NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM251866 Query DataSets for GSM251866
Status Public on Dec 01, 2008
Title Human Prostate GSK-46
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-46 treated with 0.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-46. Specimen ID: GSK-46; Treatment: 0.5 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-46 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 1.241418355 1 1 1 1 P:1 2750 9260 140 1957 2117 962 384 453 823 86 41 0 4545 4950 2580 229 236 77 98 98 0 0.364 0.367 0.377 0.361 2.098 0.346 0.856 156 799 5889 6454 -1.456 1573 4316 1733 4721 330174 772147 2.022 61.221 0 0
237242 -1.908206753 1 1 2 1 P:5 2930 9250 120 19726 18148 7954 397 403 90 100 100 0 5545 5244 2156 235 238 50 100 98 0 3.64 3.544 3.476 3.667 1.802 3.84 0.842 120 565 24639 22760 1.864 19329 5310 17751 5009 2177714 629306 197.167 100.12 0 0
237243 -2.687011104 1 1 3 1 P:9 3120 9250 100 7147 7397 1738 397 403 91 100 100 0 1435 1526 392 237 236 42 100 100 0 5.634 5.431 5.552 5.504 1.434 5.985 0.751 80 452 7948 8289 2.494 6750 1198 7000 1289 591762 122119 76.857 30.714 0 0
237244 -0.382696439 1 1 4 1 P:13 3310 9250 120 1959 1931 523 391 395 92 99 97 0 1300 1332 461 234 237 45 99 97 0 1.471 1.403 1.469 1.449 1.863 1.387 0.766 120 635 2634 2638 0.557 1568 1066 1540 1098 231760 159844 16.696 24.333 0 0
237245 -0.586964041 1 1 5 1 P:17 3500 9250 110 2052 2042 353 399 406 100 100 100 0 1217 1226 278 235 243 66 100 98 0 1.683 1.658 1.658 1.698 1.457 1.533 0.729 80 543 2635 2634 0.751 1653 982 1643 991 163348 98062 16.36 14.894 0 0
237246 4.323069032 1 1 6 1 P:21 3710 9250 100 1103 1106 153 403 416 102 100 100 0 22100 22643 8438 245 257 71 100 100 0 0.032 0.031 0.034 0.033 1.488 0.025 0.677 80 486 22555 23101 -4.964 700 21855 703 22398 88465 1811474 6.765 315.296 0 0
237247 -1.068238408 1 1 7 1 P:97 3890 9240 100 23559 25033 11025 400 408 113 100 100 0 8815 8351 3644 244 269 191 98 97 0 2.702 3.038 3.196 3.302 1.853 3.19 0.847 80 490 31730 32740 1.434 23159 8571 24633 8107 2002662 668051 217.92 42.314 0 0
237248 0.375943339 1 1 8 1 P:101 4090 9240 100 1700 1872 1680 394 414 180 100 96 0 1705 1816 544 235 250 186 100 98 0 0.888 0.935 0.863 0.843 1.838 1.739 0.315 80 496 2776 3059 -0.171 1306 1470 1478 1581 149767 145278 8.1 8.419 0 0
237249 -1.50728006 1 1 9 1 P:105 4300 9240 120 24050 22875 8825 392 412 174 100 100 0 7293 7162 2602 233 237 64 100 100 0 3.351 3.245 3.465 3.083 1.855 3.493 0.848 120 608 30718 29412 1.745 23658 7060 22483 6929 2744947 859460 129.098 108.203 0 0
237250 -0.388082617 1 1 10 1 P:109 4470 9240 110 15531 16661 5803 401 414 120 100 100 0 10362 10659 3363 231 241 68 100 100 0 1.493 1.559 1.445 1.559 1.55 1.547 0.741 80 532 25261 26688 0.579 15130 10131 16260 10428 1332889 852721 135.392 153.206 0 0
237251 0.36211681 1 1 11 1 P:113 4680 9240 110 1733 1732 262 400 408 111 100 100 0 2196 2263 355 232 244 71 100 100 0 0.679 0.656 0.655 0.653 1.289 0.628 0.823 80 566 3297 3363 -0.559 1333 1964 1332 2031 138583 181056 11.928 28.437 0 0
237252 1.174105959 1 1 12 1 P:117 4870 9240 110 1489 1528 393 379 386 91 100 100 0 3114 3338 1480 239 242 45 100 100 0 0.386 0.371 0.419 0.386 1.615 0.307 0.688 80 568 3985 4248 -1.373 1110 2875 1149 3099 122210 267048 12.549 68.8 0 0
237253 0.111731117 1 1 13 1 P:193 5080 9240 120 819 825 212 354 360 86 95 93 0 571 582 141 233 244 157 95 57 0 1.376 1.35 1.36 1.335 2.013 1.391 0.496 120 640 803 820 0.46 465 338 471 349 99052 69816 5.407 2.153 0 0
237254 -0.107430382 1 1 14 1 P:197 5260 9240 110 760 776 151 353 359 91 98 96 0 479 492 91 238 249 171 85 17 0 1.689 1.665 1.672 1.65 1.548 0.801 0.165 80 526 648 677 0.756 407 241 423 254 62112 39365 4.582 1.421 0 0
237255 0.118027024 1 1 15 1 P:201 5460 9230 110 3236 3711 1496 329 357 397 100 100 0 4472 4751 1222 230 253 427 100 100 0 0.685 0.748 0.683 0.713 1.572 0.639 0.583 80 576 7149 7903 -0.545 2907 4242 3382 4521 296849 380082 8.448 10.534 0 0
237256 1.00822397 1 1 16 1 P:205 5660 9240 110 1405 1408 542 322 328 82 100 100 0 2805 3397 2508 220 225 67 100 100 0 0.419 0.342 0.424 0.393 1.744 0.248 0.635 80 558 3668 4263 -1.255 1083 2585 1086 3177 112602 271733 13.171 47.343 0 0
237257 1.35388953 1 1 17 1 P:209 5850 9230 100 848 889 169 334 339 80 100 100 0 1547 1650 380 232 234 39 100 100 0 0.391 0.391 0.399 0.385 1.412 0.324 0.618 80 502 1829 1973 -1.355 514 1315 555 1418 71102 131989 6.875 36.308 0 0
237258 -0.492331891 1 1 18 1 P:213 6040 9230 110 4054 4215 934 331 340 87 100 100 0 4082 4182 822 238 243 61 100 100 0 0.969 0.985 1.018 0.978 1.411 0.934 0.746 80 556 7567 7828 -0.046 3723 3844 3884 3944 337197 334544 44.54 64.574 0 0
237259 0.856382041 1 1 19 1 P:289 6240 9230 130 1147 1183 316 341 348 89 99 99 0 1623 1778 559 243 250 104 100 100 0 0.584 0.549 0.519 0.536 1.555 0.53 0.686 120 706 2186 2377 -0.776 806 1380 842 1535 141952 213396 9.382 14.692 0 0
237260 0.414982604 1 1 20 1 P:293 6430 9230 100 2304 2421 722 353 358 92 100 100 0 3206 3364 1131 248 251 42 100 100 0 0.66 0.664 0.722 0.665 1.614 0.612 0.655 80 487 4909 5184 -0.6 1951 2958 2068 3116 193700 269143 22.424 74.119 0 0

Total number of rows: 15488

Table truncated, full table size 3506 Kbytes.




Supplementary file Size Download File type/resource
GSM251866.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