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Sample GSM252348 Query DataSets for GSM252348
Status Public on Dec 01, 2008
Title Human Prostate 690
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) by the laboratory of Martin Gleave. Total RNA was isolated from microdissected cells 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 690 treated with Immediate Radical Prostatectomy
Organism Homo sapiens
Characteristics Human Prostate 690. #: 690; Treatment: Immediate Radical Prostatectomy; Reference: HGSv5;
Extracted molecule total RNA
Extraction protocol Prostate samples embedded in OCT were used for laser capture microdissection (LCM) by the laboratory of Martin Gleave. Total RNA was isolated from microdissected cells 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 690 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 19, 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)
GSE9983 Prostate Cancer Gene Expression Changes with Neoadjuvant Hormone Therapy

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).
F635 CV the coefficient of variation of feature pixel intensity.
B635 the actual background value used for the feature in GenePix Pro calculations (as opposed to B635 Median, for example, which is the local median background.) This column is required because GenePix Pro 5.0 has global and negative control background subtraction methods. If you choose a non-local method, B635 is different to B635 Median
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 CV the coefficient of variation of background pixel intensity.
% > 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).
F532 CV the coefficient of variation of feature pixel intensity.
B532 the actual background value used for the feature in GenePix Pro calculations (as opposed to B532 Median, for example, which is the local median background.) This column is required because GenePix Pro 5.0 has global and negative control background subtraction methods. If you choose a non-local method, B532 is different to B532 Median.
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 CV the coefficient of variation of background pixel intensity.
% > 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.
Circularity a measure of circularity from 0 to 100, using a metric based on the variance of the distance of each boundary pixel to the centroid of the feature: 100 is most circular, 0 is most non-circular. Circular features always have a circularity of 100, square features always have a circularity of 79 (
Sum of Medians (635/532) the sum of the median intensities for each wavelength, with the median background subtracted.
Sum of Means (635/532) 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).
Autoflag reports whether or not a feature has been flagged from the Flag Features dialog box. It applies to good and bad flags only.

Data table
ID_REF VALUE MetaCol MetaRow Column Row Name X Y Dia. F635 Median F635 Mean F635 SD F635 CV B635 B635 Median B635 Mean B635 SD B635 CV % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD F532 CV B532 B532 Median B532 Mean B532 SD B532 CV % > 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 Circularity Sum of Medians (635/532) Sum of Means (635/532) 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 Autoflag
237241 -1.169045309 1 1 1 1 gi|220150|gb|D90427|D90427 3030 9950 120 1739 1741 381 21 798 798 807 126 15 100 99 0 1058 1079 375 34 392 392 395 42 10 100 95 0 1.413 1.373 1.357 1.562 1.951 1.296 0.740 120 622 100 1607 1630 0.499 941 666 943 687 208973 129505 7.413 16.286 0 0 0
237242 1 1 2 1 gi|179280|gb|M27132.1|HUMATPSYB 3230 9940 140 750 763 127 16 773 773 782 129 16 10 4 0 391 414 344 83 388 388 390 45 11 14 2 0 -7.667 -0.385 2.431 2.284 4.431 0.164 0.017 156 767 100 -20 16 Error -23 3 -10 26 118964 64515 -0.147 0.533 -50 0 0
237243 1 1 3 1 gi|12420723|gb|BG030944|BG030944 3420 9940 140 761 767 123 16 798 798 807 135 16 8 1 0 388 388 43 11 387 387 392 45 11 12 3 0 -37.000 -31.000 3.800 2.896 4.530 36.095 0.005 156 793 100 -36 -30 Error -37 1 -31 1 119575 60463 -0.296 -0.089 -50 0 0
237244 -0.125847051 1 1 4 1 gi|21536438|ref|NM_012161.2| 3610 9940 100 1325 1332 231 17 820 820 826 129 15 97 87 0 719 725 108 14 399 399 402 47 11 100 98 0 1.578 1.571 1.704 1.451 2.042 2.114 0.477 80 464 100 825 838 0.658 505 320 512 326 106544 57999 3.922 6.872 0 0 0
237245 0.050154364 1 1 5 1 gi|21536438|ref|NM_012161.2| 3800 9940 100 1283 1320 257 19 840 840 846 130 15 96 82 0 718 757 177 23 403 403 406 47 11 98 96 0 1.406 1.356 1.359 1.355 2.030 1.509 0.514 80 480 100 758 834 0.492 443 315 480 354 105601 60549 3.646 7.468 0 0 0
237246 1 1 6 1 gi|14065685|gb|BG755019|BG755019 4000 9930 140 829 834 130 15 833 833 848 178 20 8 0 0 406 403 44 10 399 399 444 1013 228 0 0 0 -0.571 0.250 3.107 2.842 4.091 9.796 0.055 156 851 100 3 5 Error -4 7 1 4 130142 62818 -0.079 -0.040 -50 0 0
237247 1 1 7 1 gi|15996756|gb|BI856009|BI856009 4200 9930 140 829 833 119 14 820 820 823 134 16 15 1 0 402 404 48 11 387 387 388 46 11 23 7 0 0.600 0.765 2.514 2.477 5.027 18.782 0.016 156 754 100 24 30 -0.737 9 15 13 17 129892 63087 0.075 0.348 -50 0 0
237248 1 1 8 1 gi|19586973|gb|BM969386|BM969386 4390 9930 140 610 585 208 35 755 755 1174 4089 348 0 0 0 307 299 72 24 361 361 670 2692 401 0 0 0 2.685 2.742 2.923 2.777 2.102 6.169 0.616 156 825 100 -199 -232 1.425 -145 -54 -170 -62 91188 46712 -0.144 -0.138 -50 0 0
237249 -2.303658984 1 1 9 1 gi|7703647|gb|AW771590| 4590 9930 100 8058 8094 4126 50 642 642 1451 5412 372 70 17 0 2200 2173 1008 46 316 316 890 3559 399 5 0 0 3.936 4.013 4.219 3.865 2.132 2.213 0.596 80 468 100 9300 9309 1.977 7416 1884 7452 1857 647523 173823 1.227 0.360 0 0 0
237250 1 1 10 1 gi|20408448|gb|BQ227048|BQ227048 4780 9930 140 807 806 122 15 817 817 814 173 21 7 0 0 396 399 77 19 389 389 408 639 156 0 0 0 -1.429 -1.100 2.318 2.041 4.991 5.580 0.110 156 863 100 -3 -1 Error -10 7 -11 10 125704 62294 -0.046 -0.014 -50 0 0
237251 0.344775787 1 1 11 1 gi|11012215|gb|AU150694|AU150694 4980 9930 100 1752 1889 578 30 857 857 874 161 18 100 93 0 1908 1989 964 48 410 410 418 57 13 100 100 0 0.597 0.654 0.689 0.694 1.574 0.556 0.724 80 453 100 2393 2611 -0.743 895 1498 1032 1579 151150 159102 6.304 27.561 0 0 0
237252 1 1 12 1 gi|17298590|gb|AC009167.8| 5170 9920 140 831 867 244 28 867 867 871 139 15 10 4 0 402 449 429 95 410 410 413 53 12 8 2 0 4.500 0.000 2.079 2.476 4.418 0.604 0.262 156 820 100 -44 39 2.170 -36 -8 0 39 135243 69973 -0.029 0.679 -50 0 0
237253 -1.063383362 1 1 13 1 gi|13477360|gb|BC005157|BC005157 5340 9920 110 1612 1649 274 16 884 884 898 168 18 100 97 0 640 659 136 20 413 413 422 76 18 95 68 0 3.207 3.110 3.445 3.436 1.644 2.883 0.656 80 506 100 955 1011 1.681 728 227 765 246 131887 52702 4.470 3.118 0 0 0
237254 1 1 14 1 UNKNOWN_4 5560 9920 140 884 886 125 14 899 899 916 158 17 8 0 0 407 412 42 10 418 418 424 64 15 6 0 0 1.364 2.167 3.179 2.812 4.092 17.166 0.023 156 849 100 -26 -19 0.447 -15 -11 -13 -6 138216 64314 -0.190 -0.187 -50 0 0
237255 1 1 15 1 gi|5031976|ref|NM_005746.1| 5760 9920 140 943 959 147 15 937 937 940 135 14 22 4 0 433 439 75 17 424 424 430 51 11 16 3 0 0.667 1.467 3.226 2.814 4.817 20.699 0.009 156 731 100 15 37 -0.585 6 9 22 15 149677 68464 0.141 0.176 -50 0 0
237256 1 1 16 1 gi|4827043|ref|NM_005121.1| 5950 9920 140 903 910 129 14 935 935 940 137 14 8 1 0 429 433 44 10 426 426 430 52 12 13 2 0 -10.667 -3.571 4.107 3.461 3.475 25.981 0.008 156 753 100 -29 -18 Error -32 3 -25 7 141886 67513 -0.219 0.058 -50 0 0
237257 1 1 17 1 BLANK 6150 9920 140 955 956 133 13 936 936 944 134 14 20 4 0 424 432 59 13 430 430 432 49 11 9 2 0 -3.167 10.000 3.487 3.173 2.889 47.802 0.002 156 762 100 13 22 Error 19 -6 20 2 149173 67376 0.090 0.000 -50 0 0
237258 1 1 18 1 UNKNOWN_6 6340 9910 140 902 902 123 13 941 941 956 249 26 1 0 0 414 417 47 11 428 428 437 107 24 1 0 0 2.786 3.545 3.211 2.333 4.601 3.037 0.449 156 811 100 -53 -50 1.478 -39 -14 -39 -11 140727 65124 -0.217 -0.187 -50 0 0
237259 0.273507177 1 1 19 1 gi|14042897|gb|AK027893|AK027893 6530 9930 110 1944 1978 302 15 938 938 947 161 17 100 100 0 3089 3556 2032 57 427 427 437 95 21 100 100 0 0.378 0.332 0.390 0.400 2.025 0.248 0.583 80 501 100 3668 4169 -1.404 1006 2662 1040 3129 158207 284452 6.404 32.832 0 0 0
237260 1 1 20 1 gi|5901981|ref|NM_006899.1| 6730 9910 140 834 846 125 14 862 862 870 144 16 10 1 0 417 433 89 20 412 412 420 85 20 9 2 0 -5.600 -0.762 2.272 2.526 4.840 9.877 0.030 156 829 100 -23 5 Error -28 5 -16 21 131919 67472 -0.167 0.153 -50 0 0

Total number of rows: 15488

Table truncated, full table size 4201 Kbytes.




Supplementary file Size Download File type/resource
GSM252348.gpr.gz 1.6 Mb (ftp)(http) GPR
Processed data included within Sample table
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