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Sample GSM251869 Query DataSets for GSM251869
Status Public on Dec 01, 2008
Title Human Prostate GSK-5
Sample type RNA
 
Channel 1
Source name Reference
Organism Homo sapiens
Characteristics Reference
Extracted molecule total RNA
Extraction protocol Prostate samples embedded in OCT were used for laser capture microdissection (LCM). Approximately 2000-3000 epithelial cells per sample were collected from 8µm sections using the Arcturus Veritas™ Laser Capture Microdissection System according to the Arcturus HistoGene LCM Frozen Section Staining Kit Protocol (Mountain View, CA). Total RNA was isolated using the Arcturus Picopure™ Kit, and the samples were treated with DNAse using the Qiagen RNase-Free DNase Set (Qiagen Inc, Valencia, CA). Total RNA was subjected to two rounds of linear amplification using the Ambion MessageAmpII Kit (Ambion Inc, Austin, TX), quantitated in a Gene-Spec III spectrophotometer (Hitachi, Tokyo) and aRNA integrity evaluated using gel electrophoresis.
Label Cy5
Label protocol Complementary DNA (cDNA) probe pairs were prepared by amino-allyl reverse transcription using 2 µg of amplified RNA from microdissected samples and 30 µg of total RNA from a reference RNA pool composed of total RNA isolated from the LNCaP, DU145, and PC3 prostate cell lines. Probes were labeled with either Cy5 or Cy3 fluors (Amersham Bioscience, Piscataway, NJ) and competitively hybridized to custom cDNA microarrays spotted in duplicate with approximately 6,700 unique cDNA clones from the Prostate Expression Database (PEDB) as previously described in Pritchard CC, Hsu L, Delrow J, and Nelson PS. Project normal: defining normal variance in mouse gene expression. Proc Natl Acad Sci U S A 2001;98:13266-13271.
 
Channel 2
Source name Human Prostate GSK-5 treated with 0.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-5. Specimen ID: GSK-5; Treatment: 0.5 mg PO qDay Dutasteride; Reference: HGSv5;
Extracted molecule total RNA
Extraction protocol Prostate samples embedded in OCT were used for laser capture microdissection (LCM). Approximately 2000-3000 epithelial cells per sample were collected from 8µm sections using the Arcturus Veritas™ Laser Capture Microdissection System according to the Arcturus HistoGene LCM Frozen Section Staining Kit Protocol (Mountain View, CA). Total RNA was isolated using the Arcturus Picopure™ Kit, and the samples were treated with DNAse using the Qiagen RNase-Free DNase Set (Qiagen Inc, Valencia, CA). Total RNA was subjected to two rounds of linear amplification using the Ambion MessageAmpII Kit (Ambion Inc, Austin, TX), quantitated in a Gene-Spec III spectrophotometer (Hitachi, Tokyo) and aRNA integrity evaluated using gel electrophoresis.
Label Cy3
Label protocol Complementary DNA (cDNA) probe pairs were prepared by amino-allyl reverse transcription using 2 µg of amplified RNA from microdissected samples and 30 µg of total RNA from a reference RNA pool composed of total RNA isolated from the LNCaP, DU145, and PC3 prostate cell lines. Probes were labeled with either Cy5 or Cy3 fluors (Amersham Bioscience, Piscataway, NJ) and competitively hybridized to custom cDNA microarrays spotted in duplicate with approximately 6,700 unique cDNA clones from the Prostate Expression Database (PEDB) as previously described in Pritchard CC, Hsu L, Delrow J, and Nelson PS. Project normal: defining normal variance in mouse gene expression. Proc Natl Acad Sci U S A 2001;98:13266-13271.
 
 
Hybridization protocol Probes were labeled with either Cy5 or Cy3 fluors (Amersham Bioscience, Piscataway, NJ) and competitively hybridized to custom cDNA microarrays spotted in duplicate with approximately 6,700 unique cDNA clones from the Prostate Expression Database (PEDB) as previously described in Nelson PS, Pritchard C, Abbott D, and Clegg N. The human (PEDB) and mouse (mPEDB) Prostate Expression Databases. Nucleic Acids Res 2002;30:218-220 and Pritchard CC, Hsu L, Delrow J, and Nelson PS. Project normal: defining normal variance in mouse gene expression. Proc Natl Acad Sci U S A 2001;98:13266-13271.
Scan protocol Fluorescence array images were collected using a GenePix 4000B fluorescent scanner (Axon Instruments, Foster City, CA) and processed as we have previously described in True L, Coleman I, Hawley S, et al. A molecular correlate to the Gleason grading system for prostate adenocarcinoma. Proc Natl Acad Sci U S A 2006;103:10991-10996.
Description Human Prostate GSK-5 from Human hybridized against Reference
Data processing Changes in gene expression were evaluated using the Statistical Analysis of Microarray (SAM) program (http://www-stat.stanford.edu/_tibs/SAM/) to perform a one-sample t-test assessing the effect of Acyline treatment on gene expression (22). An FDR (false discovery rate) of less than 5% was considered significant. Quantile normalization was performed in Bioconductor (23) to allow single channel comparison of the absolute signal intensities in the experimental channel across different arrays in the same experiment.
 
Submission date Dec 18, 2007
Last update date Dec 28, 2007
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 GPL4768
Series (1)
GSE9972 Prostate Cancer Gene Expression Changes after Treatment with Neoadjuvant Dutasteride

Data table header descriptions
ID_REF the unique identifier of the feature derived from the Array List (up to 40 characters long, contained in quotation marks).
VALUE normalized log (experiment/reference) ratio data comparable across rows and samples
MetaCol Column referring to overall organization
MetaRow Row referring to overall organization
Column the column number of the feature.
Row the row number of the feature.
Name the name of the feature derived from the Array List (up to 40 characters long, contained in quotation marks).
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.
Normalize the normalization status of the feature (included/not included).

Data table
ID_REF VALUE MetaCol MetaRow Column Row Name 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
237241 -0.428799297 1 1 1 1 P:1 2640 9670 150 2676 2860 985 733 931 985 92 48 0 1450 1638 971 375 399 121 100 96 0 1.807 1.684 1.886 1.895 1.505 1.349 0.647 156 644 3018 3390 0.854 1943 1075 2127 1263 446145 255542 1.958 10.24 0 0
237242 -4.002545311 1 1 2 1 P:5 2840 9670 140 20083 22765 13155 768 989 917 100 99 0 2257 2382 1200 395 417 133 99 98 0 10.373 11.07 12.062 11.159 1.483 11.7 0.757 156 641 21177 23984 3.375 19315 1862 21997 1987 3551309 371607 23.747 14.774 0 0
237243 -2.196754312 1 1 3 1 P:9 3060 9690 120 7548 7637 3542 763 855 532 98 95 0 1888 1887 834 395 411 111 99 95 0 4.545 4.607 5.097 4.749 1.797 4.924 0.813 120 630 8278 8366 2.184 6785 1493 6874 1492 916478 226425 12.748 13.297 0 0
237244 -0.918841744 1 1 4 1 P:13 3250 9690 130 2781 2809 626 774 801 166 100 99 0 1148 1541 972 396 414 142 98 95 0 2.669 1.777 2.435 2.239 1.814 1.381 0.627 120 622 2759 3180 1.416 2007 752 2035 1145 337098 184925 12.096 7.937 0 0
237245 -0.700254935 1 1 5 1 P:17 3450 9680 120 3116 2987 661 807 816 137 100 100 0 1455 1540 503 406 415 77 100 99 0 2.201 1.922 2.195 1.988 1.74 1.917 0.637 120 584 3358 3314 1.138 2309 1049 2180 1134 358489 184851 15.847 14.61 0 0
237246 1.818172073 1 1 6 1 P:21 3630 9670 110 1688 1694 228 800 817 142 100 100 0 2739 2889 894 411 434 145 100 100 0 0.381 0.361 0.371 0.373 1.54 0.267 0.605 80 480 3216 3372 -1.39 888 2328 894 2478 135555 231087 6.176 16.931 0 0
237247 1 1 7 1 P:97 3820 9670 140 737 734 93 782 797 150 0 0 0 376 382 67 394 412 127 1 0 0 2.5 4 2.378 1.928 4.383 4.677 0.037 156 689 -63 -60 1.322 -45 -18 -48 -12 114466 59654 -0.42 -0.236 -50 0
237248 -2.161369916 1 1 8 1 P:101 4030 9670 120 3734 3574 1211 770 787 154 100 100 0 839 829 180 379 388 69 100 97 0 6.443 6.231 6.418 6.079 1.522 6.916 0.81 120 546 3424 3254 2.688 2964 460 2804 450 428895 99433 18.097 6.391 0 0
237249 -2.564589197 1 1 9 1 P:105 4210 9670 150 19691 20060 9416 811 906 378 100 100 0 5130 5302 3520 394 435 190 100 99 0 3.986 3.922 4.455 4.34 1.587 3.943 0.721 156 695 23616 24157 1.995 18880 4736 19249 4908 3129350 827087 50.672 25.616 0 0
237250 -1.694492056 1 1 10 1 P:109 4400 9660 120 20783 20241 8769 830 1049 568 99 99 0 8122 7699 4433 414 485 184 93 92 0 2.589 2.665 2.962 3.456 2.152 2.619 0.803 120 587 27661 26696 1.372 19953 7708 19411 7285 2428880 923830 33.789 39.207 0 0
237251 1.036142483 1 1 11 1 P:113 4610 9650 140 3480 3508 1335 806 928 446 95 90 0 5875 6305 4067 417 530 317 99 94 0 0.49 0.459 0.587 0.529 2.162 0.32 0.523 156 753 8132 8590 -1.029 2674 5458 2702 5888 547265 983528 5.785 18.218 0 0
237252 2.712872254 1 1 12 1 P:117 4810 9660 110 2412 2375 418 800 813 146 100 100 0 11544 11229 4815 417 483 249 100 100 0 0.145 0.146 0.146 0.163 1.593 0.126 0.825 80 480 12739 12387 -2.787 1612 11127 1575 10812 189980 898295 10.699 43.157 0 0
237253 -0.535166502 1 1 13 1 P:193 4980 9650 130 2444 2505 573 800 834 185 100 100 0 1263 1317 558 417 450 139 100 91 0 1.943 1.894 2.161 2.198 1.585 1.048 0.39 120 682 2490 2605 0.958 1644 846 1705 900 300578 158074 9.032 6.237 0 0
237254 -0.768529497 1 1 14 1 P:197 5190 9670 110 1671 1706 388 778 787 115 100 100 0 586 619 232 404 418 78 86 61 0 4.907 4.316 4.559 5.11 2.094 4.217 0.376 80 522 1075 1143 2.295 893 182 928 215 136461 49527 7.991 2.577 0 0
237255 -3.058430418 1 1 15 1 P:201 5390 9650 150 12801 12196 6925 770 795 183 100 100 0 1946 1981 1016 401 412 69 97 94 0 7.787 7.232 7.752 7.567 1.538 7.559 0.874 156 668 13576 13006 2.961 12031 1545 11426 1580 1902643 309047 62.301 22.739 0 0
237256 1 1 16 1 P:205 5570 9640 140 717 728 105 755 779 191 3 0 0 389 394 58 402 413 72 8 2 0 2.923 3.375 1.818 1.849 4.354 7.135 0.11 156 626 -51 -35 1.547 -38 -13 -27 -8 113523 61532 -0.267 -0.264 -50 0
237257 1.22265843 1 1 17 1 P:209 5780 9640 120 1765 1791 401 759 775 134 98 97 0 2067 2633 1887 409 432 147 99 97 0 0.607 0.464 0.573 0.571 2.136 0.272 0.503 120 558 2664 3256 -0.721 1006 1658 1032 2224 214947 315959 7.582 14.973 0 0
237258 -0.7389282 1 1 18 1 P:213 5960 9640 110 5963 6635 2759 796 846 227 100 100 0 3604 3489 1377 434 491 462 97 93 0 1.63 1.911 2.054 1.947 1.525 1.632 0.67 80 518 8337 8894 0.705 5167 3170 5839 3055 530804 279130 25.502 6.489 0 0
237259 0.722838716 1 1 19 1 P:289 6160 9640 140 3201 3305 792 791 827 206 100 100 0 4091 4626 2393 434 483 396 100 99 0 0.659 0.6 0.66 0.673 1.646 0.472 0.724 156 726 6067 6706 -0.602 2410 3657 2514 4192 515583 721666 12.029 10.462 0 0
237260 -1.052527856 1 1 20 1 P:293 6360 9640 120 6299 6111 2120 801 835 199 100 100 0 3081 3102 1198 443 463 111 100 100 0 2.084 1.997 2.147 2.082 1.582 2.041 0.825 120 548 8136 7969 1.059 5498 2638 5310 2659 733263 372186 26.513 23.775 0 0

Total number of rows: 15488

Table truncated, full table size 3529 Kbytes.




Supplementary file Size Download File type/resource
GSM251869.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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