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Sample GSM251846 Query DataSets for GSM251846
Status Public on Dec 01, 2008
Title Human Prostate GSK-40
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-40 treated with Immediate Radical Prostatectomy
Organism Homo sapiens
Characteristics Human Prostate GSK-40. Specimen ID: GSK-40; 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-40 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 -0.006390991 1 1 1 1 P:1 2230 9740 110 1821 1899 633 458 496 538 92 71 0 1387 1513 693 179 188 68 100 100 0 1.128 1.08 1.182 1.124 1.734 1.045 0.725 80 586 2571 2775 0.174 1363 1208 1441 1334 151944 121010 2.608 19.485 0 0
237242 -3.148456119 1 1 2 1 P:5 2440 9720 110 18643 18118 6787 503 554 558 100 100 0 1779 1821 862 185 203 210 95 92 0 11.38 10.767 10.58 10.648 1.553 14.045 0.729 80 578 19734 19251 3.508 18140 1594 17615 1636 1449412 145659 31.477 7.705 0 0
237243 -3.153580212 1 1 3 1 P:9 2640 9720 110 5572 5567 2360 512 565 345 100 100 0 742 712 238 182 197 131 97 85 0 9.036 9.538 9.328 9.379 1.571 10.149 0.798 80 545 5620 5585 3.176 5060 560 5055 530 445330 56931 14.499 3.931 0 0
237244 -1.015656375 1 1 4 1 P:13 2810 9730 110 1568 1620 719 486 605 698 73 27 0 634 610 243 190 316 787 3 0 0 2.437 2.7 2.246 2.643 2.447 3.293 0.576 80 552 1526 1554 1.285 1082 444 1134 420 129581 48831 1.454 0.374 0 0
237245 -0.893193013 1 1 5 1 P:17 3020 9710 110 1637 1638 602 461 564 664 77 46 0 698 664 256 185 299 753 8 0 0 2.292 2.457 2.448 2.561 1.875 1.61 0.378 80 600 1689 1656 1.197 1176 513 1177 479 131042 53118 1.617 0.485 0 0
237246 1.826624548 1 1 6 1 P:21 3220 9710 110 1323 1236 318 464 472 82 100 97 0 3166 3526 1717 185 193 68 100 100 0 0.288 0.231 0.258 0.241 1.803 0.183 0.634 80 534 3840 4113 -1.795 859 2981 772 3341 98858 282110 9.317 49.015 0 0
237247 -2.808056589 1 1 7 1 P:97 3410 9710 120 14385 15759 9391 474 480 80 100 100 0 1814 1888 1118 185 193 61 96 92 0 8.54 8.975 9.416 9.059 1.806 9.464 0.829 120 636 15540 16988 3.094 13911 1629 15285 1703 1891057 226536 190.988 27.787 0 0
237248 -1.289240628 1 1 8 1 P:101 3620 9720 100 2065 2713 1656 488 507 135 100 98 0 720 807 323 185 190 41 100 100 0 2.948 3.577 3.514 3.066 2.073 5.376 0.595 80 465 2112 2847 1.56 1577 535 2225 622 217001 64588 16.341 15.049 0 0
237249 -2.839802528 1 1 9 1 P:105 3800 9700 110 18383 19743 8947 487 596 1063 100 100 0 2154 2196 960 188 214 212 98 97 0 9.103 9.59 9.549 9.878 1.932 11.074 0.701 80 541 19862 21264 3.186 17896 1966 19256 2008 1579447 175648 18.012 9.349 0 0
237250 -2.014588407 1 1 10 1 P:109 4000 9700 110 16881 16422 7385 494 576 808 100 100 0 3348 3586 2008 187 230 355 100 97 0 5.184 4.686 4.669 5.027 1.811 5.029 0.69 80 572 19548 19327 2.374 16387 3161 15928 3399 1313745 286862 19.611 9.454 0 0
237251 -1.609787754 1 1 11 1 P:113 4190 9710 120 2431 2368 875 484 536 707 90 68 0 748 790 349 188 226 328 80 37 0 3.477 3.13 3.386 3.266 1.947 3.394 0.706 120 605 2507 2486 1.798 1947 560 1884 602 284189 94758 2.591 1.72 0 0
237252 3.993175808 1 1 12 1 P:117 4380 9720 110 1528 1608 505 491 499 92 98 98 0 11761 12068 6674 192 200 67 100 100 0 0.09 0.094 0.089 0.101 2.062 0.067 0.594 80 493 12606 12993 -3.48 1037 11569 1117 11876 128660 965441 12.054 177.134 0 0
237253 -0.98814688 1 1 13 1 P:193 4580 9720 120 1200 1358 699 501 513 134 96 88 0 539 693 695 190 199 64 95 90 0 2.003 1.704 2.058 1.853 2.354 1.462 0.427 120 668 1048 1360 1.002 699 349 857 503 163010 83112 6.306 7.719 0 0
237254 -2.812527662 1 1 14 1 P:197 4790 9710 80 595 604 111 532 535 83 46 13 0 239 237 49 192 201 41 57 21 0 1.34 1.6 1.885 1.662 3.109 4.671 0.087 52 335 110 117 0.423 63 47 72 45 31391 12346 0.831 0.878 0 0
237255 -2.920751695 1 1 15 1 P:201 4970 9690 110 7089 7268 2547 553 639 927 100 100 0 1073 1240 589 199 218 162 100 97 0 7.478 6.451 7.193 6.894 1.66 7.887 0.643 80 574 7410 7756 2.903 6536 874 6715 1041 581470 99201 7.151 6.309 0 0
237256 -1.562605029 1 1 16 1 P:205 5150 9690 110 2390 3151 1946 562 650 927 95 48 0 740 790 279 200 223 172 96 83 0 3.385 4.388 3.795 4.101 1.919 5.184 0.547 80 575 2368 3179 1.759 1828 540 2589 590 252044 63226 2.698 3.297 0 0
237257 0.698150899 1 1 17 1 P:209 5370 9710 110 657 662 135 573 579 87 47 23 0 404 414 117 194 202 50 92 83 0 0.4 0.405 0.62 0.668 2.869 0.877 0.138 80 572 294 309 -1.322 84 210 89 220 52980 33087 0.954 4.24 0 0
237258 -1.829249372 1 1 18 1 P:213 5550 9690 110 3283 3214 1201 581 595 207 100 100 0 901 874 309 200 214 91 97 95 0 3.854 3.907 4.082 4.041 1.85 4.336 0.732 80 565 3403 3307 1.947 2702 701 2633 674 257117 69920 12.652 7.253 0 0
237259 1.37048666 1 1 19 1 P:289 5760 9690 120 3375 3342 1293 594 608 198 99 96 0 5199 5185 2804 207 217 86 100 99 0 0.557 0.552 0.555 0.585 1.851 0.478 0.754 120 637 7773 7726 -0.844 2781 4992 2748 4978 401061 622213 13.808 57.767 0 0
237260 -0.799774897 1 1 20 1 P:293 5940 9680 110 4385 4914 2476 636 655 133 100 100 0 2285 2142 1035 210 221 122 100 98 0 1.807 2.214 2.165 2.193 1.877 2.672 0.728 80 525 5824 6210 0.853 3749 2075 4278 1932 393152 171391 32.023 15.746 0 0

Total number of rows: 15488

Table truncated, full table size 3468 Kbytes.




Supplementary file Size Download File type/resource
GSM251846.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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