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Sample GSM252343 Query DataSets for GSM252343
Status Public on Dec 01, 2008
Title Human Prostate 646
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 646 treated with Neoadjuvant hormone suppression for 6 mo
Organism Homo sapiens
Characteristics Human Prostate 646. #: 646; Treatment: Neoadjuvant hormone suppression for 6 mo; 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 646 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 -0.303794785 1 1 1 1 gi|220150|gb|D90427|D90427 3160 9620 110 3199 3233 1009 31 844 844 842 153 18 100 100 0 1893 1937 570 29 859 859 861 86 9 98 98 0 2.278 2.216 2.473 2.392 1.793 2.074 0.513 80 548 100 3389 3467 1.187 2355 1034 2389 1078 258614 154981 15.627 12.512 0 0 0
237242 -2.809790428 1 1 2 1 gi|179280|gb|M27132.1|HUMATPSYB 3330 9610 90 31712 31727 15244 48 854 854 1437 4083 284 100 98 1 4079 4425 2106 47 863 863 1011 976 96 92 71 0 9.595 8.667 7.699 10.256 2.627 10.151 0.655 52 392 100 34074 34435 3.262 30858 3216 30873 3562 1649779 230119 7.419 3.498 0 0 0
237243 1 1 3 1 gi|12420723|gb|BG030944|BG030944 3540 9610 140 816 844 224 26 819 819 1111 2730 245 0 0 0 838 850 99 11 848 848 925 681 73 0 0 0 0.300 12.500 1.711 1.935 4.482 11.306 0.035 156 921 100 -13 27 -1.737 -3 -10 25 2 131674 132625 -0.098 -0.110 -50 0 0
237244 -1.556978183 1 1 4 1 gi|21536438|ref|NM_012161.2| 3740 9620 100 3106 3262 1642 50 761 761 772 164 21 100 100 0 1336 1396 549 39 819 819 818 93 11 76 68 0 4.536 4.334 4.944 5.222 3.280 4.870 0.542 80 489 100 2862 3078 2.181 2345 517 2501 577 260960 111678 15.183 6.215 0 0 0
237245 -1.291643439 1 1 5 1 gi|21536438|ref|NM_012161.2| 3930 9620 110 2801 3257 2011 61 712 712 733 217 29 95 91 0 1306 1410 813 57 754 754 760 88 11 67 65 0 3.784 3.880 3.715 4.076 2.754 1.282 0.281 80 528 100 2641 3201 1.920 2089 552 2545 656 260564 112812 11.631 7.386 0 0 0
237246 1 1 6 1 gi|14065685|gb|BG755019|BG755019 4120 9610 140 721 732 141 19 700 700 714 196 27 11 1 0 754 753 69 9 730 730 735 82 11 19 1 0 0.875 1.391 2.160 2.125 5.002 40.273 0.003 156 809 100 45 55 -0.193 21 24 32 23 114267 117454 0.092 0.220 -50 0 0
237247 1 1 7 1 gi|15996756|gb|BI856009|BI856009 4320 9610 140 735 752 244 32 714 714 720 148 20 20 3 0 741 752 122 16 742 742 744 72 9 16 5 0 -21.000 3.800 1.749 1.688 4.672 7.965 0.030 156 762 100 20 48 Error 21 -1 38 10 117310 117329 0.216 0.111 -50 0 0
237248 1 1 8 1 gi|19586973|gb|BM969386|BM969386 4510 9610 140 693 707 138 19 691 691 704 156 22 16 1 0 707 711 80 11 724 724 722 76 10 10 3 0 -0.118 -1.231 1.449 1.600 4.458 8.893 0.029 156 816 100 -15 3 Error 2 -17 16 -13 110360 110913 0.019 -0.145 -50 0 0
237249 -1.405160839 1 1 9 1 gi|7703647|gb|AW771590| 4700 9610 90 15545 15555 7009 45 666 666 734 467 63 100 100 0 4294 4097 2189 53 690 690 718 304 42 98 86 0 4.128 4.370 4.347 5.346 2.631 4.914 0.593 52 382 100 18483 18296 2.046 14879 3604 14889 3407 808868 213031 31.737 11.115 0 0 0
237250 1 1 10 1 gi|20408448|gb|BQ227048|BQ227048 4900 9610 140 659 699 394 56 644 644 673 320 47 3 1 0 682 687 68 9 662 662 674 208 30 0 0 0 0.750 2.200 2.200 2.380 3.854 13.051 0.079 156 900 100 35 80 -0.415 15 20 55 25 109086 107163 0.081 0.063 -50 0 0
237251 -0.316897901 1 1 11 1 gi|11012215|gb|AU150694|AU150694 5090 9610 90 3641 3456 1250 36 633 633 679 364 53 98 96 0 2158 2151 936 43 638 638 678 338 49 86 75 0 1.979 1.866 1.799 2.162 2.121 2.216 0.591 52 382 100 4528 4336 0.985 3008 1520 2823 1513 179736 111842 7.629 4.358 0 0 0
237252 1 1 12 1 gi|17298590|gb|AC009167.8| 5290 9610 140 632 641 150 23 634 634 685 860 125 0 0 0 646 656 87 13 638 638 656 234 35 1 0 0 -0.250 0.389 2.556 2.322 4.637 235.745 0.002 156 866 100 6 25 Error -2 8 7 18 99988 102397 -0.051 0.000 -50 0 0
237253 -1.508914493 1 1 13 1 gi|13477360|gb|BC005157|BC005157 5470 9610 110 1529 1608 507 31 619 619 628 136 21 100 96 0 778 829 228 27 631 631 634 67 10 75 53 0 6.190 4.995 4.838 4.917 2.090 4.652 0.373 80 519 100 1057 1187 2.630 910 147 989 198 128669 66324 7.206 2.910 0 0 0
237254 1 1 14 1 UNKNOWN_4 5680 9610 140 514 515 139 26 568 568 579 136 23 11 0 0 546 533 102 19 592 592 592 74 12 6 0 0 1.174 0.898 1.400 1.424 3.737 2.886 0.108 156 843 100 -100 -112 0.231 -54 -46 -53 -59 80336 83218 -0.471 -0.797 -50 0 0
237255 1 1 15 1 gi|5031976|ref|NM_005746.1| 5880 9610 140 557 560 122 21 531 531 542 127 23 21 3 0 549 552 62 11 558 558 560 71 12 11 0 0 -2.889 -4.833 2.339 1.844 5.410 16.940 0.004 156 757 100 17 23 Error 26 -9 29 -6 87413 86175 0.142 -0.113 -50 0 0
237256 1 1 16 1 gi|4827043|ref|NM_005121.1| 6070 9610 140 483 502 196 39 514 514 522 132 25 9 1 0 515 525 74 14 537 537 543 67 12 8 2 0 1.409 1.000 1.954 2.336 4.756 15.770 0.012 156 763 100 -53 -24 0.495 -31 -22 -12 -12 78379 81887 -0.152 -0.269 -50 0 0
237257 1 1 17 1 BLANK 6270 9610 140 507 517 133 25 520 520 531 130 24 12 1 0 514 516 65 12 531 531 539 71 13 7 2 0 0.765 0.200 1.940 2.077 3.719 5.835 0.044 156 771 100 -30 -18 -0.387 -13 -17 -3 -15 80648 80551 -0.108 -0.324 -50 0 0
237258 1 1 18 1 UNKNOWN_6 6460 9610 140 580 605 157 25 533 533 540 125 23 25 9 0 574 585 89 15 555 555 559 72 12 19 6 0 2.474 2.400 2.326 2.320 4.742 7.247 0.038 156 782 100 66 102 1.307 47 19 72 30 94354 91216 0.520 0.361 -50 0 0
237259 0.711153553 1 1 19 1 gi|14042897|gb|AK027893|AK027893 6640 9610 110 3074 3257 1321 40 492 492 502 126 25 100 100 0 3931 4761 3038 63 526 526 538 158 29 98 97 0 0.758 0.653 0.720 0.772 2.343 0.551 0.656 80 518 100 5987 7000 -0.399 2582 3405 2765 4235 260548 380913 21.865 26.728 0 0 0
237260 1 1 20 1 gi|5901981|ref|NM_006899.1| 6850 9610 140 507 506 122 24 455 455 467 127 27 25 4 0 543 544 64 11 502 502 514 161 31 3 0 0 1.268 1.214 1.797 1.775 3.619 7.529 0.029 156 896 100 93 93 0.343 52 41 51 42 78918 84895 0.307 0.186 -50 0 0

Total number of rows: 15488

Table truncated, full table size 4154 Kbytes.




Supplementary file Size Download File type/resource
GSM252343.gpr.gz 1.6 Mb (ftp)(http) GPR
Processed data included within Sample table
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