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Sample GSM251834 Query DataSets for GSM251834
Status Public on Dec 01, 2008
Title Human Prostate GSK-9
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-9 treated with 0.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-9. Specimen ID: GSK-9; Treatment: 0.5 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-9 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 -0.574896804 1 1 1 1 P:1 2450 9400 110 2240 2318 681 735 760 196 100 98 0 1284 1293 404 455 458 71 98 97 0 1.815 1.889 2.045 1.973 2.008 2.091 0.529 80 592 2334 2421 0.86 1505 829 1583 838 185440 103464 7.949 11.761 0 0
237242 -3.880470962 1 1 2 1 P:5 2640 9390 110 22980 23040 9432 774 1027 2773 100 98 0 1491 1486 643 456 485 221 83 75 0 21.455 21.617 21.59 20.87 1.649 23.333 0.702 80 570 23241 23296 4.423 22206 1035 22266 1030 1843212 118857 7.938 4.529 0 0
237243 -3.563612295 1 1 3 1 P:9 2830 9410 100 9267 8820 3904 783 1072 2931 83 70 0 895 922 288 461 489 210 81 55 0 19.548 17.434 17.655 16.797 1.74 19.571 0.639 80 511 8918 8498 4.289 8484 434 8037 461 705577 73733 2.643 2.062 0 0
237244 -1.235214631 1 1 4 1 P:13 3040 9410 110 1572 1645 606 700 745 217 92 83 0 654 632 140 442 448 67 78 65 0 4.113 4.974 4.147 4.427 2.135 5.277 0.486 80 566 1084 1135 2.04 872 212 945 190 131576 50561 4.147 2.746 0 0
237245 -1.602776861 1 1 5 1 P:17 3220 9400 100 1568 1529 392 671 685 133 97 91 0 590 584 128 426 442 101 63 37 0 5.47 5.43 5.017 5.422 2.545 5.403 0.446 80 457 1061 1016 2.451 897 164 858 158 122334 46688 6.346 1.406 0 0
237246 4.922521514 1 1 6 1 P:21 3410 9390 110 1143 1119 280 653 674 161 86 70 0 10964 10703 5583 415 448 359 100 100 0 0.046 0.045 0.047 0.051 2.21 0.036 0.471 80 570 11039 10754 -4.428 490 10549 466 10288 89516 856250 2.764 28.565 0 0
237247 -2.056179289 1 1 7 1 P:97 3610 9400 100 33692 32654 15069 627 919 3153 100 98 2 3867 3464 1543 389 523 2016 73 28 0 9.507 10.415 10.018 10.71 1.921 11.703 0.72 80 512 36543 35102 3.249 33065 3478 32027 3075 2612292 277111 10.065 1.459 0 0
237248 -1.487691263 1 1 8 1 P:101 3810 9390 100 2153 2464 1207 638 944 3155 13 0 0 850 981 528 388 502 1983 2 0 0 3.279 3.079 3.081 3.705 2.476 3.053 0.525 80 512 1977 2419 1.713 1515 462 1826 593 197114 78445 0.482 0.242 0 0
237249 -3.148890924 1 1 9 1 P:105 4000 9380 110 28836 30616 15654 608 793 1008 100 100 2 2428 2733 1978 367 397 275 85 76 0 13.696 12.683 14.192 13.375 2.098 14.094 0.574 80 550 30289 32374 3.776 28228 2061 30008 2366 2449304 218679 29.586 8.495 0 0
237250 -0.967082054 1 1 10 1 P:109 4210 9380 120 23076 21865 10941 580 745 953 99 97 0 5443 5689 3077 347 377 262 97 96 0 4.414 3.984 4.179 4.09 2.241 4.544 0.665 120 616 27592 26627 2.142 22496 5096 21285 5342 2623784 682733 22.162 20.275 0 0
237251 -0.83800797 1 1 11 1 P:113 4380 9390 110 4552 4544 1731 617 660 229 100 100 0 1991 1912 947 369 384 104 98 92 0 2.426 2.545 2.627 3.011 2.188 2.494 0.713 80 521 5557 5470 1.279 3935 1622 3927 1543 363549 152963 16.961 14.692 0 0
237252 2.148695967 1 1 12 1 P:117 4580 9390 110 2425 2360 750 634 660 179 100 97 0 5279 5459 3076 390 420 298 98 96 0 0.366 0.341 0.353 0.388 2.096 0.267 0.667 80 570 6680 6795 -1.449 1791 4889 1726 5069 188791 436686 9.497 16.909 0 0
237253 -3.269181407 1 1 13 1 P:193 4780 9360 110 1519 1446 387 605 621 166 96 87 0 421 423 101 375 384 73 45 18 0 19.87 17.521 8.51 9.366 2.117 11.911 0.174 80 558 960 889 4.312 914 46 841 48 115700 33800 4.97 0.534 0 0
237254 1 1 14 1 P:197 4970 9370 140 696 694 161 576 596 180 33 7 0 336 335 64 363 370 57 8 0 0 -4.444 -4.214 2.5 2.365 4.49 61.66 0.002 156 739 93 90 Error 120 -27 118 -28 108305 52197 0.544 -0.614 -50 0
237255 -1.199210854 1 1 15 1 P:201 5160 9390 100 8288 7935 2510 581 672 866 100 100 0 2867 2848 1303 365 415 317 97 87 0 3.08 2.962 3.103 3.417 1.979 3.057 0.718 80 447 10209 9837 1.623 7707 2502 7354 2483 634807 227841 8.387 7.675 0 0
237256 0.865359122 1 1 16 1 P:205 5370 9380 100 3904 4622 2625 548 589 450 97 93 0 4868 5349 3129 356 382 229 100 100 0 0.744 0.816 0.949 0.8 2.416 0.857 0.483 80 528 7868 9067 -0.427 3356 4512 4074 4993 369771 427915 8.962 21.69 0 0
237257 0.613683552 1 1 17 1 P:209 5570 9400 110 617 648 152 534 696 2161 0 0 0 471 451 107 343 401 868 0 0 0 0.648 1.056 1.352 1.21 3.206 2.728 0.681 80 517 211 222 -0.625 83 128 114 108 51802 36117 -0.022 0.058 0 0
237258 -2.004127737 1 1 18 1 P:213 5760 9380 110 5044 4745 1698 516 537 159 100 100 0 988 975 362 342 354 103 88 83 0 7.009 6.681 6.469 7.418 2.085 6.827 0.629 80 529 5174 4862 2.809 4528 646 4229 633 379583 77982 26.465 6.029 0 0
237259 0.968191931 1 1 19 1 P:289 5950 9360 110 5013 4988 1898 514 546 220 100 100 0 6191 5725 3049 334 386 424 98 92 0 0.768 0.83 0.845 0.966 2.376 0.72 0.73 80 552 10356 9865 -0.381 4499 5857 4474 5391 399004 458004 20.191 12.592 0 0
237260 -1.120016448 1 1 20 1 P:293 6150 9360 120 7359 7108 3151 497 543 283 100 99 0 2626 2396 1251 328 375 396 84 75 0 2.986 3.197 3.304 3.774 2.535 3.723 0.609 120 625 9160 8679 1.578 6862 2298 6611 2068 852992 287513 23.198 5.104 0 0

Total number of rows: 15488

Table truncated, full table size 3497 Kbytes.




Supplementary file Size Download File type/resource
GSM251834.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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