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Sample GSM251838 Query DataSets for GSM251838
Status Public on Dec 01, 2008
Title Human Prostate GSK-27
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-27 treated with 3.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-27. Specimen ID: GSK-27; 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-27 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 1.062660549 1 1 1 1 P:1 2560 9630 110 2272 2614 2645 1691 1744 379 75 33 0 1804 1826 669 526 541 158 98 93 0 0.455 0.71 0.476 0.512 2.734 6.029 0.055 80 612 1859 2223 -1.137 581 1278 923 1300 209114 146107 2.296 8.133 0 0
237242 -3.082769068 1 1 2 1 P:5 2760 9640 100 24468 25804 10565 1687 1785 457 100 100 0 2842 2804 1257 488 505 203 96 93 0 9.678 10.413 10.271 11.105 1.787 12.334 0.694 80 502 25135 26433 3.275 22781 2354 24117 2316 2064340 224311 52.558 11.325 0 0
237243 -3.099128726 1 1 3 1 P:9 2960 9650 100 11893 11746 4154 1590 1635 438 100 100 0 1431 1437 545 431 452 201 97 91 0 10.303 10.095 10.153 10.474 1.731 11.684 0.572 80 493 11303 11162 3.365 10303 1000 10156 1006 939691 114990 23.084 4.9 0 0
237244 0.04139131 1 1 4 1 P:13 3150 9640 100 1817 3207 5654 1590 1766 959 21 12 0 763 804 293 424 443 127 87 66 0 0.67 4.255 1.446 1.918 4.137 35.895 0.09 80 476 566 1997 -0.579 227 339 1617 380 256522 64343 1.503 2.843 0 0
237245 -1.343800464 1 1 5 1 P:17 3330 9610 110 2130 3383 4894 1562 1745 860 41 25 0 727 802 525 413 443 172 66 40 0 1.809 4.681 2.796 3.081 4.115 21.788 0.128 80 580 882 2210 0.855 568 314 1821 389 270651 64195 1.905 2.087 0 0
237246 6.230668002 1 1 6 1 P:21 3530 9630 100 1741 2425 2504 1560 1705 978 17 15 0 11568 11936 4926 406 433 154 100 100 0 0.016 0.075 0.046 0.062 4.009 0.042 0.023 80 470 11343 12395 -5.946 181 11162 865 11530 193980 954870 0.736 74.695 0 0
237247 -2.500386932 1 1 7 1 P:97 3730 9630 100 36184 37650 15524 1793 1935 957 100 100 1 3841 3820 1432 438 466 169 100 100 0 10.106 10.602 10.715 10.428 2.052 13.923 0.596 80 524 37794 39239 3.337 34391 3403 35857 3382 3012001 305564 37.32 19.846 0 0
237248 -2.772005643 1 1 8 1 P:101 3940 9620 90 4427 4956 3957 1684 1962 1504 59 40 0 809 1032 770 412 451 192 86 50 0 6.909 5.277 3.532 3.821 3.171 11.417 0.234 52 383 3140 3892 2.789 2743 397 3272 620 257713 53689 1.991 3.026 0 0
237249 -3.330408259 1 1 9 1 P:105 4100 9620 110 34853 33835 12552 1500 1728 1803 100 100 0 2827 2706 1124 378 423 283 97 91 0 13.619 13.89 13.729 14.927 1.825 15.176 0.595 80 572 35802 34663 3.768 33353 2449 32335 2328 2706831 216514 17.808 8.067 0 0
237250 -0.96543391 1 1 10 1 P:109 4320 9620 110 40345 41753 14969 1345 1490 1169 100 100 10 9728 9697 4196 355 382 210 100 98 0 4.161 4.325 4.266 4.7 2.024 4.797 0.624 80 560 48373 49750 2.057 39000 9373 40408 9342 3340229 775776 34.442 44.357 0 0
237251 -0.37972579 1 1 11 1 P:113 4490 9620 110 3752 5246 6479 1227 1253 285 100 98 0 1896 2027 808 327 374 273 100 98 0 1.609 2.364 1.538 1.784 2.069 7.733 0.195 80 560 4094 5719 0.686 2525 1569 4019 1700 419653 162173 14.011 6.055 0 0
237252 2.392786841 1 1 12 1 P:117 4710 9620 100 1703 1896 1114 1098 1113 181 73 66 0 3259 3761 2091 305 340 227 100 100 0 0.205 0.231 0.22 0.205 2.627 0.196 0.23 80 516 3559 4254 -2.288 605 2954 798 3456 151672 300866 4.326 15.07 0 0
237253 -2.326140416 1 1 13 1 P:193 4900 9620 100 1923 1909 488 968 979 157 91 86 0 544 565 173 278 290 108 80 66 0 3.59 3.279 3.024 3.43 2.237 7.713 0.149 80 453 1221 1228 1.844 955 266 941 287 152701 45234 5.924 2.546 0 0
237254 1 1 14 1 P:197 5080 9610 140 1008 1036 230 880 892 161 39 21 0 301 315 75 261 278 131 14 0 0 3.2 2.889 2.962 2.539 3.849 6.612 0.038 156 765 168 210 1.678 128 40 156 54 161539 49099 0.894 0.282 -50 0
237255 -1.561637177 1 1 15 1 P:201 5270 9610 110 4049 4228 1346 811 859 392 100 100 0 1083 1161 453 252 285 178 93 92 0 3.897 3.759 3.664 4.039 1.951 5.533 0.436 80 558 4069 4326 1.962 3238 831 3417 909 338210 92891 8.594 4.921 0 0
237256 -0.338707904 1 1 16 1 P:205 5480 9620 100 3714 4840 2960 771 805 275 98 97 0 2332 2750 1574 248 273 154 100 97 0 1.412 1.626 1.442 1.442 2.937 2.113 0.471 80 532 5027 6571 0.498 2943 2084 4069 2502 387190 220010 14.673 16.084 0 0
237257 -2.561562694 1 1 17 1 P:209 5700 9620 100 1707 3631 9046 727 755 474 85 52 0 481 703 987 243 250 63 91 83 0 4.118 6.313 4.195 4.226 2.228 29.93 0.084 80 516 1218 3364 2.042 980 238 2904 460 290449 56235 6.068 7.19 0 0
237258 -2.182539087 1 1 18 1 P:213 5880 9610 110 8203 8265 3098 679 715 264 100 100 0 1572 1459 633 236 272 262 88 82 0 5.632 6.203 5.77 6.872 1.963 6.685 0.551 80 568 8860 8809 2.494 7524 1336 7586 1223 661183 116729 28.598 4.531 0 0
237259 1.239972133 1 1 19 1 P:289 6080 9610 110 4155 4523 1759 648 689 278 100 100 0 7368 7966 4726 231 266 259 98 98 0 0.491 0.501 0.539 0.589 2.083 0.422 0.751 80 570 10644 11610 -1.025 3507 7137 3875 7735 361847 637242 13.791 29.73 0 0
237260 -0.472311671 1 1 20 1 P:293 6270 9610 100 5962 6837 3339 609 655 408 100 100 0 3900 3583 1477 227 233 47 100 100 0 1.457 1.856 1.749 1.864 2.038 2.164 0.575 80 472 9026 9584 0.543 5353 3673 6228 3356 546987 286673 15.152 71.277 0 0

Total number of rows: 15488

Table truncated, full table size 3528 Kbytes.




Supplementary file Size Download File type/resource
GSM251838.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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