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Sample GSM251853 Query DataSets for GSM251853
Status Public on Dec 01, 2008
Title Human Prostate GSK-39
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-39 treated with 0.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-39. Specimen ID: GSK-39; 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-39 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 0.102515434 1 1 1 1 P:1 2540 9600 100 1442 1473 631 434 440 111 100 91 0 1186 1224 670 122 129 40 100 100 0 0.947 0.943 0.955 0.944 2.263 0.932 0.573 80 477 2072 2141 -0.078 1008 1064 1039 1102 117847 97940 9.306 27.375 0 0
237242 -2.930457742 1 1 2 1 P:5 2710 9590 110 18290 18183 9841 438 445 94 100 100 0 2231 2062 1246 121 130 51 95 95 0 8.461 9.142 9.571 9.254 2.033 9.935 0.665 80 535 19962 19686 3.081 17852 2110 17745 1941 1454628 164931 188.702 37.882 0 0
237243 -3.024851159 1 1 3 1 P:9 2900 9570 100 5636 5622 3040 414 429 120 100 100 0 820 825 491 119 127 40 93 91 0 7.449 7.377 8.055 8.209 2.406 8.291 0.607 80 503 5923 5914 2.897 5222 701 5208 706 449730 65963 43.275 17.45 0 0
237244 -0.658931951 1 1 4 1 P:13 3090 9570 110 1045 985 349 406 410 63 86 83 0 537 486 183 121 127 37 98 92 0 1.536 1.586 1.772 1.471 2.154 1.627 0.663 80 597 1055 944 0.619 639 416 579 365 78812 38900 9.127 9.703 0 0
237245 -0.669766659 1 1 5 1 P:17 3290 9590 110 1186 1084 398 422 423 65 92 85 0 580 537 231 119 127 38 97 92 0 1.657 1.584 1.573 1.509 2.21 1.859 0.592 80 535 1225 1080 0.729 764 461 662 418 86733 42920 10.169 10.789 0 0
237246 3.116122013 1 1 6 1 P:21 3470 9570 110 1111 1048 341 428 435 71 90 87 0 6558 6618 4378 120 134 123 100 100 0 0.106 0.095 0.099 0.105 2.108 0.074 0.724 80 555 7121 7118 -3.237 683 6438 620 6498 83812 529458 8.634 52.715 0 0
237247 -1.626732705 1 1 7 1 P:97 3670 9570 100 14799 15850 9690 440 448 73 100 100 0 4148 4469 3170 122 132 50 100 100 0 3.567 3.545 4.178 4.097 2.231 3.704 0.692 80 502 18385 19757 1.835 14359 4026 15410 4347 1268012 357522 210.986 86.74 0 0
237248 -1.20457422 1 1 8 1 P:101 3860 9560 110 1572 1726 825 459 465 97 98 97 0 574 606 307 124 132 56 95 92 0 2.473 2.629 2.502 2.504 2.014 2.661 0.647 80 570 1563 1749 1.306 1113 450 1267 482 138058 48518 13 8.464 0 0
237249 -2.147078709 1 1 9 1 P:105 4050 9570 100 20392 20527 12331 480 497 134 100 100 0 3520 3381 2212 125 142 138 98 96 0 5.865 6.157 6.574 6.783 2.463 6.632 0.695 80 503 23307 23303 2.552 19912 3395 20047 3256 1642181 270495 149.478 23.471 0 0
237250 -1.242637649 1 1 10 1 P:109 4250 9560 110 17926 17320 8880 490 521 257 100 100 0 4970 5064 3204 128 169 370 100 96 0 3.601 3.41 3.635 3.732 1.794 3.399 0.764 80 566 22278 21766 1.848 17436 4842 16830 4936 1385601 405143 65.366 13.23 0 0
237251 -0.209328704 1 1 11 1 P:113 4450 9570 120 2480 2630 1346 498 517 226 95 85 0 1992 2012 1378 126 157 329 85 75 0 1.062 1.13 1.139 1.288 2.75 1.083 0.733 120 645 3848 4018 0.087 1982 1866 2132 1886 315613 241440 9.35 5.638 0 0
237252 2.342137493 1 1 12 1 P:117 4650 9590 100 1307 1291 489 506 513 82 98 86 0 4588 4700 2787 129 137 60 100 100 0 0.18 0.172 0.171 0.166 2.205 0.146 0.668 80 503 5260 5356 -2.477 801 4459 785 4571 103317 376038 9.488 76.05 0 0
237253 -1.749917744 1 1 13 1 P:193 4840 9560 100 1039 1039 333 434 432 94 91 85 0 314 300 125 123 134 66 72 63 0 3.168 3.418 3.497 3.573 2.402 4.091 0.424 80 468 796 782 1.663 605 191 605 177 83124 24000 6.457 2.515 0 0
237254 1 1 14 1 P:197 5030 9560 140 410 448 461 424 1346 6691 0 0 0 132 148 78 122 1195 7454 0 0 0 -1.4 0.923 2.814 2.675 4.617 0.853 0.6 156 815 -4 50 Error -14 10 24 26 69833 23091 -0.134 -0.14 -50 0
237255 -1.970875772 1 1 15 1 P:201 5230 9560 100 9930 9317 4653 498 506 93 100 100 0 1789 1671 970 128 139 64 98 95 0 5.679 5.715 5.611 6.255 1.994 5.896 0.737 80 504 11093 10362 2.506 9432 1661 8819 1543 745386 133713 94.742 23.938 0 0
237256 0.287030022 1 1 16 1 P:205 5430 9560 90 2192 2266 1076 525 532 91 100 96 0 2378 2372 1356 130 142 82 100 98 0 0.742 0.777 0.781 0.78 2.112 0.714 0.687 52 408 3915 3983 -0.431 1667 2248 1741 2242 117843 123357 19.055 27.195 0 0
237257 -0.793050942 1 1 17 1 P:209 5620 9560 110 735 720 197 523 528 78 75 62 0 255 260 107 128 137 68 67 47 0 1.669 1.492 1.804 2.064 2.396 2.36 0.343 80 570 339 329 0.739 212 127 197 132 57563 20803 2.462 1.809 0 0
237258 -1.314789046 1 1 18 1 P:213 5810 9560 100 2895 2671 1236 536 543 83 98 97 0 890 894 474 132 138 46 100 98 0 3.112 2.802 2.7 2.652 2.031 2.841 0.702 80 518 3117 2897 1.638 2359 758 2135 762 213646 71556 25.639 16.435 0 0
237259 0.962690639 1 1 19 1 P:289 6010 9560 110 5203 4753 2203 549 556 93 100 100 0 8118 7783 4325 135 149 89 100 100 0 0.583 0.55 0.561 0.551 2.189 0.487 0.738 80 570 12637 11852 -0.778 4654 7983 4204 7648 380234 622632 45.129 85.775 0 0
237260 -0.494714113 1 1 20 1 P:293 6200 9560 100 5932 5740 3155 572 573 74 100 100 0 2810 2684 1741 134 146 86 100 96 0 2.003 2.027 2.055 2.254 2.618 2.077 0.679 80 494 8036 7718 1.002 5360 2676 5168 2550 459206 214693 69.824 29.512 0 0

Total number of rows: 15488

Table truncated, full table size 3483 Kbytes.




Supplementary file Size Download File type/resource
GSM251853.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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