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Sample GSM251872 Query DataSets for GSM251872
Status Public on Dec 01, 2008
Title Human Prostate GSK-25
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-25 treated with Immediate Radical Prostatectomy
Organism Homo sapiens
Characteristics Human Prostate GSK-25. Specimen ID: GSK-25; 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-25 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 -0.017666918 1 1 1 1 P:1 3000 9680 120 2798 2772 443 1036 1082 489 100 95 0 1578 1706 503 303 322 251 100 99 0 1.382 1.237 1.297 1.274 1.589 1.375 0.644 120 675 3037 3139 0.467 1762 1275 1736 1403 332623 204669 3.456 5.514 0 0
237242 -4.541372066 1 1 2 1 P:5 3190 9680 120 15077 18260 9335 1099 1118 205 100 100 0 1655 1781 553 312 316 49 100 100 0 10.408 11.682 10.978 10.819 1.515 13.797 0.839 120 621 15321 18630 3.38 13978 1343 17161 1469 2191150 213737 83.62 29.898 0 0
237243 -2.606023745 1 1 3 1 P:9 3380 9680 110 6134 6314 1613 1121 1122 166 100 100 0 1007 1007 158 317 322 50 100 100 0 7.265 7.526 7.278 7.356 1.282 8.083 0.851 80 520 5703 5883 2.861 5013 690 5193 690 505158 80563 31.277 13.7 0 0
237244 -0.968929687 1 1 4 1 P:13 3580 9680 120 2721 2751 483 1100 1102 173 100 100 0 921 918 176 314 318 54 100 100 0 2.671 2.733 2.777 2.741 1.375 2.96 0.827 120 614 2228 2255 1.417 1621 607 1651 604 330093 110103 9.532 11.111 0 0
237245 -1.006526952 1 1 5 1 P:17 3770 9680 120 2745 2796 549 1044 1055 186 100 98 0 897 891 195 300 308 65 97 96 0 2.849 2.964 2.925 3.039 1.52 3.121 0.799 120 594 2298 2343 1.511 1701 597 1752 591 335505 106951 9.36 8.969 0 0
237246 2.669723673 1 1 6 1 P:21 3970 9680 120 1547 1525 406 1036 1040 154 77 66 0 2410 2726 1083 293 295 48 100 100 0 0.241 0.201 0.278 0.235 2.592 0.118 0.172 120 559 2628 2922 -2.051 511 2117 489 2433 182990 327092 3.149 50.646 0 0
237247 1 1 7 1 P:97 4150 9670 140 1015 1012 171 1098 1105 167 5 0 0 288 301 70 303 308 62 8 2 0 5.533 43 5.071 3.638 3.985 27.206 0.006 156 731 -98 -88 2.468 -83 -15 -86 -2 157838 46902 -0.557 -0.113 -50 0
237248 -1.473791534 1 1 8 1 P:101 4350 9680 80 2563 2592 348 1173 1190 181 100 100 0 595 619 97 318 326 71 100 98 0 5.018 4.714 4.592 4.781 1.516 5.426 0.623 52 322 1667 1720 2.327 1390 277 1419 301 134799 32210 7.746 4.127 0 0
237249 -1.778354016 1 1 9 1 P:105 4540 9680 120 15402 14796 3634 1170 1186 181 100 100 0 5245 5084 1758 321 328 51 100 100 0 2.89 2.861 2.92 2.998 1.353 2.817 0.916 120 676 19156 18389 1.531 14232 4924 13626 4763 1775569 610032 75.193 93.255 0 0
237250 -2.653957333 1 1 10 1 P:109 4740 9670 110 8584 9646 3573 1204 1229 290 100 100 0 2731 2985 1110 322 342 241 100 100 0 3.064 3.17 3.1 3.164 1.396 3.281 0.78 80 549 9789 11105 1.615 7380 2409 8442 2663 771678 238832 29.024 10.967 0 0
237251 0.216763766 1 1 11 1 P:113 4930 9680 120 2140 2225 484 1201 1219 271 95 85 0 1166 1156 221 323 342 225 97 95 0 1.114 1.229 1.185 1.114 1.843 1.462 0.701 120 641 1782 1857 0.156 939 843 1024 833 266951 138752 3.712 3.618 0 0
237252 0.963248602 1 1 12 1 P:117 5130 9670 100 2279 2259 407 1200 1205 176 95 95 0 1770 2100 909 322 327 53 100 100 0 0.745 0.596 0.629 0.629 1.945 0.406 0.487 80 476 2527 2837 -0.424 1079 1448 1059 1778 180733 168006 5.989 33.453 0 0
237253 -0.610317337 1 1 13 1 P:193 5320 9680 120 2216 2257 584 1163 1160 179 92 89 0 700 728 151 313 318 52 98 97 0 2.721 2.636 2.902 2.304 2.311 3.518 0.603 120 655 1440 1509 1.444 1053 387 1094 415 270816 87386 6.128 7.885 0 0
237254 -1.864469175 1 1 14 1 P:197 5520 9680 100 2521 2643 470 1134 1140 174 100 100 0 477 503 110 308 315 52 91 80 0 8.207 7.738 8.643 8.696 1.948 8.831 0.464 80 478 1556 1704 3.037 1387 169 1509 195 211468 40267 8.638 3.615 0 0
237255 -1.926081626 1 1 15 1 P:201 5710 9680 120 4587 5456 2536 1207 1210 174 100 99 0 966 1009 353 317 321 50 97 95 0 5.208 6.14 6.044 6.213 1.754 7.025 0.793 120 566 4029 4941 2.381 3380 649 4249 692 654667 121095 24.402 13.76 0 0
237256 1 1 16 1 P:205 5900 9670 140 1240 1240 165 1213 1222 169 19 3 0 314 316 46 317 320 53 12 0 0 -9 -27 3.806 3.916 3.359 54.863 0.003 156 724 24 26 Error 27 -3 27 -1 193406 49358 0.107 -0.075 -50 0
237257 0.3959366 1 1 17 1 P:209 6100 9670 110 2337 2312 294 1200 1213 174 100 100 0 1331 1345 276 318 330 119 100 100 0 1.122 1.083 1.07 1.081 1.423 1.002 0.638 80 538 2150 2139 0.167 1137 1013 1112 1027 184921 107631 6.316 8.529 0 0
237258 -0.779749228 1 1 18 1 P:213 6290 9670 100 4648 4809 750 1197 1229 266 100 100 0 2311 2401 584 322 362 287 100 98 0 1.735 1.737 1.75 1.778 1.288 1.713 0.858 80 500 5440 5691 0.795 3451 1989 3612 2079 384732 192043 13.459 7.105 0 0
237259 0.762285791 1 1 19 1 P:289 6500 9670 130 2151 2294 735 1196 1218 248 94 81 0 1438 1711 1026 317 342 225 100 98 0 0.852 0.788 0.975 0.738 2.677 0.62 0.249 120 740 2076 2492 -0.231 955 1121 1098 1394 275329 205323 4.339 6.084 0 0
237260 -0.8769465 1 1 20 1 P:293 6710 9680 110 3501 3620 917 1239 1242 195 100 100 0 1221 1300 446 319 327 70 100 100 0 2.508 2.427 2.784 2.447 1.794 2.548 0.727 80 521 3164 3362 1.326 2262 902 2381 981 289597 104033 12.195 13.9 0 0

Total number of rows: 15488

Table truncated, full table size 3501 Kbytes.




Supplementary file Size Download File type/resource
GSM251872.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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