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Sample GSM251857 Query DataSets for GSM251857
Status Public on Dec 01, 2008
Title Human Prostate GSK-36
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-36 treated with 3.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-36. Specimen ID: GSK-36; 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-36 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 -0.008029404 1 1 1 1 P:1 2480 9670 140 2696 2759 976 587 596 146 100 100 0 1806 1938 876 163 171 75 100 100 0 1.284 1.224 1.255 1.268 1.337 1.11 0.832 156 712 3752 3947 0.36 2109 1643 2172 1775 430409 302269 14.815 23.56 0 0
237242 -2.801768082 1 1 2 1 P:5 2680 9670 150 20180 22366 12275 618 664 268 100 100 0 3041 2893 1649 168 181 88 99 97 0 6.809 7.981 8.467 8.443 1.649 8.451 0.805 156 657 22435 24473 2.767 19562 2873 21748 2725 3489056 451334 80.978 30.818 0 0
237243 -2.135993063 1 1 3 1 P:9 2870 9680 120 6501 7008 3056 630 677 244 100 100 0 1440 1374 579 174 185 60 99 97 0 4.637 5.315 5.808 5.662 1.621 5.692 0.844 120 570 7137 7578 2.213 5871 1266 6378 1200 840924 164934 25.947 19.817 0 0
237244 -0.641529242 1 1 4 1 P:13 3050 9680 110 2586 2572 566 626 652 161 100 100 0 1120 1279 641 175 194 114 100 98 0 2.074 1.763 1.928 1.904 1.473 1.571 0.715 80 520 2905 3050 1.052 1960 945 1946 1104 205797 102329 11.925 9.518 0 0
237245 -0.515018004 1 1 5 1 P:17 3250 9680 120 2303 2243 496 608 623 141 100 100 0 1113 1189 464 174 204 156 100 94 0 1.805 1.611 1.856 1.686 1.543 1.568 0.75 120 653 2634 2650 0.852 1695 939 1635 1015 269150 142702 11.489 6.314 0 0
237246 4.040867889 1 1 6 1 P:21 3450 9680 110 1270 1277 186 638 882 962 2 0 0 9496 9000 2609 180 284 347 100 100 0 0.068 0.072 0.071 0.073 1.471 0.056 0.138 80 556 9948 9459 -3.882 632 9316 639 8820 102165 719985 0.411 25.118 0 0
237247 0.381417279 1 1 7 1 P:97 3640 9680 100 24615 26484 11146 660 944 1034 100 98 0 12448 12855 5536 177 262 338 100 98 0 1.952 2.037 2.304 2.097 1.694 2.179 0.647 80 500 36226 38502 0.965 23955 12271 25824 12678 2118680 1028412 24.7 37.257 0 0
237248 -0.378081502 1 1 8 1 P:101 3840 9680 100 2949 3023 872 656 719 306 100 95 0 1365 1324 464 179 190 65 100 100 0 1.933 2.067 2.195 2.095 1.459 2.129 0.825 80 461 3479 3512 0.951 2293 1186 2367 1145 241852 105934 7.529 17.446 0 0
237249 -1.252996969 1 1 9 1 P:105 4030 9670 130 34250 32201 11571 646 816 737 99 99 0 6715 6681 3393 179 210 258 98 93 0 5.141 4.853 5.314 5.467 1.578 4.666 0.821 120 646 40140 38057 2.362 33604 6536 31555 6502 3864159 801727 42.585 25.081 0 0
237250 -0.354511317 1 1 10 1 P:109 4220 9670 120 18258 17736 7362 622 766 742 100 100 0 8277 7656 3590 179 211 270 100 100 0 2.178 2.289 2.439 2.463 1.599 2.308 0.859 120 604 25734 24591 1.123 17636 8098 17114 7477 2128323 918761 22.871 27.574 0 0
237251 0.615940544 1 1 11 1 P:113 4410 9670 120 2869 3054 878 601 615 172 100 100 0 3453 3321 938 176 189 72 100 100 0 0.692 0.78 0.708 0.794 1.6 0.767 0.818 120 637 5545 5598 -0.531 2268 3277 2453 3145 366449 398526 14.18 43.5 0 0
237252 1.725826473 1 1 12 1 P:117 4620 9670 110 1965 1964 383 579 593 120 100 100 0 4227 4243 1372 177 186 61 100 100 0 0.342 0.341 0.337 0.347 1.309 0.324 0.854 80 537 5436 5451 -1.547 1386 4050 1385 4066 157156 339462 11.425 66.508 0 0
237253 -0.929789577 1 1 13 1 P:193 4800 9660 130 2029 2023 490 575 584 136 100 100 0 859 893 290 178 181 38 99 99 0 2.135 2.025 1.954 2.112 1.697 2.232 0.709 120 660 2135 2163 1.094 1454 681 1448 715 242740 107108 10.581 18.737 0 0
237254 -0.721300091 1 1 14 1 P:197 5010 9670 100 1265 1272 210 569 574 126 100 100 0 477 484 84 177 207 580 0 0 0 2.32 2.29 2.258 2.272 1.428 0.227 0.129 80 460 996 1010 1.214 696 300 703 307 101767 38694 5.54 0.478 0 0
237255 -2.505565383 1 1 15 1 P:201 5190 9670 120 10006 10010 3676 565 574 120 100 100 0 2249 2284 920 179 204 512 92 86 0 4.561 4.487 4.781 4.699 1.558 4.75 0.621 120 590 11511 11550 2.189 9441 2070 9445 2105 1201254 274075 78.633 4.063 0 0
237256 0.126411126 1 1 16 1 P:205 5390 9670 120 3659 3771 1697 565 573 89 100 100 0 3495 3577 2268 179 184 53 99 98 0 0.933 0.943 0.983 1.137 1.914 0.865 0.888 120 629 6410 6604 -0.1 3094 3316 3206 3398 452575 429257 35.933 64.019 0 0
237257 0.039924185 1 1 17 1 P:209 5590 9650 110 1772 1795 194 573 581 97 100 100 0 1234 1283 330 181 185 48 100 100 0 1.139 1.109 1.092 1.142 1.36 0.971 0.748 80 575 2252 2324 0.187 1199 1053 1222 1102 143632 102660 12.515 22.875 0 0
237258 -1.055095928 1 1 18 1 P:213 5780 9660 110 6104 6031 1167 583 630 897 100 100 0 3279 3344 623 181 200 258 100 100 0 1.782 1.722 1.744 1.715 1.215 1.706 0.872 80 556 8619 8611 0.834 5521 3098 5448 3163 482444 267490 6.021 12.186 0 0
237259 0.482333363 1 1 19 1 P:289 5980 9660 130 2403 2509 751 584 589 101 100 100 0 2405 2704 1079 184 187 47 100 100 0 0.819 0.764 0.732 0.773 1.517 0.723 0.721 120 712 4040 4445 -0.288 1819 2221 1925 2520 301053 324441 19.01 53.553 0 0
237260 -0.613475834 1 1 20 1 P:293 6180 9660 110 5358 5488 1176 575 578 102 100 100 0 3889 4077 1131 185 199 77 100 100 0 1.291 1.262 1.284 1.278 1.334 1.237 0.825 80 521 8487 8805 0.369 4783 3704 4913 3892 439024 326148 48.137 50.364 0 0

Total number of rows: 15488

Table truncated, full table size 3520 Kbytes.




Supplementary file Size Download File type/resource
GSM251857.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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