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Sample GSM251859 Query DataSets for GSM251859
Status Public on Dec 01, 2008
Title Human Prostate GSK-23
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-23 treated with 3.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-23. Specimen ID: GSK-23; 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-23 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 0.036458883 1 1 1 1 P:1 2610 9860 140 1877 2201 1644 314 340 161 100 98 0 1471 1695 1243 113 171 197 100 94 0 1.151 1.193 1.115 1.194 1.524 1.3 0.793 156 736 2921 3469 0.203 1563 1358 1887 1582 343284 264454 11.559 7.736 0 0
237242 -2.455125727 1 1 2 1 P:5 2840 9860 120 26623 26215 12517 332 363 173 100 100 0 3400 3450 1455 112 156 171 100 98 0 7.996 7.754 8.135 7.619 1.538 8.391 0.893 120 633 29579 29221 2.999 26291 3288 25883 3338 3145819 414037 149.434 19.263 0 0
237243 -1.985914645 1 1 3 1 P:9 3030 9870 110 6219 6629 2136 324 337 107 100 100 0 1391 1440 489 108 126 63 100 100 0 4.595 4.733 4.726 4.787 1.276 4.898 0.866 80 508 7178 7637 2.2 5895 1283 6305 1332 530311 115228 58.804 20.857 0 0
237244 -0.042224887 1 1 4 1 P:13 3220 9860 120 1800 1740 524 306 422 1399 55 0 0 1379 1482 648 106 167 600 90 55 0 1.174 1.042 1.133 1.125 1.555 0.983 0.813 120 606 2767 2810 0.231 1494 1273 1434 1376 208793 177796 0.942 2.192 0 0
237245 0.094078345 1 1 5 1 P:17 3410 9860 120 1871 1907 628 313 321 89 100 100 0 1502 1448 623 108 126 59 100 100 0 1.118 1.19 1.206 1.271 1.566 1.113 0.814 120 619 2952 2934 0.16 1558 1394 1594 1340 228821 173758 17.82 22.407 0 0
237246 3.880489235 1 1 6 1 P:21 3610 9860 110 862 886 232 299 309 83 100 97 0 7244 7241 2468 110 134 81 100 100 0 0.079 0.082 0.081 0.081 1.523 0.076 0.723 80 562 7697 7718 -3.664 563 7134 587 7131 70854 579313 6.952 87.741 0 0
237247 -0.174024576 1 1 7 1 P:97 3810 9860 100 28281 30440 11925 315 362 322 100 100 0 8037 8005 3060 118 147 101 100 100 0 3.532 3.82 3.961 3.912 1.552 4.138 0.789 80 500 35885 38012 1.82 27966 7919 30125 7887 2435214 640415 93.41 77.802 0 0
237248 0.170952219 1 1 8 1 P:101 4000 9860 100 1760 1796 478 320 354 254 100 97 0 1504 1680 697 112 137 91 100 100 0 1.034 0.941 0.899 1.005 1.681 0.863 0.779 80 490 2832 3044 0.049 1440 1392 1476 1568 143661 134439 5.677 16.956 0 0
237249 -0.78734732 1 1 9 1 P:105 4200 9860 120 28862 30143 8978 321 332 100 100 100 0 6237 6663 2155 111 127 57 100 100 0 4.659 4.552 4.661 4.637 1.407 4.7 0.888 120 610 34667 36374 2.22 28541 6126 29822 6552 3617186 799518 298.11 114.667 0 0
237250 0.129557086 1 1 10 1 P:109 4380 9860 100 16727 17544 5749 329 353 162 100 100 0 8327 7971 3179 115 143 110 100 100 0 1.997 2.191 2.22 2.31 1.586 2.268 0.769 80 475 24610 25071 0.998 16398 8212 17215 7856 1403549 637643 106.117 71.164 0 0
237251 0.654945252 1 1 11 1 P:113 4590 9860 120 2336 2484 1111 306 326 147 100 99 0 2913 2976 898 118 143 103 100 99 0 0.726 0.762 0.758 0.713 1.569 0.817 0.82 120 650 4825 5036 -0.461 2030 2795 2178 2858 298047 357074 14.68 27.505 0 0
237252 2.16259277 1 1 12 1 P:117 4790 9860 110 1702 1834 694 296 306 96 100 100 0 5549 6265 2774 112 128 65 100 100 0 0.259 0.25 0.259 0.252 1.589 0.218 0.677 80 527 6843 7691 -1.951 1406 5437 1538 6153 146731 501198 15.917 94.415 0 0
237253 -1.138862715 1 1 13 1 P:193 4980 9850 120 1422 1426 421 289 532 1766 6 0 0 667 721 259 104 223 802 24 0 0 2.012 1.843 1.819 1.863 1.511 1.936 0.781 120 639 1696 1754 1.009 1133 563 1137 617 171139 86538 0.506 0.621 0 0
237254 -0.379763069 1 1 14 1 P:197 5180 9860 100 601 631 287 287 297 89 92 72 0 341 347 89 106 124 63 100 91 0 1.336 1.427 1.358 1.207 2.142 2.586 0.346 80 468 549 585 0.418 314 235 344 241 50502 27725 3.753 3.54 0 0
237255 -0.333132541 1 1 15 1 P:201 5360 9850 110 8509 10476 4836 303 318 118 100 100 0 6605 8023 4142 108 141 265 100 100 0 1.263 1.285 1.233 1.329 1.502 1.143 0.816 80 555 14703 18088 0.337 8206 6497 10173 7915 838098 641821 86.085 29.743 0 0
237256 0.010020416 1 1 16 1 P:205 5560 9850 110 3388 3443 1256 293 306 110 100 100 0 3407 3724 2067 106 139 257 98 93 0 0.938 0.871 0.929 0.993 1.685 0.774 0.814 80 580 6396 6768 -0.093 3095 3301 3150 3618 275454 297924 28.518 13.949 0 0
237257 0.697167084 1 1 17 1 P:209 5760 9850 110 880 900 240 277 289 102 100 98 0 1182 1310 395 106 120 62 100 100 0 0.56 0.517 0.505 0.504 1.533 0.45 0.603 80 570 1679 1827 -0.835 603 1076 623 1204 71998 104792 5.99 19.194 0 0
237258 -1.195920992 1 1 18 1 P:213 5950 9850 100 5054 5554 1684 274 285 82 100 100 0 2375 2382 521 106 123 58 100 100 0 2.107 2.32 2.198 2.28 1.292 2.342 0.763 80 480 7049 7556 1.075 4780 2269 5280 2276 444354 190527 64.256 38.948 0 0
237259 1.08513704 1 1 19 1 P:289 6140 9840 130 1353 1522 577 272 287 133 100 100 0 2052 2318 1014 104 122 64 100 99 0 0.555 0.565 0.595 0.589 1.696 0.521 0.768 120 700 3029 3464 -0.85 1081 1948 1250 2214 182655 278126 9.286 34.313 0 0
237260 -0.653413396 1 1 20 1 P:293 6340 9840 100 3575 4132 1887 277 294 150 100 100 0 1924 2250 1176 108 124 60 100 100 0 1.816 1.8 1.71 1.85 1.495 1.766 0.796 80 486 5114 5997 0.861 3298 1816 3855 2142 330544 179978 25.587 35.433 0 0

Total number of rows: 15488

Table truncated, full table size 3474 Kbytes.




Supplementary file Size Download File type/resource
GSM251859.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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