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Sample GSM251837 Query DataSets for GSM251837
Status Public on Dec 01, 2008
Title Human Prostate GSK-7
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-7 treated with 3.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-7. Specimen ID: GSK-7; 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-7 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 0.294331137 1 1 1 1 P:1 2740 9300 110 2256 2325 1083 322 373 221 98 92 0 1369 1429 863 140 149 78 100 96 0 1.574 1.554 1.653 1.671 1.601 1.649 0.751 80 620 3163 3292 0.654 1934 1229 2003 1289 186000 114306 8.833 16.41 0 0
237242 -3.160274422 1 1 2 1 P:5 2940 9300 110 35205 32759 14065 400 751 3411 100 98 1 2364 2345 1169 149 183 238 97 91 0 15.713 14.735 14.592 15.862 1.638 15.837 0.863 80 600 37020 34555 3.974 34805 2215 32359 2196 2620733 187564 9.384 9.084 0 0
237243 -2.595174812 1 1 3 1 P:9 3140 9320 100 14081 14869 6064 409 691 3070 96 88 0 1553 1574 716 152 180 218 93 90 0 9.759 10.169 10.033 11.003 1.604 10.785 0.827 80 504 15073 15882 3.287 13672 1401 14460 1422 1189533 125924 4.618 6.394 0 0
237244 -0.875592612 1 1 4 1 P:13 3330 9320 110 1342 1304 450 370 395 174 92 87 0 454 449 156 153 160 53 93 83 0 3.229 3.155 3.056 3.007 1.91 3.799 0.622 80 536 1273 1230 1.691 972 301 934 296 104303 35927 5.224 5.453 0 0
237245 -0.816885175 1 1 5 1 P:17 3510 9310 110 1396 1307 433 358 378 177 95 87 0 490 467 177 155 173 88 87 75 0 3.099 3.042 3.075 3.285 1.727 3.53 0.641 80 568 1373 1261 1.632 1038 335 949 312 104527 37353 5.249 3.341 0 0
237246 3.438361791 1 1 6 1 P:21 3710 9320 100 1644 1712 687 345 368 127 98 95 0 11234 12782 7578 158 174 82 100 100 0 0.117 0.108 0.11 0.111 1.619 0.094 0.808 80 511 12375 13991 -3.092 1299 11076 1367 12624 136922 1022556 10.583 153.756 0 0
237247 -2.75780117 1 1 7 1 P:97 3900 9320 90 34821 37026 18401 341 487 1509 100 100 13 3039 3447 2071 157 184 280 100 98 0 11.964 11.15 11.765 12.111 1.561 11.678 0.81 52 392 37362 39975 3.581 34480 2882 36685 3290 1925359 179269 24.214 11.654 0 0
237248 -2.214393072 1 1 8 1 P:101 4110 9320 100 3245 4531 3041 348 421 335 100 100 0 489 596 301 157 164 48 98 98 0 8.726 9.528 8.913 9.415 1.575 12.252 0.66 80 472 3229 4622 3.125 2897 332 4183 439 362471 47678 12.269 9 0 0
237249 -3.160021198 1 1 9 1 P:105 4280 9310 100 41240 38770 16638 369 530 814 100 100 3 2760 2553 1260 158 183 171 97 93 0 15.708 16.034 15.887 16.154 1.485 15.814 0.857 80 495 43473 40796 3.973 40871 2602 38401 2395 3101576 204275 46.978 13.86 0 0
237250 -1.376189312 1 1 10 1 P:109 4500 9320 110 44617 43457 18255 375 520 579 100 100 21 6856 7475 4576 164 201 164 100 100 0 6.611 5.893 6.157 6.574 1.517 5.799 0.848 80 562 50934 50393 2.725 44242 6692 43082 7311 3476559 598015 74.157 44.354 0 0
237251 0.835257613 1 1 11 1 P:113 4680 9330 110 4807 5086 1991 354 429 294 100 100 0 4826 5078 2437 161 195 138 100 100 0 0.955 0.962 0.964 1.01 1.435 0.936 0.848 80 534 9118 9649 -0.067 4453 4665 4732 4917 406912 406223 15.84 35.384 0 0
237252 1.859173422 1 1 12 1 P:117 4880 9310 110 2101 2345 1289 330 351 131 100 98 0 3631 4714 3370 156 161 50 100 100 0 0.51 0.442 0.453 0.462 1.432 0.395 0.847 80 590 5246 6573 -0.972 1771 3475 2015 4558 187568 377110 15.221 91.06 0 0
237253 -1.888252861 1 1 13 1 P:193 5070 9330 110 2658 2619 830 339 364 180 100 100 0 495 503 171 155 164 126 88 67 0 6.821 6.552 6.464 7.059 1.581 5.881 0.574 80 588 2659 2628 2.77 2319 340 2280 348 209499 40260 12.528 2.69 0 0
237254 -1.549270469 1 1 14 1 P:197 5270 9330 90 775 761 270 341 358 111 86 65 0 225 229 60 153 157 35 71 50 0 6.028 5.526 4.633 5.301 2.032 5.872 0.513 52 384 506 496 2.592 434 72 420 76 39550 11920 3.631 2.057 0 0
237255 -1.227875161 1 1 15 1 P:201 5440 9340 100 6267 10257 8072 350 520 1188 100 96 0 1980 2987 2337 159 229 409 98 88 0 3.249 3.503 3.576 3.608 1.427 3.665 0.878 80 498 7738 12735 1.7 5917 1821 9907 2828 820548 238947 8.196 6.743 0 0
237256 -0.341826731 1 1 16 1 P:205 5650 9340 90 4842 5402 2821 353 414 438 100 100 0 2741 3400 2088 160 233 518 96 96 0 1.739 1.558 1.496 1.728 1.954 1.752 0.844 52 398 7070 8289 0.798 4489 2581 5049 3240 280903 176775 11.388 6.114 0 0
237257 0.211892748 1 1 17 1 P:209 5860 9320 110 793 756 270 350 397 455 47 1 0 423 427 161 160 192 274 46 3 0 1.684 1.521 1.472 1.488 1.931 1.818 0.576 80 615 706 673 0.752 443 263 406 267 60469 34139 0.789 0.858 0 0
237258 -2.291684267 1 1 18 1 P:213 6060 9330 110 8715 7860 2844 373 442 510 100 100 0 1296 1254 518 168 193 142 100 93 0 7.395 6.894 7.165 7.329 1.481 7.013 0.828 80 546 9470 8573 2.887 8342 1128 7487 1086 628821 100330 14.545 7.472 0 0
237259 0.854522185 1 1 19 1 P:289 6240 9320 110 7557 8315 3990 365 402 225 100 100 0 7548 9992 7600 167 196 227 100 100 0 0.974 0.809 0.973 0.958 1.611 0.672 0.833 80 556 14573 17775 -0.037 7192 7381 7950 9825 665192 799341 35.169 43.154 0 0
237260 -0.765196462 1 1 20 1 P:293 6440 9350 100 11535 11461 6008 382 513 1012 100 100 0 3925 3921 2362 170 213 308 98 97 0 2.97 2.954 3.048 3.3 1.87 3.418 0.69 80 506 14908 14830 1.571 11153 3755 11079 3751 916843 313706 10.818 12.039 0 0

Total number of rows: 15488

Table truncated, full table size 3518 Kbytes.




Supplementary file Size Download File type/resource
GSM251837.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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