NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM251836 Query DataSets for GSM251836
Status Public on Dec 01, 2008
Title Human Prostate GSK-2
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-2 treated with 3.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-2. Specimen ID: GSK-2; 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-2 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 0.007678185 1 1 1 1 P:1 2760 9640 110 1506 1534 487 382 554 2224 3 0 0 1001 998 408 165 180 186 95 83 0 1.344 1.383 1.494 1.453 1.565 1.422 0.74 80 604 1960 1985 0.427 1124 836 1152 833 122716 79827 0.441 4.398 0 0
237242 -3.695647091 1 1 2 1 P:5 2960 9640 100 22611 22643 8515 499 525 197 100 100 0 1630 1571 576 193 201 87 100 100 0 15.388 16.07 16.295 16.722 1.5 16.935 0.803 80 484 23549 23522 3.944 22112 1437 22144 1378 1811422 125692 112.274 15.747 0 0
237243 -3.313804399 1 1 3 1 P:9 3130 9640 100 8254 8063 3345 504 525 146 100 100 0 867 826 328 207 219 70 93 88 0 11.742 12.212 12.517 12.858 1.569 12.544 0.827 80 471 8410 8178 3.554 7750 660 7559 619 645021 66065 51.63 8.671 0 0
237244 -1.38547536 1 1 4 1 P:13 3330 9650 110 1150 1102 305 478 488 127 92 82 0 370 361 93 199 204 42 86 78 0 3.93 3.852 3.872 3.763 1.983 3.9 0.494 80 558 843 786 1.974 672 171 624 162 88172 28874 4.835 3.738 0 0
237245 -0.94540571 1 1 5 1 P:17 3520 9650 100 1028 1025 297 479 492 132 90 81 0 385 377 108 196 213 91 76 52 0 2.905 3.017 2.886 3.062 1.985 3.478 0.617 80 492 738 727 1.538 549 189 546 181 81998 30129 4.038 1.802 0 0
237246 5.026049309 1 1 6 1 P:21 3720 9650 100 1060 1038 228 481 489 117 97 95 0 14183 13029 6105 198 212 90 100 100 0 0.041 0.043 0.045 0.047 1.719 0.035 0.651 80 482 14564 13388 -4.594 579 13985 557 12831 83019 1042323 4.692 142.411 0 0
237247 -2.945321865 1 1 7 1 P:97 3900 9640 100 33186 32394 14414 463 481 146 100 100 0 2895 2664 1306 193 196 43 100 100 0 12.111 12.922 12.518 13.583 1.683 12.81 0.824 80 492 35425 34402 3.598 32723 2702 31931 2471 2591502 213111 218.582 57.395 0 0
237248 -2.370527624 1 1 8 1 P:101 4100 9640 100 2026 2566 1267 442 477 192 100 100 0 444 459 144 192 195 40 97 92 0 6.286 7.955 8.1 7.785 1.585 9.414 0.712 80 518 1836 2391 2.652 1584 252 2124 267 205265 36703 10.88 6.6 0 0
237249 -3.4115233 1 1 9 1 P:105 4310 9650 100 38622 38285 18168 446 490 222 100 100 5 2478 2583 1182 191 195 40 100 100 0 16.693 15.819 15.81 16.311 1.608 16.968 0.848 80 518 40463 40231 4.061 38176 2287 37839 2392 3062804 206647 170.248 59.7 0 0
237250 -0.629429924 1 1 10 1 P:109 4510 9650 100 31562 30322 12507 444 468 145 100 100 0 8842 8645 4740 194 201 48 100 100 0 3.598 3.535 3.669 4.109 1.954 3.524 0.834 80 470 39766 38329 1.847 31118 8648 29878 8451 2425798 691610 205.89 175.917 0 0
237251 0.283748164 1 1 11 1 P:113 4680 9650 100 3477 3391 1311 407 449 278 100 100 0 2981 2918 1643 189 209 180 100 93 0 1.1 1.093 1.128 1.254 1.666 0.986 0.827 80 484 5862 5713 0.137 3070 2792 2984 2729 271286 233471 10.583 15.05 0 0
237252 1.804882746 1 1 12 1 P:117 4900 9640 100 1894 2093 1141 392 428 273 96 86 0 4716 6655 6632 178 200 194 100 100 0 0.331 0.263 0.312 0.298 1.639 0.186 0.688 80 504 6040 8178 -1.595 1502 4538 1701 6477 167432 532428 6.099 33.273 0 0
237253 -2.029186329 1 1 13 1 P:193 5070 9650 100 1355 1417 545 399 412 103 100 96 0 353 382 149 178 182 35 100 92 0 5.463 4.99 5.493 5.168 1.642 5.043 0.682 80 488 1131 1222 2.45 956 175 1018 204 113375 30538 9.757 5.714 0 0
237254 -1.891383 1 1 14 1 P:197 5280 9650 100 577 582 133 389 403 111 75 38 0 217 221 51 175 178 36 53 28 0 4.476 4.196 3.457 3.564 3.078 6.958 0.137 80 500 230 239 2.162 188 42 193 46 46560 17662 1.613 1.194 0 0
237255 -1.064294295 1 1 15 1 P:201 5460 9650 100 6183 6104 2600 385 403 128 100 100 0 2458 2492 1332 172 180 89 100 100 0 2.536 2.465 2.705 2.774 1.616 2.373 0.87 80 500 8084 8039 1.343 5798 2286 5719 2320 488298 199323 44.539 25.978 0 0
237256 0.73446494 1 1 16 1 P:205 5670 9650 100 3506 3806 1986 383 391 96 100 100 0 4024 4073 2184 178 182 47 100 100 0 0.812 0.879 0.929 0.902 1.571 0.862 0.834 80 526 6969 7318 -0.3 3123 3846 3423 3895 304509 325817 35.573 82.787 0 0
237257 0.994206784 1 1 17 1 P:209 5880 9660 110 495 489 108 375 382 98 53 26 0 349 338 98 173 180 43 87 75 0 0.682 0.691 0.811 0.691 2.607 1.777 0.205 80 514 296 279 -0.553 120 176 114 165 39119 27014 1.092 3.674 0 0
237258 -1.954915958 1 1 18 1 P:213 6030 9660 100 5055 4882 1946 391 418 142 100 100 0 882 879 392 174 189 82 95 87 0 6.588 6.37 6.727 7.259 1.827 6.311 0.825 80 460 5372 5196 2.72 4664 708 4491 705 390579 70293 31.437 8.415 0 0
237259 0.398170296 1 1 19 1 P:289 6240 9660 100 4700 4328 1802 387 402 131 100 98 0 5711 5424 2724 174 189 83 100 100 0 0.779 0.751 0.763 0.805 1.581 0.71 0.888 80 516 9850 9191 -0.36 4313 5537 3941 5250 346275 433911 29.969 63.072 0 0
237260 -0.64015277 1 1 20 1 P:293 6450 9660 110 5167 4676 2139 376 394 129 100 100 0 2350 2220 1070 170 176 44 100 100 0 2.198 2.098 2.184 2.201 1.589 2.291 0.796 80 566 6971 6350 1.136 4791 2180 4300 2050 374098 177621 33.194 46.455 0 0

Total number of rows: 15488

Table truncated, full table size 3501 Kbytes.




Supplementary file Size Download File type/resource
GSM251836.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap