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Sample GSM251873 Query DataSets for GSM251873
Status Public on Dec 01, 2008
Title Human Prostate GSK-16
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-16 treated with 3.5 mg PO qDay Dutasteride
Organism Homo sapiens
Characteristics Human Prostate GSK-16. Specimen ID: GSK-16; 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-16 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 -0.151281606 1 1 1 1 P:1 3410 9530 130 1434 1456 281 483 499 388 98 75 0 1016 1093 338 183 188 62 100 100 0 1.142 1.069 1.101 1.094 1.394 1.027 0.789 120 676 1784 1883 0.191 951 833 973 910 174699 131152 2.466 14.597 0 0
237242 -3.064423665 1 1 2 1 P:5 3610 9520 110 13421 13953 4782 478 584 1062 100 100 0 2022 2127 821 181 264 789 97 62 0 7.03 6.924 6.785 6.978 1.437 7.007 0.846 80 535 14784 15421 2.814 12943 1841 13475 1946 1116210 170139 12.589 2.361 0 0
237243 1 1 3 1 P:9 3810 9510 140 487 499 99 515 516 106 12 1 0 185 192 41 192 198 37 14 5 0 4 100000 2.227 2.406 3.687 49.386 0.002 156 787 -35 -16 2 -28 -7 -16 0 77910 29958 -0.16 -0.162 -50 0
237244 -0.284733734 1 1 4 1 P:13 4010 9520 110 1185 1240 320 524 529 104 100 98 0 543 561 179 196 202 42 100 100 0 1.905 1.962 2.078 1.942 1.582 2.307 0.657 80 508 1008 1081 0.93 661 347 716 365 99192 44840 6.837 8.548 0 0
237245 -0.468861899 1 1 5 1 P:17 4200 9520 120 1238 1242 308 527 531 103 100 96 0 538 541 174 195 203 47 94 89 0 2.073 2.066 2.03 2.249 1.941 2.227 0.704 120 582 1054 1061 1.052 711 343 715 346 149007 64926 6.903 7.191 0 0
237246 1 1 6 1 P:21 4390 9510 140 524 519 102 527 530 101 10 1 0 202 208 69 196 202 44 14 3 0 -0.5 -0.667 2.667 2.425 4.657 45.071 0.001 156 664 3 4 Error -3 6 -8 12 81037 32465 -0.109 0.136 -50 0
237247 1 1 7 1 P:97 4580 9510 140 497 514 101 519 523 106 15 2 0 186 193 56 194 204 61 4 1 0 2.75 5 2.871 3.181 3.885 239.545 0 156 666 -30 -6 1.459 -22 -8 -5 -1 80187 30066 -0.085 -0.18 -50 0
237248 1 1 8 1 P:101 4780 9510 140 521 523 105 518 520 103 14 2 0 196 198 35 194 201 49 10 1 0 1.5 1.25 3.136 3.202 4.465 0.45 0.003 156 698 5 9 0.585 3 2 5 4 81654 30889 0.029 -0.061 -50 0
237249 -2.84151747 1 1 9 1 P:105 4980 9510 120 16156 17873 9014 513 522 105 99 99 0 2501 2503 1247 198 203 41 94 93 0 6.792 7.531 7.112 8.059 1.849 8.145 0.785 120 564 17946 19665 2.764 15643 2303 17360 2305 2144761 300347 165.248 56.098 0 0
237250 1 1 10 1 P:109 5170 9500 140 522 520 101 503 512 112 16 2 0 194 198 40 193 200 44 10 1 0 19 3.4 3.4 3.041 3.624 61.229 0.002 156 711 20 22 4.248 19 1 17 5 81059 30957 0.071 -0.045 -50 0
237251 -0.657259355 1 1 11 1 P:113 5370 9510 120 1482 1715 718 489 500 109 99 96 0 785 832 327 188 193 45 97 96 0 1.663 1.904 1.869 1.857 1.64 2.002 0.676 120 564 1590 1870 0.734 993 597 1226 644 205795 99821 11.147 14.2 0 0
237252 1 1 12 1 P:117 5560 9500 140 490 486 92 476 485 99 15 1 0 185 191 49 184 190 38 12 1 0 14 1.429 3.409 2.799 4.215 13.521 0.022 156 714 15 17 3.807 14 1 10 7 75808 29850 0.01 0.026 -50 0
237253 -0.515114553 1 1 13 1 P:193 5750 9510 120 1147 1210 301 469 475 101 100 100 0 469 488 110 186 190 33 100 100 0 2.396 2.454 2.396 2.406 1.551 2.925 0.695 120 544 961 1043 1.26 678 283 741 302 145218 58555 7.277 9.03 0 0
237254 1 1 14 1 P:197 5940 9500 140 462 478 109 463 473 100 17 5 0 182 184 32 189 195 49 6 0 0 0.143 -3 2.406 1.967 5.676 110.582 0.001 156 750 -8 10 -2.807 -1 -7 15 -5 74566 28736 0.05 -0.224 -50 0
237255 -3.169433126 1 1 15 1 P:201 6140 9500 100 7701 7925 2291 464 469 106 100 100 0 1498 1453 443 183 188 47 100 100 0 5.503 5.875 5.577 6.061 1.436 6.035 0.861 80 450 8552 8731 2.46 7237 1315 7461 1270 633989 116222 70.34 26.915 0 0
237256 1 1 16 1 P:205 6330 9500 140 460 460 96 453 459 101 14 1 0 185 191 46 180 185 32 17 7 0 1.4 0.636 2.588 2.333 4.972 35.928 0.004 156 698 12 18 0.485 7 5 7 11 71734 29844 0.01 0.188 -50 0
237257 1 1 17 1 P:209 6530 9500 140 451 463 96 440 452 98 24 3 0 190 196 71 183 187 35 17 3 0 1.571 1.769 3.2 2.277 4.879 12.203 0.015 156 678 18 36 0.652 11 7 23 13 72262 30635 0.112 0.257 -50 0
237258 1 1 18 1 P:213 6720 9500 140 458 454 91 444 454 97 18 1 0 181 194 67 183 186 35 16 5 0 -7 0.909 2.44 2.585 3.797 23.58 0.005 156 666 12 21 Error 14 -2 10 11 70867 30248 0 0.229 -50 0
237259 0.705674163 1 1 19 1 P:289 6920 9510 140 1556 1552 492 454 459 99 95 94 0 2563 2624 1204 181 188 44 97 97 0 0.463 0.449 0.46 0.477 2.129 0.391 0.699 156 632 3484 3541 -1.112 1102 2382 1098 2443 242153 409367 11.04 55.364 0 0
237260 1 1 20 1 P:293 7110 9500 140 468 460 90 443 456 136 10 0 0 187 199 83 179 187 45 19 5 0 3.125 0.85 2.575 2.832 3.879 11.093 0.037 156 678 33 37 1.644 25 8 17 20 71819 30985 0.029 0.267 -50 0

Total number of rows: 15488

Table truncated, full table size 3475 Kbytes.




Supplementary file Size Download File type/resource
GSM251873.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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