 0.593 1.542 0.599 0.878 120 594 4891 4792 -0.686 1875 3016 1807 2985 232329 372808 26.043 52.228 0 0 -0.47243984 0.47244
89666 -0.265884 2160 14650 120 1793 1782 645 133 167 150 99 97 0 1867 1957 540 115 149 154 99 99 0 0.947 0.895 0.91 0.842 1.56 0.948 0.831 120 595 3412 3491 -0.078 1660 1752 1649 1842 213803 234853 10.767 11.74 0 0 0.265884465 -0.265884
89667 -0.0657181 2350 14650 130 1676 1718 566 130 155 133 100 100 0 1984 2046 462 109 134 125 100 99 0 0.825 0.82 0.826 0.79 1.436 0.845 0.85 120 620 3421 3525 -0.278 1546 1875 1588 1937 206178 245565 11.752 15.296 0 0 0.065718076 -0.0657181
89668 -1.13788 2540 14650 140 21429 21310 6354 122 133 69 100 100 0 10430 9986 3482 107 112 31 99 98 0 2.064 2.145 2.1 2.328 1.673 2.134 0.94 156 715 31630 31067 1.045 21307 10323 21188 9879 3324287 1557763 306.913 318.516 0 0 1.137882842 -1.13788
89669 -0.65915 2740 14650 130 12263 12611 3468 124 131 65 100 100 0 8374 8547 2368 108 113 31 100 100 0 1.469 1.48 1.487 1.483 1.214 1.507 0.868 120 620 20405 20926 0.554 12139 8266 12487 8439 1513297 1025645 192 272.065 0 0 0.659149988 -0.65915
89670 -1.80268 2930 14650 140 2661 2746 809 125 133 71 100 100 0 1041 1052 324 108 114 35 98 98 0 2.718 2.776 2.723 2.809 1.508 2.877 0.83 156 699 3469 3565 1.443 2536 933 2621 944 428356 164161 36.803 26.8 0 0 1.802683013 -1.80268
89671 -0.0611526 3120 14650 130 9967 10332 2722 123 136 72 100 100 0 10258 10565 2790 112 119 46 100 100 0 0.97 0.977 0.963 0.978 1.253 0.945 0.904 120 634 19990 20662 -0.044 9844 10146 10209 10453 1239822 1267808 141.611 227.087 0 0 0.061152572 -0.0611526
89672 0.553446 3330 14650 140 8738 8571 2842 121 131 68 100 100 0 13707 13704 3704 111 117 42 100 100 0 0.634 0.622 0.631 0.589 1.468 0.626 0.922 156 722 22213 22043 -0.658 8617 13596 8450 13593 1337040 2137762 124.118 323.5 0 0 -0.553446303 0.553446
89673 0.399708 3520 14640 130 2760 2742 774 122 131 65 100 100 0 3951 3906 1129 109 115 36 100 100 0 0.687 0.69 0.692 0.691 1.267 0.672 0.901 120 594 6480 6417 -0.542 2638 3842 2620 3797 329057 468668 40.169 105.306 0 0 -0.399707541 0.399708
89674 -0.720559 3710 14640 150 757 804 413 122 129 66 98 92 0 453 471 212 108 115 36 96 95 0 1.841 1.879 1.786 1.801 1.863 2.023 0.791 156 758 980 1045 0.88 635 345 682 363 125454 73524 10.227 9.889 0 0 0.720558881 -0.720559
89675 -0.218597 3910 14640 140 5070 5106 1568 117 127 66 100 100 0 4726 4542 1418 107 111 33 98 98 0 1.072 1.125 1.095 1.2 1.809 1.122 0.902 156 692 9572 9424 0.101 4953 4619 4989 4435 796562 708526 75.439 134.273 0 0 0.218597117 -0.218597
89676 0.46132 4100 14640 120 608 727 491 118 130 68 98 93 0 734 876 557 107 111 35 100 98 0 0.781 0.792 0.722 0.769 1.857 0.797 0.658 120 548 1117 1378 -0.356 490 627 609 769 87239 105116 8.779 21.857 0 0 -0.461319745 0.46132
89677 0.696322 4300 14650 140 9151 9627 3417 119 129 63 100 100 0 15817 16006 4691 107 113 35 100 100 0 0.575 0.598 0.581 0.587 1.396 0.598 0.903 156 665 24742 25407 -0.799 9032 15710 9508 15899 1501835 2496958 150.762 454.086 0 0 -0.696321994 0.696322
89678 -0.535262 4490 14640 150 9587 9818 4419 125 137 80 100 100 0 7129 7076 3198 110 122 63 99 98 0 1.348 1.391 1.383 1.441 1.526 1.392 0.906 156 771 16481 16659 0.431 9462 7019 9693 6966 1531592 1103796 121.013 110.381 0 0 0.535262251 -0.535262
89679 0.41281 4700 14640 120 981 1011 406 127 142 90 98 97 0 1493 1558 506 111 126 72 100 100 0 0.618 0.611 0.595 0.564 1.804 0.617 0.769 120 546 2236 2331 -0.694 854 1382 884 1447 121273 186979 9.656 19.889 0 0 -0.4128101 0.41281
89680 0.353889 4880 14640 140 6153 6377 2003 121 130 83 100 100 0 8431 8565 2949 108 113 35 100 100 0 0.725 0.74 0.756 0.77 1.586 0.714 0.884 156 658 14355 14713 -0.464 6032 8323 6256 8457 994839 1336187 75.265 241.486 0 0 -0.353889275 0.353889
89681 0.834583 5080 14640 140 5243 5085 1352 122 129 64 100 100 0 9969 9812 2136 110 113 33 100 100 0 0.519 0.512 0.511 0.502 1.394 0.506 0.909 156 652 14980 14665 -0.945 5121 9859 4963 9702 793313 1530697 77.438 293.909 0 0 -0.834582861 0.834583
89682 0.240003 5280 14640 140 4528 4458 1410 120 130 66 100 100 0 5746 5680 1331 109 114 36 100 100 0 0.782 0.779 0.781 0.744 1.428 0.798 0.916 156 642 10045 9909 -0.355 4408 5637 4338 5571 695484 886015 65.576 154.611 0 0 -0.240002814 0.240003

Total number of rows: 15488

Table truncated, full table size 3518 Kbytes.




Supplementary file Size Download File type/resource
GSM115782.gpr.gz 1.3 Mb (ftp)(http) GPR

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