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Sample GSM251831 Query DataSets for GSM251831
Status Public on Dec 01, 2008
Title Human Prostate GSK-3
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-3 treated with Immediate Radical Prostatectomy
Organism Homo sapiens
Characteristics Human Prostate GSK-3. Specimen ID: GSK-3; 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-3 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 0.353874516 1 1 1 1 P:1 2340 9130 110 2753 2831 1189 384 536 694 96 81 0 2366 2418 1145 87 121 365 100 92 0 1.039 1.05 1.045 1.071 1.462 0.993 0.54 80 562 4648 4778 0.056 2369 2279 2447 2331 226460 193479 3.307 6.293 0 0
237242 -2.722080077 1 1 2 1 P:5 2530 9130 120 21998 20777 9877 453 683 1029 100 98 0 2656 2614 1511 90 109 85 97 93 0 8.396 8.052 8.961 9.359 2.064 8.562 0.754 120 641 24111 22848 3.07 21545 2566 20324 2524 2493253 313737 19.528 29.471 0 0
237243 -3.133359096 1 1 3 1 P:9 2730 9130 110 14455 14608 6431 452 556 520 100 100 0 1294 1379 654 90 155 1156 55 8 0 11.63 10.982 10.988 11.414 1.468 10.945 0.789 80 544 15207 15445 3.54 14003 1204 14156 1289 1168647 110326 27.023 1.059 0 0
237244 -0.605330677 1 1 4 1 P:13 2920 9120 110 1677 1706 533 404 487 890 78 15 0 520 551 233 90 196 1248 0 0 0 2.96 2.824 2.589 2.924 1.687 0.372 0.025 80 543 1703 1763 1.566 1273 430 1302 461 136519 44103 1.37 0.284 0 0
237245 -0.359259886 1 1 5 1 P:17 3110 9120 110 1643 1640 459 399 469 433 95 83 0 595 569 229 89 179 608 30 0 0 2.458 2.585 2.332 2.752 1.817 2.699 0.714 80 553 1750 1721 1.298 1244 506 1241 480 131203 45493 2.704 0.641 0 0
237246 3.944325768 1 1 6 1 P:21 3310 9110 110 1841 1937 540 397 459 561 100 76 0 20208 20866 10892 90 173 600 100 100 0 0.072 0.074 0.075 0.082 1.717 0.057 0.718 80 570 21562 22316 -3.8 1444 20118 1540 20776 154967 1669309 2.635 34.488 0 0
237247 -2.822546393 1 1 7 1 P:97 3500 9110 100 51078 47959 17522 414 497 618 100 100 22 4385 4084 2373 90 101 77 100 97 0 11.796 11.904 11.281 14.277 1.922 11.092 0.79 80 488 54959 51539 3.56 50664 4295 47545 3994 3836714 326724 76.799 51.727 0 0
237248 -1.223563552 1 1 8 1 P:101 3700 9110 100 2977 3184 1328 417 602 1021 97 68 0 696 779 334 89 99 54 100 100 0 4.217 4.01 3.74 3.98 1.666 5.183 0.567 80 474 3167 3457 2.076 2560 607 2767 690 254695 62334 2.529 12.593 0 0
237249 -3.918309587 1 1 9 1 P:105 3890 9100 110 40106 38063 17590 444 733 1395 100 100 7 2340 2496 1527 92 126 267 93 86 0 17.643 15.649 15.934 18.136 1.677 14.491 0.824 80 570 41910 40023 4.141 39662 2248 37619 2404 3045051 199649 26.76 8.876 0 0
237250 -1.381325162 1 1 10 1 P:109 4090 9100 110 54509 49809 15989 450 615 991 100 100 17 12021 11571 5734 95 132 263 100 100 0 4.533 4.301 4.086 4.771 1.743 4.214 0.784 80 538 65985 60835 2.18 54059 11926 49359 11476 3984689 925676 49.641 43.494 0 0
237251 0.322397991 1 1 11 1 P:113 4270 9100 120 4487 4385 1927 397 454 342 98 97 0 3611 3717 2224 94 125 294 99 99 0 1.163 1.101 1.118 1.164 1.914 1.018 0.758 120 623 7607 7611 0.218 4090 3517 3988 3623 526248 446024 11.494 12.218 0 0
237252 1.371367885 1 1 12 1 P:117 4480 9100 110 1995 2438 1140 397 430 225 100 100 0 3179 4770 3345 94 109 138 100 100 0 0.518 0.436 0.475 0.486 1.573 0.364 0.839 80 569 4683 6717 -0.949 1598 3085 2041 4676 195075 381601 8.924 33.775 0 0
237253 -1.291969038 1 1 13 1 P:193 4690 9100 100 3500 3851 1761 404 436 228 100 100 0 832 995 704 90 102 100 100 100 0 4.173 3.809 4.14 4.108 1.492 4.008 0.625 80 500 3838 4352 2.061 3096 742 3447 905 308110 79594 14.978 8.93 0 0
237254 -1.009378272 1 1 14 1 P:197 4880 9100 100 1309 1344 389 390 403 109 100 100 0 309 323 103 92 96 24 100 100 0 4.235 4.13 4.02 4.146 1.547 4.701 0.694 80 474 1136 1185 2.082 919 217 954 231 107508 25854 8.633 9.458 0 0
237255 0.633954903 1 1 15 1 P:201 5060 9090 110 2888 3246 1607 419 435 131 100 100 0 2835 3676 2793 101 144 274 100 97 0 0.903 0.791 0.763 0.883 1.671 0.667 0.805 80 576 5203 6402 -0.147 2469 2734 2827 3575 259673 294105 21.458 12.891 0 0
237256 1.168952875 1 1 16 1 P:205 5270 9090 100 3243 3511 1572 430 450 125 100 100 0 4133 5315 3482 102 134 230 96 95 0 0.698 0.591 0.612 0.718 3.005 0.421 0.459 80 511 6844 8294 -0.519 2813 4031 3081 5213 280889 425199 24.488 22.526 0 0
237257 0.965332302 1 1 17 1 P:209 5460 9090 100 1002 1025 249 451 478 173 96 75 0 640 670 265 105 114 49 100 98 0 1.03 1.016 1.082 1.028 1.759 0.974 0.6 80 502 1086 1139 0.043 551 535 574 565 81981 53620 3.162 11.347 0 0
237258 -1.859126241 1 1 18 1 P:213 5660 9090 100 9645 9764 3049 482 522 271 100 100 0 2420 2448 863 114 129 122 100 100 0 3.974 3.977 3.956 4.043 1.419 4.099 0.804 80 488 11469 11616 1.99 9163 2306 9282 2334 781138 195854 34.103 19.008 0 0
237259 0.650126692 1 1 19 1 P:289 5850 9080 110 7772 7452 2197 507 529 230 100 100 0 9698 10254 5368 119 129 109 100 100 0 0.758 0.685 0.723 0.772 1.574 0.588 0.826 80 570 16844 17080 -0.399 7265 9579 6945 10135 596136 820283 30.1 92.89 0 0
237260 0.373114072 1 1 20 1 P:293 6050 9080 100 6986 7682 2977 527 573 386 100 100 0 6351 6154 3277 124 130 38 100 100 0 1.037 1.187 1.273 1.315 1.896 1.251 0.573 80 502 12686 13185 0.053 6459 6227 7155 6030 614525 492296 18.417 158.526 0 0

Total number of rows: 15488

Table truncated, full table size 3548 Kbytes.




Supplementary file Size Download File type/resource
GSM251831.gpr.gz 1.4 Mb (ftp)(http) GPR
Processed data included within Sample table
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