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Sample GSM251867 Query DataSets for GSM251867
Status Public on Dec 01, 2008
Title Human Prostate GSK-60
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-60 treated with 0.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-60. Specimen ID: GSK-60; 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-60 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 0.610536604 1 1 1 1 P:1 2780 9160 90 25087 22762 10795 308 678 2962 94 90 0 28959 26993 14561 227 372 557 98 98 0 0.862 0.839 0.79 0.896 1.791 0.805 0.906 52 399 53511 49220 -0.214 24779 28732 22454 26766 1183619 1403652 7.456 47.794 0 0
237242 -3.935749314 1 1 2 1 P:5 2940 9220 110 17970 19446 8170 381 618 2547 100 100 0 1667 1762 576 269 345 410 100 88 0 12.582 12.77 12.458 12.596 1.354 13.644 0.827 80 524 18987 20558 3.653 17589 1398 19065 1493 1555672 140949 7.392 3.456 0 0
237243 -3.431858128 1 1 3 1 P:9 3130 9210 100 5144 5954 4045 395 436 384 100 100 0 541 580 162 283 311 163 82 33 0 18.407 18.717 18.257 17.756 1.468 24.469 0.592 80 512 5007 5856 4.202 4749 258 5559 297 476342 46390 14.37 1.65 0 0
237244 -0.966665556 1 1 4 1 P:13 3330 9200 110 1356 1828 1106 377 408 477 92 51 0 556 605 193 284 315 219 67 23 0 3.599 4.52 3.866 4.262 1.658 5.766 0.589 80 590 1251 1772 1.848 979 272 1451 321 146252 48368 2.977 1.324 0 0
237245 -1.293563198 1 1 5 1 P:17 3530 9210 110 1018 1083 572 359 366 92 86 78 0 435 461 197 275 297 97 67 43 0 4.119 3.892 4.2 3.955 2.28 4.528 0.398 80 558 819 910 2.042 659 160 724 186 86619 36849 7.793 1.691 0 0
237246 4.319620824 1 1 6 1 P:21 3710 9200 90 750 786 375 412 417 95 90 82 0 5787 6324 2612 311 394 604 100 100 0 0.062 0.062 0.051 0.055 1.979 0.056 0.403 52 394 5814 6387 -4.018 338 5476 374 6013 40858 328858 3.884 9.818 0 0
237247 -3.697019498 1 1 7 1 P:97 3910 9200 90 21132 21553 5873 417 446 292 100 100 0 2125 2064 365 294 315 105 100 100 0 11.313 11.941 11.792 11.757 1.234 13.91 0.881 52 406 22546 22906 3.5 20715 1831 21136 1770 1120779 107312 72.284 16.657 0 0
237248 -1.49059829 1 1 8 1 P:101 4100 9200 90 2466 2518 470 426 454 256 100 100 0 691 720 156 300 316 95 96 94 0 5.217 4.981 4.987 5.376 1.737 5.848 0.658 52 407 2431 2512 2.383 2040 391 2092 420 130937 37419 8.063 4.253 0 0
237249 -2.918073705 1 1 9 1 P:105 4310 9190 110 15845 17167 6969 437 470 335 100 100 0 2514 2720 1006 307 325 103 100 100 0 6.981 6.933 6.978 6.842 1.438 7.743 0.84 80 574 17615 19143 2.804 15408 2207 16730 2413 1373398 217577 49.842 23.252 0 0
237250 -2.329199176 1 1 10 1 P:109 4490 9190 100 18085 17775 7264 437 462 179 100 100 0 3838 3664 1660 295 316 93 100 100 0 4.981 5.146 5.118 5.471 1.606 5.155 0.817 80 493 21191 20707 2.316 17648 3543 17338 3369 1422009 293124 96.721 36 0 0
237251 -1.156554112 1 1 11 1 P:113 4690 9180 110 1328 1375 257 419 434 175 100 100 0 531 526 138 301 317 97 80 57 0 3.952 4.249 4.312 4.867 1.959 5.349 0.395 80 590 1139 1181 1.983 909 230 956 225 110008 42057 5.377 2.155 0 0
237252 1.876418953 1 1 12 1 P:117 4880 9180 90 843 958 408 399 423 161 94 76 0 1289 1825 1416 298 331 183 100 100 0 0.448 0.366 0.368 0.385 1.765 0.263 0.685 52 402 1435 2086 -1.158 444 991 559 1527 49835 94914 3.323 8.164 0 0
237253 -0.155578832 1 1 13 1 P:193 5070 9180 110 956 977 265 384 396 132 100 90 0 576 576 133 274 302 154 87 47 0 1.894 1.964 1.836 1.982 1.681 2.269 0.534 80 590 874 895 0.921 572 302 593 302 78127 46078 4.402 1.779 0 0
237254 0.169664139 1 1 14 1 P:197 5270 9180 100 620 639 161 387 395 107 83 56 0 443 473 134 282 301 95 75 40 0 1.447 1.319 1.423 1.373 2.378 1.635 0.288 80 502 394 443 0.533 233 161 252 191 51120 37827 2.28 1.811 0 0
237255 -2.279282007 1 1 15 1 P:201 5460 9180 100 3590 4445 2614 402 411 82 100 100 0 644 657 177 295 313 90 96 86 0 9.135 11.169 10.222 10.931 1.766 16.7 0.582 80 510 3537 4405 3.191 3188 349 4043 362 355565 52536 49.195 3.822 0 0
237256 -1.350500715 1 1 16 1 P:205 5660 9180 90 2725 2806 645 397 397 107 100 100 0 776 815 184 276 291 95 100 100 0 4.656 4.469 4.536 4.577 1.316 4.964 0.793 52 420 2828 2948 2.219 2328 500 2409 539 145932 42369 22.514 5.516 0 0
237257 -0.648050831 1 1 17 1 P:209 5860 9170 90 996 1109 669 378 379 91 100 100 0 496 509 154 264 282 87 92 63 0 2.664 2.984 2.682 2.906 2.092 4.694 0.342 52 414 850 976 1.413 618 232 731 245 57662 26460 8.022 2.609 0 0
237258 -1.469271723 1 1 18 1 P:213 6050 9180 100 2916 3152 997 379 383 78 100 100 0 966 1016 350 271 289 83 97 96 0 3.65 3.722 3.76 3.993 1.678 3.912 0.755 80 491 3232 3518 1.868 2537 695 2773 745 252133 81254 35.5 8.759 0 0
237259 0.947192524 1 1 19 1 P:289 6250 9170 120 1436 1655 769 376 380 79 100 99 0 1367 1941 1364 275 299 127 97 95 0 0.971 0.768 0.855 0.869 1.67 0.648 0.788 120 658 2152 2945 -0.043 1060 1092 1279 1666 198624 232872 16.139 12.929 0 0
237260 0.083769027 1 1 20 1 P:293 6440 9170 100 3108 3605 1677 383 388 81 100 100 0 2424 2384 901 281 305 141 100 100 0 1.272 1.532 1.497 1.485 1.351 1.624 0.821 80 480 4868 5325 0.347 2725 2143 3222 2103 288415 190695 39.716 14.745 0 0

Total number of rows: 15488

Table truncated, full table size 3482 Kbytes.




Supplementary file Size Download File type/resource
GSM251867.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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