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Sample GSM251835 Query DataSets for GSM251835
Status Public on Dec 01, 2008
Title Human Prostate GSK-18
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-18 treated with 0.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-18. Specimen ID: GSK-18; 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-18 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 -0.651808154 1 1 1 1 P:1 2360 9320 100 2752 2669 790 652 696 250 100 95 0 1271 1251 383 405 406 54 100 97 0 2.425 2.384 2.308 2.507 1.527 2.448 0.775 80 515 2966 2863 1.278 2100 866 2017 846 213533 100114 7.892 15.648 0 0
237242 -3.74398974 1 1 2 1 P:5 2560 9310 100 20663 19830 6310 719 773 277 100 100 0 1832 1811 658 419 420 55 100 100 0 14.115 13.729 14.299 14.805 1.477 14.243 0.825 80 491 21357 20503 3.819 19944 1413 19111 1392 1586383 144885 68.798 25.291 0 0
237243 -3.241754276 1 1 3 1 P:9 2730 9310 110 8484 7713 3160 671 716 443 100 100 0 1012 954 287 415 418 70 93 88 0 13.087 13.065 13.279 13.728 1.585 14.984 0.788 80 563 8410 7581 3.71 7813 597 7042 539 617031 76325 15.795 7.657 0 0
237244 -1.565981167 1 1 4 1 P:13 2940 9310 110 1498 1652 1386 654 666 145 95 83 0 558 581 144 410 413 56 77 66 0 5.703 5.836 4.93 5.731 1.936 10.817 0.34 80 588 992 1169 2.512 844 148 998 171 132152 46486 6.8 3 0 0
237245 -1.462288536 1 1 5 1 P:17 3140 9310 100 1403 1357 363 643 654 144 93 83 0 557 578 132 417 453 185 37 6 0 5.429 4.435 3.842 4.343 2.337 4.275 0.279 80 492 900 875 2.441 760 140 714 161 108568 46202 4.882 0.676 0 0
237246 4.956024768 1 1 6 1 P:21 3330 9310 100 1342 1305 293 647 664 153 95 86 0 18015 18102 9257 420 457 185 100 100 0 0.039 0.037 0.036 0.039 1.699 0.031 0.682 80 494 18290 18340 -4.662 695 17595 658 17682 104393 1448172 4.19 95.378 0 0
237247 -1.978691075 1 1 7 1 P:97 3510 9300 90 32633 30252 13704 653 935 2377 100 100 0 4624 4354 2237 411 479 506 96 86 0 7.591 7.507 8.031 8.075 1.568 7.904 0.87 52 394 36193 33542 2.924 31980 4213 29599 3943 1573101 226398 12.334 7.658 0 0
237248 -0.256542939 1 1 8 1 P:101 3720 9300 100 1588 1815 675 640 824 694 70 37 0 995 1144 503 404 427 202 98 70 0 1.604 1.588 1.554 1.622 1.752 2.512 0.385 80 494 1539 1915 0.682 948 591 1175 740 145197 91482 1.428 3.55 0 0
237249 -2.839393264 1 1 9 1 P:105 3890 9300 110 45519 41012 19282 537 1065 3191 100 100 15 3470 3430 1915 335 387 386 96 85 0 14.348 13.078 13.58 14.863 1.685 13.237 0.849 80 554 48117 43570 3.843 44982 3135 40475 3095 3280952 274388 12.519 7.883 0 0
237250 -0.410521629 1 1 10 1 P:109 4110 9290 120 29592 26539 13262 520 892 2906 94 91 0 9622 9833 5761 345 399 352 97 96 0 3.134 2.742 2.94 2.886 1.751 2.793 0.83 120 653 38349 35507 1.648 29072 9277 26019 9488 3184721 1180011 8.826 26.801 0 0
237251 -0.059009184 1 1 11 1 P:113 4280 9290 110 1770 1857 416 565 795 837 85 17 0 1232 1280 425 379 550 791 56 6 0 1.413 1.434 1.512 1.523 1.584 1.141 0.599 80 517 2058 2193 0.498 1205 853 1292 901 148558 102437 1.269 0.923 0 0
237252 0.587799222 1 1 12 1 P:117 4490 9300 110 1449 1653 766 560 786 898 48 10 0 1360 1687 1093 371 546 833 61 22 0 0.899 0.831 0.847 0.876 2.038 0.858 0.565 80 537 1878 2409 -0.154 889 989 1093 1316 132248 134970 0.965 1.37 0 0
237253 -2.096882237 1 1 13 1 P:193 4680 9290 120 1671 1666 597 563 580 146 95 91 0 513 538 174 377 383 114 55 25 0 8.147 6.851 7.762 7.118 2.849 7.037 0.411 120 647 1244 1264 3.026 1108 136 1103 161 199964 64590 7.438 1.36 0 0
237254 -2.770156266 1 1 14 1 P:197 4890 9290 100 865 892 217 573 590 154 76 48 0 398 403 81 384 386 57 26 13 0 20.857 16.789 5.539 5.232 3.295 11.442 0.081 80 488 306 338 4.382 292 14 319 19 71398 32202 1.961 0.298 0 0
237255 -0.070470226 1 1 15 1 P:201 5080 9290 120 2943 3280 1703 557 580 146 99 99 0 1981 2187 1202 391 392 57 99 98 0 1.501 1.516 1.553 1.61 1.628 1.507 0.82 120 626 3976 4519 0.586 2386 1590 2723 1796 393567 262385 18.493 31.491 0 0
237256 0.785687722 1 1 16 1 P:205 5270 9290 100 3744 4360 2217 565 591 178 100 100 0 5422 5498 2528 394 407 177 100 100 0 0.632 0.744 0.686 0.709 1.548 0.715 0.784 80 468 8207 8899 -0.661 3179 5028 3795 5104 348808 439871 21.174 28.763 0 0
237257 0.82344946 1 1 17 1 P:209 5470 9290 120 848 856 186 578 593 134 75 50 0 628 608 164 389 399 97 70 58 0 1.13 1.269 1.249 1.362 2.344 1.654 0.371 120 628 509 497 0.176 270 239 278 219 102661 72941 1.963 2.155 0 0
237258 -1.666640708 1 1 18 1 P:213 5650 9270 110 6185 6066 2276 578 625 405 100 100 0 1657 1596 688 387 405 137 96 87 0 4.415 4.539 4.482 5.252 1.768 4.354 0.872 80 548 6877 6697 2.142 5607 1270 5488 1209 485279 127648 13.435 8.693 0 0
237259 0.482094994 1 1 19 1 P:289 5860 9270 110 4285 4120 1601 562 591 161 100 100 0 5518 5436 3010 387 401 133 100 100 0 0.726 0.705 0.739 0.806 1.612 0.65 0.865 80 588 8854 8607 -0.463 3723 5131 3558 5049 329592 434863 21.919 37.857 0 0
237260 -0.528855688 1 1 20 1 P:293 6050 9260 110 5590 5587 2129 561 602 238 100 100 0 3593 3527 1757 378 409 197 100 98 0 1.564 1.596 1.67 1.761 1.691 1.733 0.752 80 579 8244 8175 0.645 5029 3215 5026 3149 446956 282196 20.945 15.827 0 0

Total number of rows: 15488

Table truncated, full table size 3525 Kbytes.




Supplementary file Size Download File type/resource
GSM251835.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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