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Sample GSM251852 Query DataSets for GSM251852
Status Public on Dec 01, 2008
Title Human Prostate GSK-37
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-37 treated with 0.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-37. Specimen ID: GSK-37; 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-37 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 -1.048115133 1 1 1 1 P:1 2510 9810 120 2520 2751 945 985 1175 1707 42 5 0 976 1090 575 178 288 1636 11 0 0 1.924 1.936 2.118 2.134 2.082 0.273 0.077 120 664 2333 2678 0.944 1535 798 1766 912 330113 130768 0.923 0.49 0 0
237242 -3.211982686 1 1 2 1 P:5 2700 9780 110 19585 20598 9211 1011 1120 1156 100 100 0 2710 2656 1027 180 201 131 100 100 0 7.342 7.911 7.439 7.905 1.601 8.414 0.693 80 545 21104 22063 2.876 18574 2530 19587 2476 1647826 212463 16.849 18.74 0 0
237243 -2.340463743 1 1 3 1 P:9 2890 9780 100 6824 7134 3028 979 1089 1276 97 87 0 1528 1584 645 182 216 333 95 83 0 4.342 4.39 4.3 4.333 1.623 5.783 0.548 80 492 7191 7557 2.119 5845 1346 6155 1402 570756 126681 4.737 4.108 0 0
237244 -0.16564572 1 1 4 1 P:13 3090 9780 120 1701 1846 655 962 1007 365 77 50 0 747 834 491 175 211 338 76 32 0 1.292 1.341 1.277 1.298 2.085 1.382 0.497 120 669 1311 1543 0.37 739 572 884 659 221552 100078 2.299 1.843 0 0
237245 0.126771631 1 1 5 1 P:17 3290 9780 110 1540 1615 546 910 939 207 86 71 0 751 894 1432 168 189 123 93 82 0 1.081 0.971 1.221 1.122 2.147 0.448 0.328 80 527 1213 1431 0.112 630 583 705 726 129234 71488 3.266 5.732 0 0
237246 3.907368433 1 1 6 1 P:21 3470 9770 110 1774 1757 404 917 982 632 66 16 0 14791 17923 11681 174 288 1032 100 100 0 0.059 0.047 0.049 0.052 1.923 0.035 0.156 80 554 15474 18589 -4.092 857 14617 840 17749 140584 1433843 1.226 17.088 0 0
237247 -1.607796458 1 1 7 1 P:97 3670 9770 100 19234 19913 9357 889 951 652 100 100 0 6152 6675 3263 176 228 540 100 100 0 3.07 2.927 2.984 2.953 1.544 2.762 0.497 80 500 24321 25523 1.618 18345 5976 19024 6499 1593010 533962 29.083 11.939 0 0
237248 0.751879116 1 1 8 1 P:101 3860 9770 100 1633 1719 477 852 867 192 100 90 0 1548 1727 713 166 181 90 100 100 0 0.565 0.555 0.575 0.534 1.65 0.507 0.648 80 519 2163 2428 -0.823 781 1382 867 1561 137552 138144 4.438 17.178 0 0
237249 -2.288714795 1 1 9 1 P:105 4060 9760 110 19921 25197 15230 783 898 1442 100 100 1 4823 5618 3387 169 222 435 100 100 0 4.112 4.48 4.415 4.492 1.63 5.355 0.711 80 554 23792 29863 2.04 19138 4654 24414 5449 2015745 449407 16.851 12.405 0 0
237250 -1.162460236 1 1 10 1 P:109 4240 9760 110 25696 27400 13783 790 1127 2355 100 100 0 7844 9990 6526 173 450 1595 91 85 0 3.247 2.711 2.666 3.097 2.335 2.68 0.737 80 582 32577 36427 1.699 24906 7671 26610 9817 2192020 799207 11.156 5.981 0 0
237251 0.107240196 1 1 11 1 P:113 4450 9770 120 3001 3211 1628 730 936 1790 63 20 0 2943 3578 2421 168 360 1283 85 58 0 0.818 0.728 0.775 0.728 2.141 0.661 0.668 120 656 5046 5891 -0.289 2271 2775 2481 3410 385272 429414 1.271 2.508 0 0
237252 0.546955289 1 1 12 1 P:117 4650 9760 110 2010 1904 638 672 693 245 96 81 0 2262 2748 1795 156 180 242 100 98 0 0.635 0.475 0.517 0.523 1.849 0.376 0.603 80 535 3444 3824 -0.654 1338 2106 1232 2592 152302 219845 4.943 10.612 0 0
237253 -1.912520865 1 1 13 1 P:193 4840 9770 120 1775 1732 487 637 673 508 84 60 0 397 392 138 151 178 218 54 7 0 4.626 4.544 5.095 4.835 2.155 5.331 0.226 120 653 1384 1336 2.21 1138 246 1095 241 207859 47014 2.085 0.982 0 0
237254 -0.097677145 1 1 14 1 P:197 5020 9790 90 782 804 136 623 639 123 65 34 0 226 233 68 154 164 60 59 19 0 2.208 2.291 2.355 2.561 3.387 4.476 0.248 52 365 231 260 1.143 159 72 181 79 41810 12137 1.341 1.15 0 0
237255 0.847958675 1 1 15 1 P:201 5230 9760 110 3222 4225 2808 625 644 195 100 100 0 6578 11351 9311 154 195 441 100 100 0 0.404 0.322 0.313 0.324 1.537 0.264 0.736 80 584 9021 14797 -1.307 2597 6424 3600 11197 338025 908064 18.364 25.297 0 0
237256 0.532522239 1 1 16 1 P:205 5410 9760 90 3084 3121 868 605 725 626 100 92 0 4075 4431 2157 152 403 1350 92 80 0 0.632 0.588 0.569 0.702 2.882 0.471 0.634 52 401 6402 6795 -0.662 2479 3923 2516 4279 162287 230427 3.827 2.984 0 0
237257 0.28690669 1 1 17 1 P:209 5630 9760 100 992 986 172 586 666 859 0 0 0 468 509 198 150 237 574 11 0 0 1.277 1.114 1.144 1.148 1.953 0.382 0.263 80 506 724 759 0.352 406 318 400 359 78859 40753 0.373 0.474 0 0
237258 -1.73508641 1 1 18 1 P:213 5810 9760 110 4505 4292 1452 613 646 402 100 100 0 1353 1443 729 153 192 273 98 86 0 3.243 2.852 3.178 3.019 1.505 3.062 0.527 80 556 5092 4969 1.697 3892 1200 3679 1290 343341 115449 9.07 4.582 0 0
237259 0.930596561 1 1 19 1 P:289 6020 9760 120 3068 3686 2014 625 635 115 99 99 0 5552 7439 5795 154 169 129 99 99 0 0.453 0.42 0.508 0.462 1.897 0.349 0.758 120 623 7841 10346 -1.144 2443 5398 3061 7285 442291 892678 26.53 56.357 0 0
237260 -1.01183465 1 1 20 1 P:293 6200 9750 110 5802 5934 2461 646 679 377 100 100 0 3696 3781 2043 151 200 365 100 98 0 1.454 1.457 1.564 1.552 1.495 1.506 0.795 80 537 8701 8918 0.54 5156 3545 5288 3630 474688 302503 13.939 9.811 0 0

Total number of rows: 15488

Table truncated, full table size 3518 Kbytes.




Supplementary file Size Download File type/resource
GSM251852.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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