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Sample GSM251840 Query DataSets for GSM251840
Status Public on Dec 01, 2008
Title Human Prostate GSK-30
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-30 treated with 3.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-30. Specimen ID: GSK-30; 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-30 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 -0.608434843 1 1 1 1 P:1 1950 9650 110 1786 1838 691 325 357 171 97 93 0 1091 1109 496 156 165 69 98 98 0 1.563 1.588 1.594 1.672 1.951 1.584 0.704 80 592 2396 2466 0.644 1461 935 1513 953 147070 88747 8.661 13.681 0 0
237242 -3.375824298 1 1 2 1 P:5 2140 9650 100 18514 18621 7305 385 423 196 100 100 0 1777 1783 719 159 172 74 100 100 0 11.205 11.229 11.527 11.57 1.614 13.596 0.729 80 502 19747 19860 3.486 18129 1618 18236 1624 1489671 142601 92.847 21.77 0 0
237243 -2.060800147 1 1 3 1 P:9 2340 9650 100 5581 5643 2197 347 370 132 100 100 0 1174 1164 444 165 170 41 100 98 0 5.187 5.301 5.423 5.423 1.604 5.828 0.772 80 492 6243 6295 2.375 5234 1009 5296 999 451459 93084 39.947 24.244 0 0
237244 -0.466749524 1 1 4 1 P:13 2530 9640 110 820 807 273 334 339 101 88 83 0 429 410 143 163 169 44 91 82 0 1.827 1.915 1.715 1.765 2.135 2.376 0.613 80 580 752 720 0.87 486 266 473 247 64576 32789 4.634 5.477 0 0
237245 -0.481644743 1 1 5 1 P:17 2730 9640 110 890 889 296 320 328 99 96 92 0 486 457 175 168 176 60 85 73 0 1.792 1.969 1.766 2.341 2.544 2.253 0.554 80 570 888 858 0.842 570 318 569 289 71157 36559 5.667 4.683 0 0
237246 3.848545627 1 1 6 1 P:21 2920 9640 100 962 956 292 313 323 92 97 88 0 7372 6758 2863 171 182 63 100 100 0 0.09 0.098 0.098 0.098 1.453 0.087 0.767 80 494 7850 7230 -3.472 649 7201 643 6587 76499 540677 6.88 104.381 0 0
237247 -2.105110638 1 1 7 1 P:97 3100 9630 90 25660 27280 12191 340 682 3040 100 98 0 4266 4168 2151 172 292 808 94 82 0 6.185 6.742 5.994 6.985 2.027 7.876 0.718 52 407 29414 30936 2.629 25320 4094 26940 3996 1418539 216714 8.749 4.797 0 0
237248 -1.361744624 1 1 8 1 P:101 3310 9640 100 1532 1801 1043 353 466 597 78 50 0 531 634 322 173 223 411 42 16 0 3.293 3.141 2.824 3.133 2.029 4.217 0.494 80 516 1537 1909 1.72 1179 358 1448 461 144043 50751 2.236 1 0 0
237249 -2.537619779 1 1 9 1 P:105 3500 9630 110 36595 35211 15721 364 429 279 100 100 2 3749 3627 2103 179 190 105 100 100 0 10.149 10.106 9.535 11.144 1.759 9.932 0.769 80 570 39801 38295 3.343 36231 3570 34847 3448 2816864 290148 124.667 32.733 0 0
237250 -0.510531462 1 1 10 1 P:109 3690 9640 100 26064 23190 9280 363 404 211 100 100 0 8970 8204 4018 184 194 110 100 100 0 2.925 2.846 2.901 3.035 1.625 2.935 0.764 80 484 34487 30847 1.549 25701 8786 22827 8020 1855176 656350 107.991 72.818 0 0
237251 0.29667025 1 1 11 1 P:113 3880 9630 110 2612 2492 827 338 363 148 100 100 0 2365 2325 1013 175 182 51 100 100 0 1.038 1.002 1.058 1.058 1.597 0.953 0.754 80 570 4464 4304 0.054 2274 2190 2154 2150 199330 185989 14.385 42.02 0 0
237252 0.849676428 1 1 12 1 P:117 4080 9630 100 1768 1691 567 334 341 101 98 98 0 2413 2301 1089 170 177 45 100 100 0 0.639 0.637 0.592 0.691 2.063 0.559 0.682 80 511 3677 3488 -0.645 1434 2243 1357 2131 135284 184057 13.366 47.2 0 0
237253 -1.871390904 1 1 13 1 P:193 4280 9640 100 1631 1556 448 299 315 108 100 100 0 436 414 99 163 168 49 97 91 0 4.879 5.008 4.875 5.168 1.55 5.47 0.672 80 511 1605 1508 2.287 1332 273 1257 251 124449 33148 11.491 5.02 0 0
237254 -1.404815658 1 1 14 1 P:197 4480 9640 100 606 595 165 304 321 117 85 60 0 251 258 70 163 170 50 75 42 0 3.432 3.063 2.804 3.121 2.452 4.958 0.255 80 492 390 386 1.779 302 88 291 95 47592 20610 2.342 1.76 0 0
237255 -0.909049039 1 1 15 1 P:201 4660 9630 100 5801 5393 1961 310 319 105 100 100 0 2507 2465 1150 167 176 73 100 100 0 2.347 2.212 2.25 2.394 1.546 2.262 0.806 80 492 7831 7381 1.231 5491 2340 5083 2298 431469 197203 48.324 31.356 0 0
237256 0.003892186 1 1 16 1 P:205 4850 9630 90 2247 2531 1494 308 320 104 100 98 0 1868 2141 1267 165 190 201 100 92 0 1.139 1.125 1.04 1.098 1.621 1.298 0.656 52 408 3642 4199 0.187 1939 1703 2223 1976 131591 111349 21.26 9.706 0 0
237257 -0.773729966 1 1 17 1 P:209 5050 9630 100 664 664 164 290 307 98 93 86 0 328 324 79 166 177 132 63 6 0 2.309 2.367 2.488 2.597 2.301 3.001 0.484 80 510 536 532 1.207 374 162 374 158 53149 25898 3.643 1.114 0 0
237258 -2.231982832 1 1 18 1 P:213 5240 9630 100 6050 5622 1814 304 320 102 100 100 0 1177 1043 450 170 177 54 98 96 0 5.706 6.092 5.523 6.752 1.98 6.156 0.751 80 492 6753 6191 2.512 5746 1007 5318 873 449756 83434 51.98 16.037 0 0
237259 1.208332463 1 1 19 1 P:289 5440 9630 110 3830 3555 1276 303 318 102 100 100 0 6592 6312 2673 169 177 52 100 100 0 0.549 0.529 0.525 0.542 1.633 0.487 0.804 80 580 9950 9395 -0.865 3527 6423 3252 6143 284387 504977 31.735 117.981 0 0
237260 -0.869979699 1 1 20 1 P:293 5630 9620 90 4385 3953 1777 313 346 238 100 100 0 2060 1925 1005 168 188 178 100 90 0 2.152 2.072 2.387 2.194 1.736 2.881 0.649 52 414 5964 5397 1.106 4072 1892 3640 1757 205569 100117 15.155 9.758 0 0

Total number of rows: 15488

Table truncated, full table size 3478 Kbytes.




Supplementary file Size Download File type/resource
GSM251840.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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