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Sample GSM251839 Query DataSets for GSM251839
Status Public on Dec 01, 2008
Title Human Prostate GSK-28
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-28 treated with 3.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-28. Specimen ID: GSK-28; 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-28 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 -0.573158905 1 1 1 1 P:1 2620 9720 120 1791 1791 582 345 410 337 96 90 0 1402 1498 513 182 192 53 99 99 0 1.185 1.099 1.213 1.078 1.853 1.181 0.655 120 665 2666 2762 0.245 1446 1220 1446 1316 214912 179713 4.098 24.642 0 0
237242 -2.794180923 1 1 2 1 P:5 2810 9710 120 14637 15654 8352 391 450 331 99 98 0 2611 2656 1355 194 207 67 98 98 0 5.894 6.199 6.598 6.472 2.041 7.818 0.599 120 601 16663 17725 2.559 14246 2417 15263 2462 1878537 318703 45.934 36.552 0 0
237243 -2.998268882 1 1 3 1 P:9 3000 9720 100 6016 6712 2435 390 443 241 100 100 0 1240 1375 564 198 202 44 100 100 0 5.399 5.371 5.431 5.527 1.349 5.706 0.714 80 445 6668 7499 2.433 5626 1042 6322 1177 536973 109975 26.012 26.659 0 0
237244 -0.560536858 1 1 4 1 P:13 3200 9710 150 807 849 394 399 722 937 11 0 0 447 515 285 204 956 2523 0 0 0 1.679 1.447 1.515 1.691 2.584 0.483 0.312 156 676 651 761 0.748 408 243 450 311 132468 80263 0.136 -0.175 0 0
237245 1 1 5 1 P:17 3370 9690 140 756 761 349 407 1107 1699 0 0 0 456 461 249 218 1490 3176 0 0 0 1.466 1.457 1.717 1.9 2.341 0.464 0.373 156 601 587 597 0.552 349 238 354 243 118748 71851 -0.204 -0.324 -50 0
237246 1 1 6 1 P:21 3580 9700 150 1946 5441 8542 389 983 2024 44 30 0 3655 5028 5252 214 863 2446 64 35 0 0.452 1.049 0.804 0.644 4.195 1.425 0.365 156 706 4998 9866 -1.144 1557 3441 5052 4814 848854 784298 2.203 1.703 -50 0
237247 1 1 7 1 P:97 3770 9710 110 7513 10004 8150 408 1154 3122 85 56 0 1759 2329 1798 214 513 1813 42 15 0 4.599 4.537 4.796 4.729 2.381 4.806 0.29 80 516 8650 11711 2.201 7105 1545 9596 2115 800287 186353 2.835 1.002 -50 0
237248 1 1 8 1 P:101 3950 9710 90 9892 11335 7392 460 1960 5133 75 44 0 1654 1931 1161 231 547 979 69 30 0 6.628 6.397 6.412 5.844 2.503 7.024 0.554 52 394 10855 12575 2.729 9432 1423 10875 1700 589415 100402 1.826 1.414 -50 0
237249 -3.733454772 1 1 9 1 P:105 4150 9690 110 14236 17381 11744 437 1484 4203 95 73 0 1479 1951 1448 225 434 779 62 48 0 11.004 9.817 10.691 10.416 2.176 9.549 0.592 80 600 15053 18670 3.46 13799 1254 16944 1726 1390452 156092 3.782 1.947 0 0
237250 -0.159551478 1 1 10 1 P:109 4350 9700 100 26663 26375 9171 444 984 2647 100 98 0 13584 13112 6110 231 328 474 100 100 0 1.964 2.013 2.138 2.177 1.749 2.079 0.695 80 493 39572 38812 0.973 26219 13353 25931 12881 2110001 1048973 9.592 26.97 0 0
237251 0.418963748 1 1 11 1 P:113 4540 9700 100 2152 2221 440 439 475 225 100 100 0 3974 4483 1940 236 258 158 100 100 0 0.458 0.42 0.437 0.448 1.43 0.306 0.689 80 492 5451 6029 -1.126 1713 3738 1782 4247 177706 358627 7.76 26.741 0 0
237252 1.633064829 1 1 12 1 P:117 4740 9700 100 1185 1263 441 425 434 105 100 100 0 3209 3652 1774 238 245 74 100 100 0 0.256 0.245 0.241 0.246 1.604 0.211 0.724 80 511 3731 4252 -1.967 760 2971 838 3414 101027 292192 7.895 46.041 0 0
237253 -1.518050959 1 1 13 1 P:193 4940 9690 110 1349 1381 273 417 434 114 100 100 0 514 546 136 238 242 58 100 98 0 3.377 3.13 3.287 3.265 1.55 3.46 0.581 80 580 1208 1272 1.756 932 276 964 308 110454 43693 8.307 5.241 0 0
237254 -1.3205388 1 1 14 1 P:197 5140 9690 110 691 719 181 420 431 118 85 60 0 349 357 74 235 239 44 90 66 0 2.377 2.451 2.48 2.276 2.464 4.237 0.3 80 570 385 421 1.249 271 114 299 122 57550 28582 2.441 2.682 0 0
237255 0.785727138 1 1 15 1 P:201 5330 9690 110 1917 2096 682 418 425 111 100 100 0 4586 4854 1327 238 244 60 100 100 0 0.345 0.364 0.352 0.354 1.407 0.305 0.735 80 570 5847 6294 -1.536 1499 4348 1678 4616 167653 388324 15.054 76.833 0 0
237256 0.167674053 1 1 16 1 P:205 5530 9700 100 3942 4256 1683 396 416 186 100 100 0 5003 5618 3080 231 246 137 100 98 0 0.743 0.717 0.7 0.805 2.287 0.604 0.677 80 509 8318 9247 -0.428 3546 4772 3860 5387 340440 449454 20.645 39.212 0 0
237257 1.790941149 1 1 17 1 P:209 5740 9700 100 667 739 261 347 361 121 91 65 0 1196 1366 714 209 216 81 100 100 0 0.324 0.339 0.352 0.327 2.001 0.244 0.467 80 490 1307 1549 -1.625 320 987 392 1157 59109 109265 3.124 14.198 0 0
237258 -1.832871791 1 1 18 1 P:213 5910 9690 100 5426 5498 1075 266 289 176 100 100 0 2347 2393 789 164 191 212 98 98 0 2.364 2.347 2.288 2.475 1.552 2.235 0.719 80 478 7343 7461 1.241 5160 2183 5232 2229 439856 191466 29.597 10.387 0 0
237259 1.039238221 1 1 19 1 P:289 6110 9690 110 3095 3396 1119 272 297 190 100 100 0 6809 8271 4514 168 219 414 100 100 0 0.425 0.386 0.43 0.417 1.589 0.312 0.748 80 568 9464 11227 -1.234 2823 6641 3124 8103 271643 661701 16.311 19.449 0 0
237260 0.057117088 1 1 20 1 P:293 6300 9680 90 4111 4816 2039 365 409 245 100 100 0 4906 5588 2517 205 271 592 100 100 0 0.797 0.827 0.901 0.845 1.426 0.874 0.695 52 400 8447 9834 -0.328 3746 4701 4451 5383 250417 290600 17.988 8.981 0 0

Total number of rows: 15488

Table truncated, full table size 3509 Kbytes.




Supplementary file Size Download File type/resource
GSM251839.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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