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Sample GSM251860 Query DataSets for GSM251860
Status Public on Dec 01, 2008
Title Human Prostate GSK-59
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-59 treated with 3.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-59. Specimen ID: GSK-59; 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-59 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 0.829579501 1 1 1 1 P:1 2530 9520 130 1227 1428 659 101 107 37 100 100 0 956 1096 559 103 123 74 99 98 0 1.32 1.336 1.406 1.415 1.678 1.326 0.786 120 762 1979 2320 0.401 1126 853 1327 993 171351 131571 35.703 13.149 0 0
237242 -5.066929477 1 1 2 1 P:5 2730 9520 110 20803 20236 7304 115 136 116 100 100 0 1155 1203 510 108 130 95 100 98 0 19.759 18.375 19.035 18.507 1.493 18.739 0.702 80 538 21735 21216 4.304 20688 1047 20121 1095 1618840 96250 173.276 11.295 0 0
237243 -2.027141334 1 1 3 1 P:9 2920 9510 110 4822 5164 1726 113 132 114 100 100 0 575 626 244 110 133 86 98 98 0 10.127 9.789 10.087 10.296 1.549 10.722 0.722 80 538 5174 5567 3.34 4709 465 5051 516 413086 50068 44.14 5.733 0 0
237244 -0.047433623 1 1 4 1 P:13 3110 9510 120 1841 1921 748 109 113 34 100 100 0 912 992 518 103 128 86 94 92 0 2.141 2.038 2.053 2.301 1.982 2.079 0.671 120 638 2541 2701 1.098 1732 809 1812 889 230575 119066 53.176 10.047 0 0
237245 0.166526115 1 1 5 1 P:17 3310 9510 110 1924 2097 821 114 118 38 100 100 0 1031 1135 558 108 137 93 100 100 0 1.961 1.931 2.078 2.016 1.548 1.809 0.707 80 556 2733 3010 0.972 1810 923 1983 1027 167793 90815 52.079 10.731 0 0
237246 2.918956654 1 1 6 1 P:21 3520 9510 110 400 440 168 114 120 40 100 96 0 1556 1616 580 113 143 89 100 100 0 0.198 0.217 0.218 0.205 1.66 0.198 0.676 80 538 1729 1829 -2.335 286 1443 326 1503 35190 129310 8 16.551 0 0
237247 -4.902488874 1 1 7 1 P:97 3680 9500 90 18282 19699 5966 120 314 1321 100 100 0 1092 1040 383 121 166 154 98 92 0 18.704 21.305 19.914 22.876 1.505 21.162 0.821 52 375 19133 20498 4.225 18162 971 19579 919 1024337 54088 14.674 5.675 0 0
237248 0.187665653 1 1 8 1 P:101 3890 9500 90 2093 2062 558 122 134 71 100 100 0 1060 1095 383 114 135 83 100 100 0 2.084 1.978 2.095 2.056 1.322 2.027 0.789 52 400 2917 2921 1.059 1971 946 1940 981 107222 56945 27.155 11.566 0 0
237249 -4.381726517 1 1 9 1 P:105 4090 9500 120 14526 14063 3650 125 152 182 100 100 0 579 592 169 111 252 1732 0 0 0 30.771 28.977 29.907 28.876 1.418 38.172 0.014 120 652 14869 14419 4.944 14401 468 13938 481 1687508 71037 76.434 0.196 0 0
237250 -3.28293798 1 1 10 1 P:109 4280 9510 100 10059 11436 4876 125 135 69 100 100 0 1223 1273 464 110 138 108 100 98 0 8.925 9.726 9.298 9.667 1.549 10.584 0.736 80 456 11047 12474 3.158 9934 1113 11311 1163 914879 101864 163.783 10.509 0 0
237251 0.322274531 1 1 11 1 P:113 4470 9500 120 1081 1134 441 119 127 46 100 99 0 725 721 268 111 132 73 95 93 0 1.567 1.664 1.619 1.739 1.701 1.725 0.784 120 626 1576 1625 0.648 962 614 1015 610 136021 86504 21.891 8.068 0 0
237252 5.576460009 1 1 12 1 P:117 4670 9490 110 546 626 249 119 123 41 100 100 0 9271 10492 4896 110 137 161 100 100 0 0.047 0.049 0.047 0.049 1.468 0.041 0.747 80 548 9588 10889 -4.423 427 9161 507 10382 50074 839331 12.268 64.317 0 0
237253 0.231981241 1 1 13 1 P:193 4870 9490 120 770 824 250 118 122 39 100 100 0 593 609 205 113 136 113 98 92 0 1.358 1.423 1.38 1.44 1.678 1.475 0.614 120 672 1132 1202 0.442 652 480 706 496 98912 73075 18 4.186 0 0
237254 -1.057105855 1 1 14 1 P:197 5070 9490 110 336 350 106 111 190 610 0 0 0 252 281 110 109 230 860 0 0 0 1.573 1.39 1.659 1.564 2.199 2.399 0.41 80 566 368 411 0.654 225 143 239 172 28033 22485 0.262 0.059 0 0
237255 -1.093703348 1 1 15 1 P:201 5260 9490 110 4760 6058 3265 112 193 616 100 100 0 1181 1568 933 116 239 868 75 21 0 4.364 4.095 4.141 4.201 1.625 3.523 0.426 80 556 5713 7398 2.126 4648 1065 5946 1452 484618 125466 9.521 1.531 0 0
237256 -1.20738256 1 1 16 1 P:205 5450 9490 110 1909 2139 1535 117 123 41 100 100 0 474 572 539 114 138 80 95 86 0 4.978 4.415 4.826 5.258 1.831 6.685 0.243 80 548 2152 2480 2.316 1792 360 2022 458 171139 45729 49.171 5.425 0 0
237257 -1.702208031 1 1 17 1 P:209 5640 9480 110 1911 2011 462 118 122 43 100 100 0 417 419 117 113 133 71 97 95 0 5.898 6.186 5.694 6.401 1.562 6.646 0.63 80 580 2097 2199 2.56 1793 304 1893 306 160890 33550 43.93 4.028 0 0
237258 -1.992861806 1 1 18 1 P:213 5840 9490 110 3803 3842 566 115 121 46 100 100 0 539 565 188 117 139 78 96 96 0 8.739 8.319 8.752 8.711 1.515 8.51 0.663 80 561 4110 4175 3.128 3688 422 3727 448 307390 45184 80.891 5.462 0 0
237259 0.414492996 1 1 19 1 P:289 6050 9490 130 800 934 397 116 119 34 100 100 0 724 786 268 114 138 80 100 100 0 1.121 1.217 1.195 1.193 1.526 1.355 0.675 120 682 1294 1490 0.165 684 610 818 672 112065 94284 23.971 8.1 0 0
237260 -0.140025953 1 1 20 1 P:293 6230 9480 110 2328 2773 1410 119 130 166 100 100 0 959 1037 407 115 140 88 100 100 0 2.617 2.879 2.881 2.784 1.681 3.374 0.64 80 525 3053 3576 1.388 2209 844 2654 922 221806 82975 15.922 10.193 0 0

Total number of rows: 15488

Table truncated, full table size 3409 Kbytes.




Supplementary file Size Download File type/resource
GSM251860.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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