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Sample GSM251848 Query DataSets for GSM251848
Status Public on Dec 01, 2008
Title Human Prostate GSK-26
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-26 treated with 0.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-26. Specimen ID: GSK-26; 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-26 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 0.019128423 1 1 1 1 P:1 2110 9770 110 1760 1841 596 503 534 248 100 93 0 1565 1664 832 204 214 76 100 100 0 0.924 0.916 0.94 0.993 1.729 0.967 0.579 80 580 2618 2798 -0.115 1257 1361 1338 1460 147283 133127 5.27 19.079 0 0
237242 -3.520063871 1 1 2 1 P:5 2300 9760 100 19006 17742 9106 553 869 2258 100 86 0 2682 2614 1345 209 234 228 100 95 0 7.462 7.147 7.276 7.237 1.996 9.058 0.647 80 506 20926 19594 2.9 18453 2473 17189 2405 1419394 209157 7.473 10.439 0 0
237243 -2.067927336 1 1 3 1 P:9 2520 9770 100 3933 4226 2338 455 594 1045 91 72 0 1254 1463 926 192 204 71 93 93 0 3.275 2.967 3.147 3.172 2.146 3.092 0.739 80 498 4540 5042 1.711 3478 1062 3771 1271 338051 117036 3.476 17.732 0 0
237244 -0.105280004 1 1 4 1 P:13 2690 9760 100 910 1245 2598 464 488 161 92 70 0 839 867 499 199 220 148 91 78 0 0.697 1.169 0.77 0.823 2.294 5.87 0.211 80 473 1086 1449 -0.521 446 640 781 668 99595 69359 4.702 4.372 0 0
237245 -0.153106215 1 1 5 1 P:17 2880 9770 100 904 910 327 467 497 251 71 42 0 815 770 308 201 221 125 91 81 0 0.712 0.779 0.757 0.768 2.132 1.151 0.354 80 476 1051 1012 -0.491 437 614 443 569 72812 61620 1.645 4.392 0 0
237246 3.723984099 1 1 6 1 P:21 3080 9760 100 1038 1102 332 471 480 119 97 91 0 11937 13676 9826 196 261 529 100 100 0 0.048 0.047 0.06 0.056 2.08 0.034 0.543 80 515 12308 14111 -4.372 567 11741 631 13480 88164 1094106 5.227 25.359 0 0
237247 -1.399692676 1 1 7 1 P:97 3300 9760 100 16316 17642 9958 462 485 188 100 100 0 6283 6081 2677 197 225 189 100 98 0 2.605 2.92 2.727 2.708 2.521 3.541 0.698 80 486 21940 23064 1.381 15854 6086 17180 5884 1411345 486460 91.261 30.984 0 0
237248 0.909843289 1 1 8 1 P:101 3460 9760 90 816 888 313 456 498 220 80 40 0 1191 1304 594 194 267 402 94 57 0 0.361 0.389 0.382 0.348 2.165 0.324 0.55 52 369 1357 1542 -1.47 360 997 432 1110 46178 67792 1.773 2.58 0 0
237249 -2.19900628 1 1 9 1 P:105 3650 9750 110 24139 23571 14780 464 606 1088 100 100 0 4851 5347 3414 200 261 365 100 90 0 5.09 4.489 4.533 4.639 1.768 4.993 0.76 80 580 28326 28254 2.348 23675 4651 23107 5147 1885712 427772 21.108 13.934 0 0
237250 -0.334189945 1 1 10 1 P:109 3850 9750 100 13325 14552 7961 428 800 1928 98 92 0 9178 10153 5404 195 269 584 100 100 0 1.436 1.418 1.516 1.382 2.123 1.694 0.657 80 492 21880 24082 0.522 12897 8983 14124 9958 1164173 812204 7.133 16.925 0 0
237251 -0.472390211 1 1 11 1 P:113 4030 9750 110 2508 2461 1040 398 720 1721 56 10 0 2391 2557 1605 187 288 609 82 70 0 0.957 0.87 0.946 0.993 1.99 1.658 0.245 80 556 4314 4433 -0.063 2110 2204 2063 2370 196856 204561 1.012 3.726 0 0
237252 0.977847437 1 1 12 1 P:117 4240 9760 100 1675 1651 622 389 452 341 95 78 0 3971 4048 2184 179 221 263 100 100 0 0.339 0.326 0.333 0.335 1.926 0.284 0.682 80 516 5078 5131 -1.56 1286 3792 1262 3869 132080 323868 3.516 14.551 0 0
237253 -2.212023526 1 1 13 1 P:193 4450 9760 100 1055 1039 285 364 383 162 95 87 0 416 411 130 176 181 52 92 85 0 2.879 2.872 2.824 3.094 2.061 3.137 0.526 80 522 931 910 1.526 691 240 675 235 83093 32912 4.049 4.423 0 0
237254 -2.037140728 1 1 14 1 P:197 4670 9750 90 474 477 118 355 363 90 55 28 0 224 234 72 171 194 237 1 0 0 2.245 1.937 1.55 1.907 2.595 3.546 0.134 52 377 172 185 1.167 119 53 122 63 24825 12144 1.267 0.169 0 0
237255 -0.216490374 1 1 15 1 P:201 4830 9750 110 5165 5090 2191 362 522 1040 100 86 0 7124 7894 4761 178 300 954 96 88 0 0.691 0.613 0.594 0.713 2.553 0.516 0.502 80 554 11749 12444 -0.532 4803 6946 4728 7716 407195 631514 4.392 7.96 0 0
237256 0.017901532 1 1 16 1 P:205 5040 9750 100 2230 2292 1137 350 495 969 80 47 0 3095 3085 1831 172 250 727 91 73 0 0.643 0.667 0.657 0.62 2.915 0.661 0.696 80 500 4803 4855 -0.637 1880 2923 1942 2913 183375 246781 1.854 3.9 0 0
237257 0.115875834 1 1 17 1 P:209 5230 9750 100 505 514 119 328 338 84 78 53 0 445 446 140 164 170 45 95 88 0 0.63 0.66 0.681 0.652 2.611 0.802 0.381 80 470 458 468 -0.667 177 281 186 282 41143 35643 2.095 6.133 0 0
237258 -1.791246634 1 1 18 1 P:213 5410 9740 100 3209 3084 1349 335 370 238 100 100 0 1057 1071 562 172 187 96 95 88 0 3.247 3.058 3.142 3.339 2.163 3.406 0.628 80 502 3759 3648 1.699 2874 885 2749 899 246701 85691 11.403 9.208 0 0
237259 1.231956918 1 1 19 1 P:289 5610 9740 100 2871 2665 1165 349 391 244 98 96 0 9005 8013 4304 178 201 176 100 100 0 0.286 0.296 0.302 0.317 2.19 0.253 0.693 80 518 11349 10151 -1.807 2522 8827 2316 7835 213177 641074 9.32 44.386 0 0
237260 -0.683196214 1 1 20 1 P:293 5810 9740 100 3522 3294 1483 353 394 214 98 97 0 2912 2608 1460 171 188 108 96 95 0 1.156 1.207 1.291 1.325 2.993 1.288 0.582 80 510 5910 5378 0.209 3169 2741 2941 2437 263531 208634 13.551 22.407 0 0

Total number of rows: 15488

Table truncated, full table size 3498 Kbytes.




Supplementary file Size Download File type/resource
GSM251848.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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