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Sample GSM251850 Query DataSets for GSM251850
Status Public on Dec 01, 2008
Title Human Prostate GSK-47
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-47 treated with Immediate Radical Prostatectomy
Organism Homo sapiens
Characteristics Human Prostate GSK-47. Specimen ID: GSK-47; 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-47 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 0.362514663 1 1 1 1 P:1 2500 10020 120 1407 1495 465 468 549 831 61 9 0 1148 1203 471 225 234 60 99 99 0 1.017 1.05 1.067 1.086 1.674 0.989 0.738 120 702 1862 2005 0.025 939 923 1027 978 179432 144359 1.138 16.15 0 0
237242 -2.13498288 1 1 2 1 P:5 2700 10020 110 15031 17553 10124 503 626 1215 100 100 0 2497 2831 1403 239 262 240 100 98 0 6.434 6.578 6.683 6.563 1.402 7.137 0.867 80 558 16786 19642 2.686 14528 2258 17050 2592 1404222 226471 13.932 10.704 0 0
237243 -1.766280755 1 1 3 1 P:9 2890 10010 110 5270 5209 1946 510 516 109 100 100 0 1249 1289 554 241 252 97 98 96 0 4.722 4.484 4.441 4.873 1.855 4.853 0.755 80 531 5768 5747 2.239 4760 1008 4699 1048 416729 103144 43.055 10.691 0 0
237244 0.032056962 1 1 4 1 P:13 3070 10020 100 940 1025 422 533 535 109 86 78 0 619 679 350 249 260 100 90 80 0 1.1 1.144 1.086 1.066 2.327 1.267 0.749 80 484 777 922 0.138 407 370 492 430 82036 54296 4.495 4.19 0 0
237245 0.00761088 1 1 5 1 P:17 3260 10010 110 1000 976 292 529 532 98 85 82 0 664 690 233 250 267 105 93 86 0 1.138 1.016 1.11 1.013 1.74 1.081 0.702 80 589 885 887 0.186 471 414 447 440 78099 55237 4.531 4.029 0 0
237246 2.565066864 1 1 6 1 P:21 3470 10020 100 2052 1936 590 541 545 84 100 100 0 9150 9090 4309 255 266 69 100 100 0 0.17 0.158 0.161 0.16 1.68 0.137 0.791 80 510 10406 10230 -2.557 1511 8895 1395 8835 154903 727208 16.56 127.884 0 0
237247 -1.749401449 1 1 7 1 P:97 3650 10010 90 15744 16794 8314 565 760 1695 100 100 0 3093 3268 1801 256 351 581 94 78 0 5.35 5.388 5.433 5.603 1.947 6.089 0.795 52 407 18016 19241 2.42 15179 2837 16229 3012 873287 169961 9.46 5.021 0 0
237248 -1.99438541 1 1 8 1 P:101 3840 10010 90 2927 3373 1170 574 695 645 100 100 0 690 764 334 258 332 394 53 9 0 5.447 5.532 5.628 5.939 1.639 6.231 0.753 52 414 2785 3305 2.445 2353 432 2799 506 175398 39719 4.152 1.096 0 0
237249 -2.597435852 1 1 9 1 P:105 4050 10020 110 21529 21611 8042 575 632 415 100 100 0 2651 2612 898 258 281 127 100 100 0 8.756 8.936 8.934 8.935 1.363 9.473 0.847 80 586 23347 23390 3.13 20954 2393 21036 2354 1728856 208980 50.552 18.354 0 0
237250 -1.183217606 1 1 10 1 P:109 4240 10030 100 28720 27766 12232 584 595 105 100 100 0 8362 8134 3645 261 271 66 100 100 0 3.473 3.453 3.379 3.48 1.464 3.775 0.844 80 493 36237 35055 1.796 28136 8101 27182 7873 2221305 650752 258.771 119.136 0 0
237251 0.193907587 1 1 11 1 P:113 4440 10020 100 3844 3859 962 594 594 97 100 100 0 3242 3385 1280 262 272 66 100 100 0 1.091 1.045 1.094 1.101 1.481 0.909 0.754 80 493 6230 6388 0.125 3250 2980 3265 3123 308730 270813 33.66 47.167 0 0
237252 1.890914466 1 1 12 1 P:117 4610 10020 90 2253 2099 779 608 619 156 100 94 0 4629 4592 2255 267 323 418 100 98 0 0.377 0.345 0.343 0.342 1.443 0.327 0.848 52 393 6007 5816 -1.407 1645 4362 1491 4325 109154 238764 9.487 10.213 0 0
237253 -2.08608544 1 1 13 1 P:193 4830 10020 120 1478 1753 1656 590 603 148 98 94 0 448 513 378 268 304 328 15 3 0 4.933 4.747 4.819 5.328 2.129 4.944 0.73 120 695 1068 1408 2.303 888 180 1163 245 210416 61564 7.77 0.637 0 0
237254 -0.36680336 1 1 14 1 P:197 5020 10050 80 634 677 184 605 613 93 40 26 0 296 313 107 274 279 64 34 17 0 1.318 1.846 2.765 2.428 3.848 2.964 0.147 52 314 51 111 0.399 29 22 72 39 35226 16269 0.688 0.531 0 0
237255 0.041508223 1 1 15 1 P:201 5210 10030 100 5018 5395 2536 583 591 87 100 100 0 4614 5043 2005 274 284 68 100 100 0 1.022 1.009 1.022 0.964 1.472 0.997 0.774 80 504 8775 9581 0.031 4435 4340 4812 4769 431636 403424 55.218 69.985 0 0
237256 0.58928449 1 1 16 1 P:205 5390 10030 90 3465 3809 1320 594 626 344 100 100 0 3783 3982 1712 284 353 620 98 96 0 0.821 0.869 0.82 0.907 1.716 0.831 0.805 52 400 6370 6913 -0.285 2871 3499 3215 3698 198051 207067 9.253 5.853 0 0
237257 1.390703725 1 1 17 1 P:209 5610 10040 110 669 703 212 586 596 142 33 16 0 426 638 566 270 286 111 68 33 0 0.532 0.318 0.59 0.604 3.51 0.309 0.305 80 580 239 485 -0.91 83 156 117 368 56259 51039 0.754 3.171 0 0
237258 -1.569489652 1 1 18 1 P:213 5800 10040 110 4163 4081 1828 577 596 162 100 100 0 1302 1426 860 270 288 147 97 93 0 3.475 3.031 3.632 3.232 1.873 3.104 0.626 80 560 4618 4660 1.797 3586 1032 3504 1156 326491 114059 21.512 7.741 0 0
237259 0.885886218 1 1 19 1 P:289 5990 10030 110 6917 6962 3269 586 593 103 100 100 0 8583 8589 5191 275 289 89 100 100 0 0.762 0.767 0.845 0.839 1.75 0.693 0.822 80 580 14639 14690 -0.392 6331 8308 6376 8314 556968 687107 61.835 93.258 0 0
237260 -0.060557655 1 1 20 1 P:293 6190 10040 100 7634 7959 4517 594 598 109 100 100 0 4926 4670 2218 280 295 80 100 100 0 1.515 1.678 1.745 1.618 1.642 1.962 0.799 80 503 11686 11755 0.6 7040 4646 7365 4390 636733 373577 67.532 54.688 0 0

Total number of rows: 15488

Table truncated, full table size 3486 Kbytes.




Supplementary file Size Download File type/resource
GSM251850.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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