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Sample GSM251833 Query DataSets for GSM251833
Status Public on Dec 01, 2008
Title Human Prostate GSK-8
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-8 treated with 0.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-8. Specimen ID: GSK-8; 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-8 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 -0.154699123 1 1 1 1 P:1 2250 9390 110 2723 2711 426 1064 1187 683 100 76 0 1544 1578 498 380 390 111 96 95 0 1.425 1.375 1.419 1.546 2.094 1.565 0.465 80 557 2823 2845 0.511 1659 1164 1647 1198 216916 126209 2.231 10.703 0 0
237242 -3.478676956 1 1 2 1 P:5 2440 9390 120 28521 26432 12150 1037 1263 1646 98 92 0 2011 1994 1101 369 386 127 97 89 0 16.738 15.628 16.825 17.461 1.525 15.156 0.768 120 621 29126 27020 4.065 27484 1642 25395 1625 3171864 239246 15.291 12.661 0 0
237243 -3.912895236 1 1 3 1 P:9 2630 9400 100 13731 13704 3689 1039 1091 305 100 100 0 1175 1217 344 371 375 51 100 100 0 15.786 14.97 15.346 15.487 1.358 16.127 0.806 80 480 13496 13511 3.981 12692 804 12665 846 1096352 97399 41.354 16.51 0 0
237244 -0.751763449 1 1 4 1 P:13 2820 9400 110 1870 1999 761 955 974 182 98 93 0 677 761 315 370 374 53 98 97 0 2.98 2.67 2.518 2.849 1.829 2.806 0.688 80 570 1222 1435 1.576 915 307 1044 391 159901 60888 5.632 7.302 0 0
237245 -0.653727713 1 1 5 1 P:17 3020 9390 110 1903 1948 599 875 892 167 96 93 0 726 737 174 367 369 53 100 97 0 2.864 2.9 2.768 2.729 1.652 3.246 0.636 80 539 1387 1443 1.518 1028 359 1073 370 155868 58947 6.323 6.943 0 0
237246 4.038791105 1 1 6 1 P:21 3210 9380 110 1681 1659 335 855 897 458 82 37 0 14667 14055 4853 355 371 227 100 100 0 0.058 0.059 0.057 0.059 1.675 0.055 0.682 80 553 15138 14504 -4.115 826 14312 804 13700 132755 1124379 1.664 60.282 0 0
237247 -2.018148106 1 1 7 1 P:97 3410 9390 100 42427 42749 14310 856 926 544 100 100 10 4980 5292 2086 358 387 296 100 100 0 8.994 8.491 8.858 8.667 1.526 9.146 0.795 80 505 46193 46827 3.169 41571 4622 41893 4934 3419924 423373 76.881 16.571 0 0
237248 -0.31511162 1 1 8 1 P:101 3600 9390 100 2222 2748 1329 846 1089 1273 58 32 0 1189 1335 519 352 375 161 95 95 0 1.644 1.935 1.616 1.691 2.308 2.207 0.684 80 470 2213 2885 0.717 1376 837 1902 983 219829 106836 1.303 5.963 0 0
237249 -2.960485698 1 1 9 1 P:105 3800 9370 120 36071 35294 13249 825 1115 1704 100 100 0 3204 3201 1230 348 386 322 100 99 0 12.341 12.082 12.509 12.227 1.75 13.476 0.748 120 641 38102 37322 3.625 35246 2856 34469 2853 4235286 384080 20.058 8.742 0 0
237250 -0.699272257 1 1 10 1 P:109 4000 9370 120 43784 39980 16630 810 986 1450 100 99 5 9620 9278 3931 351 368 156 100 100 0 4.636 4.388 4.794 4.38 1.808 4.842 0.778 120 584 52243 48097 2.213 42974 9269 39170 8927 4797608 1113375 26.892 57.115 0 0
237251 -0.263090989 1 1 11 1 P:113 4190 9370 120 4375 4414 1274 784 929 968 95 91 0 2176 2235 820 350 472 1112 86 23 0 1.967 1.926 2 2.052 1.735 1.927 0.806 120 611 5417 5515 0.976 3591 1826 3630 1885 529722 268200 3.6 1.585 0 0
237252 1.389538398 1 1 12 1 P:117 4380 9360 110 1818 1875 645 769 791 166 97 87 0 2383 3045 2026 343 357 177 100 100 0 0.514 0.409 0.429 0.431 1.627 0.337 0.708 80 563 3089 3808 -0.96 1049 2040 1106 2702 149965 243566 6.53 15.186 0 0
237253 -2.083013049 1 1 13 1 P:193 4580 9360 110 2249 3406 3647 745 760 175 100 100 0 531 910 1213 339 350 150 65 25 0 7.833 4.66 7.486 7.837 2.285 4.274 0.566 80 580 1696 3232 2.97 1504 192 2661 571 272500 72779 15.12 3.733 0 0
237254 -2.015547201 1 1 14 1 P:197 4780 9360 100 1129 1153 279 701 714 146 88 71 0 399 398 65 334 339 44 61 35 0 6.585 7.063 5.431 6.308 2.518 10.027 0.208 80 466 493 516 2.719 428 65 452 64 92223 31856 3.007 1.341 0 0
237255 1.192635809 1 1 15 1 P:201 4950 9350 110 3016 3112 948 703 765 417 100 100 0 4407 4848 1882 336 511 1051 100 96 0 0.568 0.534 0.542 0.536 1.416 0.46 0.769 80 555 6384 6921 -0.816 2313 4071 2409 4512 248960 387848 5.628 4.127 0 0
237256 0.028734204 1 1 16 1 P:205 5160 9370 100 4051 5412 3248 673 714 290 100 100 0 3794 5103 3639 336 452 781 92 88 0 0.977 0.994 0.947 1.096 2.293 0.824 0.679 80 520 6836 9506 -0.034 3378 3458 4739 4767 432955 408252 16.2 5.955 0 0
237257 1.727342695 1 1 17 1 P:209 5360 9360 110 1188 1188 287 656 684 228 86 56 0 1430 1582 706 331 357 349 98 76 0 0.484 0.425 0.424 0.411 1.735 0.303 0.551 80 558 1631 1783 -1.047 532 1099 532 1251 95077 126595 2.211 3.51 0 0
237258 -1.751465067 1 1 18 1 P:213 5550 9340 110 6990 7008 1383 637 679 252 100 100 0 1796 1850 665 325 340 180 96 93 0 4.319 4.178 4.3 4.745 2.008 4.016 0.745 80 552 7824 7896 2.111 6353 1471 6371 1525 560646 147965 25.115 8.389 0 0
237259 0.714385768 1 1 19 1 P:289 5750 9340 130 4617 5238 1995 639 658 167 100 100 0 5352 6005 3500 323 338 220 98 97 0 0.791 0.809 0.807 0.949 2.02 0.719 0.796 120 690 9007 10281 -0.338 3978 5029 4599 5682 628598 720622 27.425 25.759 0 0
237260 -0.826127036 1 1 20 1 P:293 5940 9340 120 8824 9615 4805 632 645 159 100 100 0 3383 3419 2015 317 319 41 97 95 0 2.672 2.896 3.126 3.313 2.06 3.051 0.703 120 578 11258 12085 1.418 8192 3066 8983 3102 1153795 410324 56.415 75.61 0 0

Total number of rows: 15488

Table truncated, full table size 3542 Kbytes.




Supplementary file Size Download File type/resource
GSM251833.gpr.gz 1.4 Mb (ftp)(http) GPR
Processed data included within Sample table
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