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Sample GSM251832 Query DataSets for GSM251832
Status Public on Dec 01, 2008
Title Human Prostate GSK-1
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-1 treated with 0.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-1. Specimen ID: GSK-1; 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-1 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 0.709890355 1 1 1 1 P:1 2310 9310 110 2499 2622 475 1465 1653 1244 35 0 0 2038 2120 377 1045 1065 128 100 100 0 1.041 1.076 1.064 1.045 1.426 2.63 0.317 80 550 2027 2232 0.058 1034 993 1157 1075 209795 169566 0.779 8.242 0 0
237242 -2.591120351 1 1 2 1 P:5 2500 9310 120 18509 18661 7373 1381 2144 5327 94 83 0 2636 2929 1091 1011 1069 379 98 90 0 10.54 9.009 10.484 9.077 1.752 9.31 0.803 120 611 18753 19198 3.398 17128 1625 17280 1918 2239333 351457 3.101 4.908 0 0
237243 -4.055794984 1 1 3 1 P:9 2690 9300 120 13347 14061 5087 1303 1405 578 100 100 0 1537 1610 312 979 1001 222 97 69 0 21.584 20.219 21.787 20.688 1.61 22.747 0.712 120 616 12602 13389 4.432 12044 558 12758 631 1687352 193207 21.896 2.743 0 0
237244 -0.49458849 1 1 4 1 P:13 2890 9300 120 2219 2612 1149 1219 1242 209 96 88 0 1198 1292 301 964 966 71 85 69 0 4.274 4.247 4.369 4.531 2.411 4.645 0.709 120 606 1234 1721 2.095 1000 234 1393 328 313466 155033 6.555 4.592 0 0
237245 -0.657191235 1 1 5 1 P:17 3080 9290 120 2249 2503 985 1148 1175 168 95 91 0 1177 1245 315 935 950 209 55 25 0 4.55 4.371 4.46 4.788 2.4 4.21 0.584 120 591 1343 1665 2.186 1101 242 1355 310 300343 149379 7.905 1.411 0 0
237246 4.701130659 1 1 6 1 P:21 3270 9290 110 1718 1721 256 1118 1126 156 96 87 0 13085 13508 4776 921 963 477 100 100 0 0.049 0.048 0.046 0.049 1.654 0.044 0.604 80 513 12764 13190 -4.342 600 12164 603 12587 137657 1080655 3.814 26.3 0 0
237247 -2.838652486 1 1 7 1 P:97 3450 9290 100 35911 40489 15388 1097 1463 3393 100 98 12 3530 4295 1893 912 1000 639 97 96 0 13.298 11.644 12.07 12.461 1.59 11.993 0.846 80 492 37432 42775 3.733 34814 2618 39392 3383 3239090 343572 11.502 5.156 0 0
237248 -1.754498496 1 1 8 1 P:101 3670 9290 100 2718 3636 2310 1058 1514 2034 38 22 0 1051 1246 483 886 929 296 43 31 0 10.061 7.161 7.839 7.745 2.396 8.584 0.53 80 507 1825 2938 3.331 1660 165 2578 360 290874 99653 1.043 1.071 0 0
237249 -3.812892168 1 1 9 1 P:105 3850 9280 110 29660 30675 6697 1003 1397 1970 100 100 0 2376 2584 775 849 877 192 100 100 0 18.767 17.102 18.505 17.947 1.322 16.323 0.836 80 544 30184 31407 4.23 28657 1527 29672 1735 2453989 206713 14.862 8.891 0 0
237250 -1.401163642 1 1 10 1 P:109 4040 9280 110 44091 43805 11250 986 1436 3839 100 100 3 9190 9763 3494 849 1011 1122 98 98 0 5.168 4.804 4.838 5.076 1.403 4.756 0.889 80 531 51446 51733 2.37 43105 8341 42819 8914 3504369 781058 11.036 7.8 0 0
237251 -0.235903302 1 1 11 1 P:113 4220 9280 110 3708 3884 947 935 1370 3680 18 0 0 2245 2464 740 830 1038 1139 80 21 0 1.96 1.805 1.862 1.883 1.314 1.618 0.662 80 564 4188 4583 0.971 2773 1415 2949 1634 310723 197109 0.683 1.252 0 0
237252 1.851187343 1 1 12 1 P:117 4440 9280 120 1606 1690 452 867 930 356 87 52 0 2260 2735 1350 794 866 467 95 79 0 0.504 0.424 0.469 0.455 1.667 0.345 0.711 120 691 2205 2764 -0.988 739 1466 823 1941 202768 328236 2.135 4.002 0 0
237253 -3.094712251 1 1 13 1 P:193 4640 9280 110 2167 2160 373 825 836 148 100 100 0 773 779 124 766 765 56 32 17 0 191.714 102.692 17.21 17.501 2.24 12.965 0.235 80 508 1349 1348 7.583 1342 7 1335 13 172771 62338 8.946 0.25 0 0
237254 1 1 14 1 P:197 4820 9270 140 1016 1058 275 791 810 173 57 34 0 636 638 113 753 765 86 2 0 0 -1.923 -2.322 3.479 2.752 5.746 0.165 0.104 156 750 108 152 Error 225 -117 267 -115 165057 99545 1.434 -1.477 -50 0
237255 -0.127818501 1 1 15 1 P:201 5010 9270 110 3096 3065 669 791 825 261 100 100 0 2001 2190 653 755 799 267 100 100 0 1.85 1.585 1.637 1.64 1.424 1.485 0.733 80 546 3551 3709 0.887 2305 1246 2274 1435 245203 175161 8.582 5.21 0 0
237256 1.103898148 1 1 16 1 P:205 5210 9270 90 2879 4212 3546 776 810 293 100 100 0 3639 5172 3569 751 814 583 100 100 0 0.728 0.777 0.745 0.72 1.423 0.861 0.78 52 400 4991 7857 -0.458 2103 2888 3436 4421 219038 268924 11.611 7.475 0 0
237257 2.682801526 1 1 17 1 P:209 5400 9270 110 1216 1235 293 742 822 531 42 5 0 2197 2393 943 730 843 1220 65 16 0 0.323 0.296 0.284 0.284 2.113 0.382 0.287 80 588 1941 2156 -1.63 474 1467 493 1663 98773 191415 0.778 1.27 0 0
237258 -1.040070111 1 1 18 1 P:213 5610 9270 110 7807 7852 1287 717 767 332 100 100 0 2726 2848 755 712 732 136 100 100 0 3.52 3.34 3.454 3.48 1.322 3.187 0.794 80 560 9104 9271 1.816 7090 2014 7135 2136 628147 227826 21.34 15.559 0 0
237259 0.954618893 1 1 19 1 P:289 5800 9260 110 6239 6319 2165 688 708 138 100 100 0 8096 8255 4097 684 701 196 100 100 0 0.749 0.744 0.755 0.816 1.49 0.683 0.853 80 556 12963 13202 -0.417 5551 7412 5631 7571 505489 660368 40.659 38.541 0 0
237260 0.800332875 1 1 20 1 P:293 5990 9260 100 5686 6925 3602 669 691 159 100 100 0 5821 6100 2843 674 683 154 100 100 0 0.975 1.153 1.135 1.211 1.616 1.252 0.774 80 494 10164 11682 -0.037 5017 5147 6256 5426 554038 487994 39.208 35.175 0 0

Total number of rows: 15488

Table truncated, full table size 3529 Kbytes.




Supplementary file Size Download File type/resource
GSM251832.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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