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Sample GSM251851 Query DataSets for GSM251851
Status Public on Dec 01, 2008
Title Human Prostate GSK-58
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-58 treated with Immediate Radical Prostatectomy
Organism Homo sapiens
Characteristics Human Prostate GSK-58. Specimen ID: GSK-58; Treatment: Immediate Radical Prostatectomy; 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-58 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 1.724231633 1 1 1 1 P:1 2240 9650 120 1740 1678 663 462 929 4509 0 0 0 2630 2652 1208 251 278 208 100 97 0 0.537 0.506 0.517 0.485 2.071 0.443 0.651 120 663 3657 3617 -0.896 1278 2379 1216 2401 201357 318262 0.166 11.413 0 0
237242 -3.088445175 1 1 2 1 P:5 2410 9640 110 19227 17782 6612 492 1315 5151 96 83 0 1442 1384 538 263 337 367 88 80 0 15.891 15.424 15.421 15.226 1.852 21.168 0.662 80 514 19914 18411 3.99 18735 1179 17290 1121 1422558 110752 3.197 2.853 0 0
237243 -2.714932679 1 1 3 1 P:9 2600 9640 110 7839 7221 3278 487 1254 4815 72 20 0 821 792 250 273 341 342 72 25 0 13.416 12.975 13.074 12.303 1.775 15.387 0.643 80 552 7900 7253 3.746 7352 548 6734 519 577641 63360 1.239 1.319 0 0
237244 -0.752689302 1 1 4 1 P:13 2800 9650 120 1792 1787 822 484 572 748 74 37 0 767 768 361 268 331 606 29 4 0 2.621 2.606 2.585 2.605 2.295 2.771 0.562 120 636 1807 1803 1.39 1308 499 1303 500 214442 92180 1.624 0.721 0 0
237245 -0.639680002 1 1 5 1 P:17 3000 9640 120 2183 2096 1081 483 497 108 96 90 0 859 828 364 267 282 105 85 79 0 2.872 2.875 2.78 2.924 2.101 3.16 0.683 120 615 2292 2174 1.522 1700 592 1613 561 251525 99333 14.806 5.2 0 0
237246 2.447754531 1 1 6 1 P:21 3190 9640 110 1323 1317 402 496 507 103 98 93 0 3002 3187 1908 273 298 170 100 98 0 0.303 0.282 0.287 0.317 1.978 0.22 0.62 80 506 3556 3735 -1.722 827 2729 821 2914 105381 254936 7.864 16.994 0 0
237247 -2.344748348 1 1 7 1 P:97 3380 9640 120 12989 14437 8975 502 509 91 100 100 0 1541 1634 922 267 288 151 90 85 0 9.801 10.194 10.89 10.152 2.422 12.522 0.618 120 634 13761 15302 3.293 12487 1274 13935 1367 1732442 196068 153.055 8.914 0 0
237248 -1.051539093 1 1 8 1 P:101 3580 9640 100 2532 3032 1560 518 527 98 100 100 0 788 916 339 271 282 78 100 98 0 3.896 3.898 3.527 3.69 1.725 4.731 0.644 80 464 2531 3159 1.962 2014 517 2514 645 242550 73277 25.561 8.128 0 0
237249 -2.734973742 1 1 9 1 P:105 3770 9650 120 17059 16418 8567 514 523 95 100 100 0 1599 1579 677 274 287 84 95 95 0 12.487 12.187 11.79 11.721 2.135 13.975 0.746 120 620 17870 17209 3.642 16545 1325 15904 1305 1970151 189482 167.316 15.381 0 0
237250 -3.091548722 1 1 10 1 P:109 3970 9630 110 23572 25269 12657 520 630 1398 100 100 0 1905 2123 1572 277 313 211 95 88 0 14.16 13.407 14.346 14.567 1.879 15.247 0.601 80 536 24680 26595 3.824 23052 1628 24749 1846 2021535 169820 17.624 8.578 0 0
237251 -0.368284284 1 1 11 1 P:113 4160 9640 120 2827 2760 979 529 658 1377 77 29 0 1362 1331 493 291 363 570 80 42 0 2.146 2.145 2.202 2.135 1.993 2.269 0.781 120 667 3369 3271 1.101 2298 1071 2231 1040 331162 159749 1.527 1.698 0 0
237252 2.37687879 1 1 12 1 P:117 4370 9640 110 1538 1589 548 534 589 638 76 31 0 3200 3385 1835 290 332 284 100 92 0 0.345 0.341 0.403 0.345 1.9 0.346 0.251 80 543 3914 4150 -1.535 1004 2910 1055 3095 127113 270784 1.567 10.75 0 0
237253 -1.062199141 1 1 13 1 P:193 4540 9630 110 1649 1598 445 540 558 135 100 97 0 620 621 191 284 305 106 90 75 0 3.301 3.139 3.312 3.294 1.756 3.271 0.625 80 517 1445 1395 1.723 1109 336 1058 337 127840 49718 7.704 2.981 0 0
237254 1 1 14 1 P:197 4740 9630 140 626 642 119 560 582 140 30 5 0 327 345 98 287 314 114 21 8 0 1.65 1.414 1.759 1.638 3.921 1.879 0.098 156 761 106 140 0.722 66 40 82 58 100165 53754 0.429 0.272 -50 0
237255 -1.999247283 1 1 15 1 P:201 4940 9630 120 6103 6623 3383 579 587 99 100 99 0 991 1065 444 298 313 88 96 94 0 7.971 7.88 7.373 7.919 1.836 9.236 0.704 120 603 6217 6811 2.995 5524 693 6044 767 794757 127787 60.97 8.545 0 0
237256 -2.062498494 1 1 16 1 P:205 5130 9630 100 3889 4220 1904 583 589 93 100 100 0 726 803 299 311 326 95 95 86 0 7.966 7.392 7.377 7.978 1.938 8.112 0.629 80 475 3721 4129 2.994 3306 415 3637 492 337572 64257 39.043 5.021 0 0
237257 1.308318932 1 1 17 1 P:209 5330 9640 110 710 737 124 583 600 181 42 3 0 560 632 366 311 331 109 78 58 0 0.51 0.48 0.575 0.611 3.484 0.147 0.174 80 553 376 475 -0.971 127 249 154 321 58991 50547 0.757 2.761 0 0
237258 -1.570605137 1 1 18 1 P:213 5520 9630 110 4077 3908 1480 587 603 197 100 100 0 1009 1001 345 306 331 151 93 85 0 4.964 4.778 5.152 4.888 1.623 5.048 0.665 80 576 4193 4016 2.312 3490 703 3321 695 312633 80099 16.777 4.437 0 0
237259 0.634555168 1 1 19 1 P:289 5730 9630 120 4350 4729 2714 589 611 215 97 95 0 3512 4187 2760 307 329 142 98 97 0 1.173 1.067 1.008 1.057 2.072 1.037 0.808 120 651 6966 8020 0.231 3761 3205 4140 3880 567525 502498 19.153 27.169 0 0
237260 -0.870306558 1 1 20 1 P:293 5920 9630 110 8721 8556 4246 607 645 265 100 100 0 2677 2549 1097 326 338 95 100 100 0 3.451 3.576 3.714 3.536 1.623 4.071 0.771 80 524 10465 10172 1.787 8114 2351 7949 2223 684512 203917 29.853 23.274 0 0

Total number of rows: 15488

Table truncated, full table size 3506 Kbytes.




Supplementary file Size Download File type/resource
GSM251851.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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