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Sample GSM251864 Query DataSets for GSM251864
Status Public on Dec 01, 2008
Title Human Prostate GSK-14
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-14 treated with 0.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-14. Specimen ID: GSK-14; 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-14 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 0.227438337 1 1 1 1 P:1 2630 9310 130 2829 2789 439 1237 1255 266 99 98 0 2088 2389 1275 197 215 82 100 98 0 0.842 0.708 0.811 0.838 1.823 0.572 0.7 120 726 3483 3744 -0.248 1592 1891 1552 2192 334725 286716 5.767 26.512 0 0
237242 -0.717976487 1 1 2 1 P:5 2820 9300 120 17579 19791 9166 1238 1252 194 100 100 0 7089 7386 2941 200 213 56 100 100 0 2.372 2.582 2.461 2.534 1.593 2.874 0.824 120 604 23230 25739 1.246 16341 6889 18553 7186 2374875 886301 95.562 128.089 0 0
237243 -3.24158397 1 1 3 1 P:9 3010 9300 110 12964 14240 4543 1233 1248 212 100 100 0 2169 2278 715 206 223 80 100 100 0 5.976 6.278 5.932 6.26 1.279 7.091 0.782 80 534 13694 15079 2.579 11731 1963 13007 2072 1139177 182217 61.283 25.688 0 0
237244 0.006593176 1 1 4 1 P:13 3210 9310 120 2603 2654 485 1199 1212 198 100 99 0 1501 1740 861 211 233 98 100 100 0 1.088 0.952 1.052 1.015 1.555 0.871 0.661 120 629 2694 2984 0.122 1404 1290 1455 1529 318519 208790 7.283 15.378 0 0
237245 -0.279140721 1 1 5 1 P:17 3410 9300 120 2758 2786 428 1151 1166 190 100 99 0 1449 1709 776 216 240 140 100 97 0 1.303 1.095 1.214 1.194 1.594 0.929 0.682 120 621 2840 3128 0.382 1607 1233 1635 1493 334322 205065 8.526 10.493 0 0
237246 3.681795561 1 1 6 1 P:21 3600 9290 110 1879 1942 342 1171 1175 190 100 90 0 14880 17760 9665 227 289 694 100 100 0 0.048 0.044 0.045 0.045 1.806 0.032 0.481 80 539 15361 18304 -4.371 708 14653 771 17533 155375 1420808 4.037 25.174 0 0
237247 0.195744064 1 1 7 1 P:97 3780 9300 90 27160 27495 7672 1188 1312 1234 100 100 0 10505 11000 2848 234 366 1151 100 100 0 2.529 2.444 2.49 2.42 1.355 2.342 0.763 52 383 36243 37073 1.338 25972 10271 26307 10766 1429750 571989 21.218 9.239 0 0
237248 1.017244074 1 1 8 1 P:101 3980 9290 90 2007 2011 225 1081 1177 731 82 0 0 1717 1845 487 208 244 168 100 100 0 0.614 0.568 0.578 0.573 1.416 0.492 0.609 52 414 2435 2567 -0.705 926 1509 930 1637 104591 95960 1.141 9.53 0 0
237249 -1.183474574 1 1 9 1 P:105 4190 9290 120 31752 32087 7434 995 1116 832 100 100 0 6341 6242 1646 204 247 314 100 99 0 5.012 5.149 5.07 5.264 1.433 5.398 0.873 120 661 36894 37130 2.325 30757 6137 31092 6038 3850406 749088 37.225 19.092 0 0
237250 0.048692781 1 1 10 1 P:109 4380 9300 110 29354 31346 10440 1127 1160 377 100 100 0 10011 10797 3865 227 247 115 100 100 0 2.885 2.859 3.057 2.87 1.313 2.942 0.876 80 526 38011 40789 1.529 28227 9784 30219 10570 2507687 863747 80.069 91.739 0 0
237251 1.263341968 1 1 11 1 P:113 4570 9290 120 2843 2867 410 1125 1162 342 100 99 0 7270 7377 1424 235 341 1301 100 98 0 0.244 0.244 0.24 0.243 1.315 0.227 0.841 120 640 8753 8884 -2.034 1718 7035 1742 7142 344018 885195 4.985 5.408 0 0
237252 1.295625059 1 1 12 1 P:117 4770 9290 110 2383 2414 268 1096 1098 161 100 100 0 4015 4223 1674 234 249 71 100 100 0 0.34 0.33 0.337 0.354 1.503 0.272 0.697 80 534 5068 5307 -1.555 1287 3781 1318 3989 193141 337831 8.174 55.972 0 0
237253 -0.473542915 1 1 13 1 P:193 4960 9290 130 2502 2621 559 1096 1177 436 98 90 0 854 926 295 244 276 136 100 99 0 2.305 2.236 2.395 2.255 1.533 2.666 0.621 120 678 2016 2207 1.205 1406 610 1525 682 314549 111079 3.312 4.779 0 0
237254 0.689847236 1 1 14 1 P:197 5160 9300 130 1344 1572 990 1036 1083 302 51 13 0 456 490 234 245 265 110 79 44 0 1.46 2.188 1.512 1.64 2.501 7.013 0.189 120 678 519 781 0.546 308 211 536 245 188634 58789 1.619 2.045 0 0
237255 -1.384722705 1 1 15 1 P:201 5350 9290 110 6209 6524 1949 1037 1050 170 100 100 0 3556 3860 1265 237 253 80 100 100 0 1.558 1.514 1.462 1.498 1.268 1.43 0.869 80 549 8491 9110 0.64 5172 3319 5487 3623 521945 308761 32.2 45.088 0 0
237256 0.263285293 1 1 16 1 P:205 5550 9290 100 4866 5177 2041 1042 1056 152 100 100 0 7996 8478 4411 237 246 63 100 100 0 0.493 0.502 0.501 0.515 1.441 0.475 0.922 80 500 11583 12376 -1.021 3824 7759 4135 8241 414132 678268 27.112 130.667 0 0
237257 0.613109909 1 1 17 1 P:209 5750 9280 120 2504 2465 436 1065 1082 232 100 96 0 2670 2898 1311 237 247 67 100 100 0 0.591 0.526 0.563 0.572 1.71 0.439 0.725 120 642 3872 4061 -0.758 1439 2433 1400 2661 295752 347768 5.961 39.567 0 0
237258 -0.60522928 1 1 18 1 P:213 5930 9280 110 5900 14953 20604 1130 1218 540 100 100 12 5403 6493 3457 249 312 555 98 97 0 0.925 2.214 0.951 1.336 2.156 4.625 0.538 80 520 9924 20067 -0.112 4770 5154 13823 6244 1196200 519475 25.435 11.137 0 0
237259 0.168023623 1 1 19 1 P:289 6140 9280 140 3604 6084 9900 1108 1184 503 96 94 1 4848 5781 4557 242 306 499 94 92 0 0.542 0.898 0.568 0.685 2.617 3.263 0.121 156 743 7102 10515 -0.884 2496 4606 4976 5539 949104 901902 9.742 10.972 0 0
237260 0.261592433 1 1 20 1 P:293 6330 9280 110 3916 4717 3445 1113 1210 619 100 100 0 6160 6749 2678 243 272 150 100 100 0 0.474 0.554 0.493 0.51 1.593 0.757 0.389 80 520 8720 10110 -1.078 2803 5917 3604 6506 377340 539953 5.666 43.18 0 0

Total number of rows: 15488

Table truncated, full table size 3534 Kbytes.




Supplementary file Size Download File type/resource
GSM251864.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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