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Sample GSM251868 Query DataSets for GSM251868
Status Public on Dec 01, 2008
Title Human Prostate GSK-4
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-4 treated with 3.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-4. Specimen ID: GSK-4; 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-4 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 0.612576424 1 1 1 1 P:1 2430 9790 140 2768 2772 671 844 864 184 99 99 0 2453 2622 1410 293 322 202 100 98 0 0.891 0.828 0.896 0.917 1.614 0.597 0.624 156 625 4084 4257 -0.167 1924 2160 1928 2329 432397 408958 10.37 11.386 0 0
237242 -2.412312573 1 1 2 1 P:5 2630 9790 150 29628 25936 14574 852 882 205 100 100 0 4598 3960 2041 301 323 107 98 97 0 6.697 6.855 7.189 6.884 1.489 7.281 0.903 156 631 33073 28743 2.743 28776 4297 25084 3659 4046056 617688 122.215 33.991 0 0
237243 -1.946484904 1 1 3 1 P:9 2820 9790 130 9195 9083 3478 870 924 338 100 100 0 1935 1975 790 314 340 106 100 100 0 5.136 4.945 5.256 5.111 1.46 5.211 0.828 120 631 9946 9874 2.361 8325 1621 8213 1661 1090011 236963 24.139 15.425 0 0
237244 0.42426394 1 1 4 1 P:13 3020 9790 120 2221 2154 375 816 871 327 98 96 0 1321 1469 618 301 320 134 100 98 0 1.377 1.146 1.283 1.213 1.501 1.143 0.57 120 613 2425 2506 0.462 1405 1020 1338 1168 258431 176311 3.924 8.575 0 0
237245 0.629026051 1 1 5 1 P:17 3220 9790 120 2031 2054 412 781 796 154 100 97 0 1299 1497 769 292 325 222 99 96 0 1.241 1.056 1.227 1.147 1.647 0.838 0.643 120 615 2257 2478 0.312 1250 1007 1273 1205 246518 179615 8.169 5.279 0 0
237246 4.264599782 1 1 6 1 P:21 3400 9790 110 1741 1745 249 790 819 182 100 100 0 19358 20625 9818 309 661 1783 100 97 0 0.05 0.047 0.05 0.052 1.992 0.028 0.421 80 532 20000 21271 -4.324 951 19049 955 20316 139578 1650020 5.088 11.197 0 0
237247 -0.419934691 1 1 7 1 P:97 3610 9780 130 21383 20661 12676 776 798 171 100 100 0 9967 9921 6880 298 540 1558 85 75 0 2.131 2.066 2.405 2.121 1.755 2.229 0.664 120 690 30276 29508 1.092 20607 9669 19885 9623 2479325 1190504 116.158 6.021 0 0
237248 0.730697684 1 1 8 1 P:101 3790 9780 90 2728 2690 399 775 774 147 100 100 0 2756 2697 620 294 343 251 100 100 0 0.793 0.797 0.768 0.808 1.301 0.695 0.771 52 361 4415 4318 -0.334 1953 2462 1915 2403 139872 140253 13.034 9.378 0 0
237249 -1.278273174 1 1 9 1 P:105 4000 9780 130 30861 29960 7878 790 846 357 100 100 0 7589 7682 2891 285 346 292 100 100 0 4.117 3.943 4.203 4.096 1.4 4.04 0.788 120 685 37375 36567 2.042 30071 7304 29170 7397 3595248 921887 81.552 25.123 0 0
237250 -0.122363224 1 1 10 1 P:109 4190 9790 120 26308 26052 11820 788 832 348 100 100 0 11951 11744 5384 285 339 266 100 100 0 2.188 2.205 2.466 2.289 1.565 2.32 0.841 120 562 37186 36723 1.129 25520 11666 25264 11459 3126278 1409324 72.471 42.876 0 0
237251 0.54800982 1 1 11 1 P:113 4380 9770 130 4220 4305 1192 759 791 230 100 100 0 3949 3944 1412 277 322 186 100 99 0 0.943 0.967 0.973 1.016 1.442 0.921 0.863 120 646 7133 7213 -0.085 3461 3672 3546 3667 516593 473323 15.278 19.473 0 0
237252 0.880631617 1 1 12 1 P:117 4570 9780 110 3213 3205 394 734 746 155 100 100 0 3743 3861 1515 274 300 154 100 100 0 0.715 0.689 0.679 0.764 1.61 0.551 0.786 80 509 5948 6058 -0.485 2479 3469 2471 3587 256429 308862 15.865 23.123 0 0
237253 -0.73311312 1 1 13 1 P:193 4770 9770 130 3007 3014 680 747 790 270 100 100 0 1074 1112 351 271 290 136 100 99 0 2.814 2.696 2.989 2.806 1.524 2.853 0.768 120 696 3063 3108 1.493 2260 803 2267 841 361721 133392 8.237 6.044 0 0
237254 -0.758668516 1 1 14 1 P:197 4960 9760 110 2333 2356 322 830 839 151 100 100 0 644 655 125 284 287 55 100 100 0 4.175 4.113 4.457 4.258 1.502 4.507 0.72 80 537 1863 1897 2.062 1503 360 1526 371 188484 52415 10.046 6.691 0 0
237255 -2.401605064 1 1 15 1 P:201 5160 9760 130 12447 12508 5431 844 882 249 100 100 0 2694 2691 1039 288 303 76 100 100 0 4.823 4.854 5.041 4.92 1.512 5.27 0.81 120 728 14009 14067 2.27 11603 2406 11664 2403 1501001 322895 46.691 31.421 0 0
237256 0.184258709 1 1 16 1 P:205 5380 9770 90 1023 1332 755 840 869 229 46 40 0 384 490 307 289 303 75 51 36 0 1.926 2.448 2.751 2.986 3.793 2.634 0.227 52 375 278 693 0.946 183 95 492 201 69282 25471 2.022 2.493 0 0
237257 -0.92319696 1 1 17 1 P:209 5550 9750 110 3363 3453 435 851 875 187 100 100 0 1089 1104 245 289 350 263 98 90 0 3.14 3.193 3.227 3.309 1.408 2.786 0.668 80 559 3312 3417 1.651 2512 800 2602 815 276248 88305 13.786 2.867 0 0
237258 -1.092972389 1 1 18 1 P:213 5750 9750 110 9415 9257 1739 800 841 217 100 100 0 4707 4629 1369 282 324 235 100 100 0 1.947 1.945 2.001 2.045 1.43 1.907 0.807 80 534 13040 12804 0.961 8615 4425 8457 4347 740563 370295 38.783 18.319 0 0
237259 0.828182944 1 1 19 1 P:289 5940 9750 140 3640 3833 1220 777 801 179 99 99 0 4108 4219 1924 284 317 245 99 98 0 0.749 0.777 0.789 0.809 1.794 0.694 0.687 156 747 6687 6991 -0.418 2863 3824 3056 3935 597928 658153 16.939 15.927 0 0
237260 -0.544754171 1 1 20 1 P:293 6140 9750 100 7359 7783 1750 787 800 150 100 100 0 5181 5333 1496 295 308 95 100 100 0 1.345 1.389 1.366 1.412 1.362 1.292 0.807 80 464 11458 12034 0.428 6572 4886 6996 5038 622628 426625 46.553 52.895 0 0

Total number of rows: 15488

Table truncated, full table size 3562 Kbytes.




Supplementary file Size Download File type/resource
GSM251868.gpr.gz 1.4 Mb (ftp)(http) GPR
Processed data included within Sample table
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