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Sample GSM251844 Query DataSets for GSM251844
Status Public on Dec 01, 2008
Title Human Prostate GSK-19
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-19 treated with Immediate Radical Prostatectomy
Organism Homo sapiens
Characteristics Human Prostate GSK-19. Specimen ID: GSK-19; 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-19 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 0.16760084 1 1 1 1 P:1 2550 9530 100 1385 1739 1539 701 850 2019 5 3 0 1059 1169 579 154 166 99 100 100 0 0.756 1.023 0.795 0.832 1.9 2.683 0.248 80 484 1589 2053 -0.404 684 905 1038 1015 139116 93501 0.44 10.131 0 0
237242 -3.262058911 1 1 2 1 P:5 2720 9530 110 26289 27816 11623 735 1968 6573 100 90 0 2672 2738 1259 158 306 712 91 83 0 10.165 10.497 10.512 11.054 1.715 12.55 0.63 80 540 28068 29661 3.345 25554 2514 27081 2580 2225288 219014 3.932 3.416 0 0
237243 -2.723546309 1 1 3 1 P:9 2930 9530 100 10531 10095 4193 710 1748 6070 77 26 0 1793 1815 886 154 277 629 83 63 0 5.992 5.65 5.893 5.963 1.61 6.172 0.756 80 500 11460 11046 2.583 9821 1639 9385 1661 807574 145233 1.375 2.445 0 0
237244 -0.008230782 1 1 4 1 P:13 3120 9530 100 958 1031 474 684 714 206 55 22 0 507 525 240 153 192 298 57 10 0 0.774 0.933 0.812 0.816 2.326 1.513 0.465 80 492 628 719 -0.37 274 354 347 372 82465 41971 1.539 1.117 0 0
237245 -0.043854706 1 1 5 1 P:17 3320 9530 110 991 1229 1243 689 725 216 61 32 0 524 621 414 153 195 193 78 46 0 0.814 1.154 0.802 0.768 2.656 3.168 0.281 80 559 673 1008 -0.297 302 371 540 468 98302 49694 2.333 2.207 0 0
237246 2.533248687 1 1 6 1 P:21 3510 9530 100 1680 1606 325 718 755 261 97 80 0 9502 10247 4810 161 232 474 100 100 0 0.103 0.088 0.092 0.092 1.63 0.07 0.677 80 474 10303 10974 -3.279 962 9341 888 10086 128441 819734 3.261 21.129 0 0
237247 -2.220053161 1 1 7 1 P:97 3680 9520 90 29862 29309 12990 737 2872 9466 90 71 0 4546 4229 2337 165 660 1804 73 59 0 6.648 7.031 6.536 7.516 1.967 6.735 0.829 52 394 33506 32636 2.733 29125 4381 28572 4064 1524068 219887 2.793 1.978 0 0
237248 -0.77550599 1 1 8 1 P:101 3880 9520 90 1603 1851 714 759 1483 4820 0 0 0 727 799 334 165 380 1172 5 0 0 1.502 1.722 1.566 1.611 1.495 2.597 0.74 52 414 1406 1726 0.587 844 562 1092 634 96231 41532 0.076 0.358 0 0
237249 -2.211128835 1 1 9 1 P:105 4090 9530 110 30490 30611 13915 807 1203 2036 100 100 0 4571 4542 2118 171 289 572 100 96 0 6.746 6.819 6.806 6.921 1.671 7.443 0.797 80 586 34083 34175 2.754 29683 4400 29804 4371 2448847 363327 14.444 7.435 0 0
237250 -0.736384786 1 1 10 1 P:109 4280 9530 100 35339 33605 13446 824 1555 3475 100 100 0 9213 8824 4698 175 486 1527 97 83 0 3.819 3.79 4.071 4.17 1.799 3.933 0.775 80 502 43553 41430 1.933 34515 9038 32781 8649 2688401 705894 9.223 5.46 0 0
237251 -0.704577652 1 1 11 1 P:113 4480 9530 100 3618 3602 1267 792 1174 2601 56 3 0 2341 2422 911 168 372 1265 83 31 0 1.301 1.247 1.237 1.229 1.483 1.462 0.618 80 511 4999 5064 0.379 2826 2173 2810 2254 288174 193795 0.933 1.621 0 0
237252 1.4743335 1 1 12 1 P:117 4680 9530 100 1922 1949 549 755 779 147 100 97 0 3897 4202 2166 164 184 137 100 100 0 0.313 0.296 0.301 0.302 1.841 0.222 0.549 80 502 4900 5232 -1.678 1167 3733 1194 4038 155924 336172 7.959 29.328 0 0
237253 -2.193671521 1 1 13 1 P:193 4870 9530 100 1739 1725 365 729 737 127 100 96 0 414 408 104 159 169 47 100 93 0 3.961 4 4.165 4.033 1.481 4.583 0.705 80 467 1265 1245 1.986 1010 255 996 249 138035 32624 7.78 5.085 0 0
237254 1 1 14 1 P:197 5060 9520 140 807 822 142 731 747 168 28 5 0 213 214 56 165 185 115 10 1 0 1.583 1.857 2.107 1.999 3.122 3.772 0.153 156 752 124 140 0.663 76 48 91 49 128298 33412 0.446 0.252 -50 0
237255 -0.384488782 1 1 15 1 P:201 5250 9530 100 3529 3507 1080 737 760 212 100 100 0 3713 4137 1714 170 231 643 100 100 0 0.788 0.698 0.709 0.687 1.48 0.694 0.632 80 476 6335 6737 -0.344 2792 3543 2770 3967 280521 330927 12.958 6.075 0 0
237256 -0.015998711 1 1 16 1 P:205 5430 9530 90 3102 3582 1654 767 1108 1400 84 40 0 4044 4309 2052 173 683 1860 90 51 0 0.603 0.681 0.574 0.689 2.379 0.623 0.568 52 401 6206 6951 -0.729 2335 3871 2815 4136 186279 224089 1.767 1.949 0 0
237257 1.067694951 1 1 17 1 P:209 5640 9540 100 971 1403 1436 767 972 1147 11 8 0 712 936 596 171 469 1414 11 1 0 0.377 0.831 0.355 0.408 4.014 3.193 0.098 80 525 745 1401 -1.407 204 541 636 765 112244 74897 0.376 0.33 0 0
237258 -2.510388014 1 1 18 1 P:213 5840 9530 110 6031 5938 1834 773 790 163 100 100 0 1410 1446 651 171 195 152 100 98 0 4.244 4.051 4.111 4.326 1.656 4.04 0.571 80 591 6497 6440 2.085 5258 1239 5165 1275 475014 115712 31.583 8.23 0 0
237259 1.60937202 1 1 19 1 P:289 6040 9530 100 5013 5096 2253 780 796 168 100 100 0 11766 11803 6135 172 190 140 100 100 0 0.365 0.371 0.38 0.393 1.867 0.303 0.651 80 511 15827 15947 -1.454 4233 11594 4316 11631 407713 944246 25.595 82.95 0 0
237260 0.322311108 1 1 20 1 P:293 6240 9530 100 6801 6466 2700 802 840 450 100 100 0 6166 5819 2979 169 183 166 95 95 0 1 1.002 1.016 1.113 2.3 1.005 0.714 80 480 11996 11314 0 5999 5997 5664 5650 517264 465535 12.502 33.952 0 0

Total number of rows: 15488

Table truncated, full table size 3510 Kbytes.




Supplementary file Size Download File type/resource
GSM251844.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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