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Sample GSM251865 Query DataSets for GSM251865
Status Public on Dec 01, 2008
Title Human Prostate GSK-42
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-42 treated with 0.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-42. Specimen ID: GSK-42; 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-42 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 1.425765429 1 1 1 1 P:1 2630 9520 130 2327 2375 878 712 733 201 94 91 0 3959 4416 2075 284 296 88 100 97 0 0.439 0.402 0.431 0.378 1.859 0.362 0.722 120 731 5290 5795 -1.186 1615 3675 1663 4132 285043 529891 8.169 46.818 0 0
237242 -1.849945329 1 1 2 1 P:5 2810 9520 120 16305 19813 13016 756 771 171 100 100 0 4573 5002 2599 300 313 98 98 95 0 3.639 4.053 3.678 3.884 1.937 4.956 0.726 120 605 19822 23759 1.864 15549 4273 19057 4702 2377604 600261 111.357 47.847 0 0
237243 -2.091796419 1 1 3 1 P:9 3000 9510 110 6866 7915 2754 793 799 144 100 100 0 1555 1731 740 302 317 100 100 97 0 4.847 4.984 4.824 5.339 1.732 5.558 0.653 80 561 7326 8551 2.277 6073 1253 7122 1429 633219 138461 49.417 14.14 0 0
237244 -0.404316849 1 1 4 1 P:13 3210 9520 120 2439 2594 1020 779 792 161 99 95 0 1290 1393 590 296 331 250 92 86 0 1.67 1.655 1.66 1.695 2.293 1.789 0.536 120 654 2654 2912 0.74 1660 994 1815 1097 311238 167198 11.193 4.248 0 0
237245 -0.411543295 1 1 5 1 P:17 3390 9510 110 2521 2850 875 784 809 173 100 100 0 1313 1490 641 292 339 282 98 93 0 1.701 1.725 1.698 1.829 1.786 1.591 0.611 80 535 2758 3264 0.767 1737 1021 2066 1198 227997 119162 11.798 4.082 0 0
237246 3.779608321 1 1 6 1 P:21 3590 9510 110 1647 1657 274 807 847 270 98 86 0 21503 25434 13857 324 395 284 100 100 0 0.04 0.034 0.04 0.037 1.854 0.023 0.427 80 580 22019 25960 -4.656 840 21179 850 25110 132523 2034719 3 88.165 0 0
237247 -1.415326837 1 1 7 1 P:97 3770 9520 90 24085 24423 5374 824 950 937 100 100 0 6719 6557 2236 307 396 621 100 98 0 3.628 3.776 3.519 4.045 1.68 3.705 0.755 52 383 29673 29849 1.859 23261 6412 23599 6250 1270004 340980 25.051 9.921 0 0
237248 -0.563903697 1 1 8 1 P:101 3970 9520 90 2401 2501 562 806 821 208 100 100 0 1095 1120 279 291 310 107 100 100 0 1.984 2.045 1.936 2.04 1.425 2.049 0.701 52 400 2399 2524 0.988 1595 804 1695 829 130048 58243 8.077 7.57 0 0
237249 -2.34957217 1 1 9 1 P:105 4160 9510 110 21878 26924 13123 813 837 194 100 100 2 4051 4656 2269 285 298 97 100 100 0 5.593 5.974 5.501 5.985 1.477 6.344 0.783 80 581 24831 30482 2.484 21065 3766 26111 4371 2153886 372506 134.469 44.928 0 0
237250 -0.202326066 1 1 10 1 P:109 4360 9530 110 19351 19512 8071 823 947 1033 100 100 0 11085 12771 6347 281 443 1508 98 98 0 1.715 1.496 1.564 1.538 1.722 1.508 0.661 80 570 29332 31179 0.778 18528 10804 18689 12490 1560952 1021719 17.972 8.175 0 0
237251 0.315050617 1 1 11 1 P:113 4560 9510 110 2420 5661 12223 796 830 207 100 100 1 1847 2188 1504 288 310 107 100 98 0 1.042 2.561 1.005 1.204 2.161 8.188 0.433 80 591 3183 6765 0.059 1624 1559 4865 1900 452913 175042 23.338 17.551 0 0
237252 1.319507185 1 1 12 1 P:117 4760 9520 110 1979 2232 1729 767 772 137 100 98 0 2790 3370 2073 289 303 91 100 100 0 0.485 0.475 0.493 0.474 2.156 0.499 0.401 80 553 3713 4546 -1.045 1212 2501 1465 3081 178559 269589 10.657 33.703 0 0
237253 -0.115719167 1 1 13 1 P:193 4950 9510 120 1718 2692 3868 750 756 130 97 96 0 811 945 692 280 289 92 94 91 0 1.823 2.92 1.829 2.042 2.289 9.158 0.242 120 646 1499 2607 0.866 968 531 1942 665 322999 113353 14.892 7.13 0 0
237254 0.619733021 1 1 14 1 P:197 5150 9520 100 1056 1089 222 750 759 137 88 57 0 477 493 127 284 296 78 86 61 0 1.585 1.622 1.549 1.679 2.607 2.494 0.278 80 490 499 548 0.665 306 193 339 209 87148 39433 2.409 2.526 0 0
237255 -1.249876641 1 1 15 1 P:201 5350 9520 110 4329 5158 2755 768 780 144 100 100 0 1676 2196 1460 291 304 81 100 97 0 2.571 2.304 2.269 2.49 2.063 2.375 0.574 80 566 4946 6295 1.362 3561 1385 4390 1905 412659 175684 30.403 23.358 0 0
237256 1.002841977 1 1 16 1 P:205 5540 9530 100 2993 2973 674 768 780 136 100 100 0 4878 5136 2136 299 310 75 100 100 0 0.486 0.456 0.467 0.494 1.777 0.391 0.778 80 493 6804 7042 -1.041 2225 4579 2205 4837 237820 410900 16.125 64.347 0 0
237257 0.74134669 1 1 17 1 P:209 5740 9520 100 1594 2444 4530 794 803 144 100 100 0 1152 1311 625 293 304 80 100 100 0 0.931 1.621 0.89 1 1.951 30.291 0.086 80 503 1659 2668 -0.103 800 859 1650 1018 195487 104866 11.396 12.588 0 0
237258 -0.866396653 1 1 18 1 P:213 5930 9510 110 4945 5362 2983 803 808 143 100 100 0 2461 2503 678 306 319 91 100 100 0 1.922 2.075 1.928 1.967 1.43 2.552 0.556 80 566 6297 6756 0.943 4142 2155 4559 2197 428943 200247 31.846 24 0 0
237259 0.495271296 1 1 19 1 P:289 6130 9510 120 2595 4330 7673 817 829 151 99 96 0 2734 3366 2169 310 322 97 96 95 0 0.733 1.15 0.688 0.835 2.653 5.124 0.172 120 660 4202 6569 -0.447 1778 2424 3513 3056 519603 403872 23.185 31.381 0 0
237260 -0.187425282 1 1 20 1 P:293 6320 9530 100 3925 5899 6926 859 875 192 100 100 0 2622 2912 1822 307 332 226 98 97 0 1.324 1.935 1.453 1.662 2.355 4.238 0.315 80 487 5381 7645 0.405 3066 2315 5040 2605 471944 232976 26.167 11.416 0 0

Total number of rows: 15488

Table truncated, full table size 3533 Kbytes.




Supplementary file Size Download File type/resource
GSM251865.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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