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Sample GSM251870 Query DataSets for GSM251870
Status Public on Dec 01, 2008
Title Human Prostate GSK-10
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-10 treated with 3.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-10. Specimen ID: GSK-10; Treatment: 3.5 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-10 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 0.068976306 1 1 1 1 P:1 2900 9580 100 3293 3398 847 1514 1543 305 98 95 0 1325 1520 903 337 342 43 97 93 0 1.801 1.593 1.715 1.988 2.057 1.392 0.68 80 526 2767 3067 0.848 1779 988 1884 1183 271832 121635 6.082 27.395 0 0
237242 -3.46432119 1 1 2 1 P:5 3080 9570 90 23709 23424 15217 1701 1966 1679 100 98 0 1841 1916 1267 368 400 222 76 67 0 14.941 14.033 17.275 16.553 1.72 14.558 0.808 52 401 23481 23271 3.901 22008 1473 21723 1548 1218063 99628 12.78 6.829 0 0
237243 -2.825935318 1 1 3 1 P:9 3260 9570 90 7637 8873 5211 1800 2069 1388 88 71 0 909 1114 706 385 436 266 61 50 0 11.139 9.702 11.458 12.384 2.251 9.621 0.757 52 414 6361 7802 3.478 5837 524 7073 729 461411 57951 4.902 2.549 0 0
237244 -0.253175436 1 1 4 1 P:13 3480 9570 80 2592 2613 530 1835 1865 271 78 61 0 567 581 151 392 395 48 80 61 0 4.326 4.116 3.937 4.175 2.08 2.743 0.153 52 316 932 967 2.113 757 175 778 189 135864 30205 2.76 3.875 0 0
237245 1 1 5 1 P:17 3660 9570 140 2296 2447 487 1805 1800 269 77 45 0 505 528 130 384 386 50 72 57 0 4.058 4.458 4.166 4.551 2.111 5.883 0.532 156 800 612 786 2.021 491 121 642 144 381675 82408 2.405 2.84 -50 0
237246 3.678134458 1 1 6 1 P:21 3860 9570 100 2713 2739 285 1868 1873 241 98 95 0 13029 14045 9335 390 393 45 100 100 0 0.067 0.064 0.064 0.085 2.529 0.031 0.349 80 453 13484 14526 -3.903 845 12639 871 13655 219116 1123595 3.593 303.378 0 0
237247 1 1 7 1 P:97 4050 9560 140 1715 1714 206 1748 1762 235 11 0 0 366 371 36 373 375 44 11 0 0 4.714 17 4.935 5.045 3.382 20.882 0.059 156 793 -40 -36 2.237 -33 -7 -34 -2 267425 57806 -0.204 -0.091 -50 0
237248 0.199363909 1 1 8 1 P:101 4260 9570 100 2463 2511 394 1698 1715 227 95 80 0 677 768 338 364 366 39 97 86 0 2.444 2.012 2.524 2.625 2.479 2.188 0.456 80 482 1078 1217 1.289 765 313 813 404 200906 61466 3.507 10.308 0 0
237249 -2.862804459 1 1 9 1 P:105 4430 9560 90 41456 41162 21461 1719 2003 1565 100 100 25 3526 3760 2426 371 414 281 96 84 0 12.595 11.639 12.369 14.086 2.056 11.328 0.796 52 398 42892 42832 3.655 39737 3155 39443 3389 2140439 195518 25.022 11.907 0 0
237250 -1.339113832 1 1 10 1 P:109 4630 9570 100 33941 33536 18176 1624 1813 1206 100 100 1 6407 8369 5797 365 390 221 100 100 0 5.349 3.987 4.143 4.466 1.608 3.816 0.865 80 518 38359 39916 2.419 32317 6042 31912 8004 2682850 669547 26.304 36.104 0 0
237251 0.586907097 1 1 11 1 P:113 4830 9570 100 4004 3986 1271 1568 1609 303 100 90 0 3511 3973 3039 360 361 40 100 100 0 0.773 0.669 0.797 0.844 1.807 0.523 0.711 80 519 5587 6031 -0.371 2436 3151 2418 3613 318886 317860 7.845 90.3 0 0
237252 1.825982341 1 1 12 1 P:117 5020 9560 90 2903 3078 611 1599 1616 328 100 92 0 3362 4298 3355 362 389 314 100 98 0 0.435 0.376 0.475 0.494 1.828 0.27 0.62 52 414 4304 5415 -1.202 1304 3000 1479 3936 160062 223500 4.457 12.449 0 0
237253 -0.916080393 1 1 13 1 P:193 5220 9570 100 2570 2567 634 1532 1556 201 88 81 0 531 533 137 358 376 231 30 3 0 6 5.914 5.364 5.667 2.27 6.942 0.534 80 474 1211 1210 2.585 1038 173 1035 175 205388 42613 5.03 0.68 0 0
237254 1 1 14 1 P:197 5410 9550 140 1708 1762 414 1508 1521 189 50 30 0 359 363 62 355 358 39 25 12 0 50 31.75 7.16 5.877 3.879 21.04 0.078 156 767 204 262 5.644 200 4 254 8 274946 56666 1.275 0.128 -50 0
237255 0.698932047 1 1 15 1 P:201 5610 9560 100 3771 4015 1117 1502 1513 187 100 100 0 4381 4117 2056 356 358 39 100 100 0 0.564 0.668 0.785 0.741 1.904 0.565 0.64 80 462 6294 6274 -0.827 2269 4025 2513 3761 321167 329355 13.38 96.385 0 0
237256 1 1 16 1 P:205 5800 9550 140 1464 1482 166 1511 1529 206 5 1 0 348 349 32 357 361 48 7 0 0 5.222 3.625 5.259 4.92 3.421 28.486 0.021 156 758 -56 -37 2.385 -47 -9 -29 -8 231118 54478 -0.228 -0.25 -50 0
237257 1 1 17 1 P:209 6000 9550 140 1789 1810 274 1579 1605 356 32 4 0 403 431 99 367 380 182 8 2 0 5.833 3.609 3.453 3.885 3.236 3.892 0.144 156 772 246 295 2.544 210 36 231 64 282436 67159 0.576 0.28 -50 0
237258 -0.949274872 1 1 18 1 P:213 6200 9560 100 4516 4966 1926 1670 1701 415 100 97 0 1140 1336 756 380 392 227 77 67 0 3.745 3.448 3.843 4.163 1.741 3.335 0.716 80 480 3606 4252 1.905 2846 760 3296 956 397315 106844 7.867 4.159 0 0
237259 0.172326467 1 1 19 1 P:289 6390 9550 110 4401 4280 905 1683 1682 216 100 100 0 3794 4036 1952 383 392 126 100 100 0 0.797 0.711 0.759 0.785 1.771 0.641 0.735 80 580 6129 6250 -0.328 2718 3411 2597 3653 342413 322897 12.028 28.921 0 0
237260 -0.180016502 1 1 20 1 P:293 6590 9550 100 4683 10449 14969 1588 1590 233 95 92 1 3102 4824 5262 365 368 44 100 98 0 1.131 1.987 1.337 1.322 2.289 2.805 0.796 80 510 5832 13320 0.177 3095 2737 8861 4459 835953 385882 38.021 101.273 0 0

Total number of rows: 15488

Table truncated, full table size 3533 Kbytes.




Supplementary file Size Download File type/resource
GSM251870.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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