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Sample GSM252347 Query DataSets for GSM252347
Status Public on Dec 01, 2008
Title Human Prostate 687
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 687 treated with Immediate Radical Prostatectomy
Organism Homo sapiens
Characteristics Human Prostate 687. #: 687; 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 687 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 2.947240859 1 1 1 1 gi|220150|gb|D90427|D90427 3370 9960 130 2211 2305 555 24 2170 2170 2171 194 8 37 30 0 796 825 369 44 412 412 418 62 14 87 76 0 0.107 0.327 1.286 1.026 7.243 2.867 0.046 120 756 100 425 548 -3.227 41 384 135 413 276566 98958 0.691 6.565 0 0 0
237242 -2.539547126 1 1 2 1 gi|179280|gb|M27132.1|HUMATPSYB 3530 9950 50 3248 3698 1281 34 2162 2162 2228 361 16 91 75 0 804 908 411 45 397 397 448 252 56 66 41 0 2.668 3.006 2.833 3.255 2.087 3.613 0.652 12 104 100 1493 2047 1.416 1086 407 1536 511 44375 10891 4.072 1.825 0 0 0
237243 1 1 3 1 gi|12420723|gb|BG030944|BG030944 3760 9950 140 1862 1822 268 14 2036 2036 2052 234 11 2 0 0 368 377 76 20 399 399 412 115 27 4 0 0 5.613 9.727 3.659 3.615 4.267 13.036 0.050 156 969 100 -205 -236 2.489 -174 -31 -214 -22 284282 58773 -0.983 -0.304 -50 0 0
237244 -1.272072577 1 1 4 1 gi|21536438|ref|NM_012161.2| 3960 9970 100 2436 2457 492 20 2028 2028 2030 186 9 63 52 0 650 656 164 25 390 390 397 70 17 90 76 0 1.569 1.613 1.873 1.648 2.660 2.923 0.441 80 490 100 668 695 0.650 408 260 429 266 196531 52504 2.296 3.700 0 0 0
237245 -0.844235071 1 1 5 1 gi|21536438|ref|NM_012161.2| 4150 9970 100 2245 2339 484 20 1936 1936 1943 167 8 61 45 0 626 628 167 26 380 380 392 125 31 71 48 0 1.256 1.625 2.200 2.033 3.147 3.170 0.193 80 480 100 555 651 0.329 309 246 403 248 187130 50265 2.371 1.888 0 0 0
237246 1 1 6 1 gi|14065685|gb|BG755019|BG755019 4350 9960 140 1802 1819 172 9 1857 1857 1862 171 9 8 2 0 360 370 72 19 372 372 382 111 29 4 0 0 4.583 19.000 2.821 2.619 4.432 6.835 0.011 156 744 100 -67 -40 2.196 -55 -12 -38 -2 283776 57744 -0.251 -0.108 -50 0 0
237247 1 1 7 1 gi|15996756|gb|BI856009|BI856009 4540 9960 140 1763 1772 383 21 1782 1782 1780 168 9 18 5 0 356 369 97 26 358 358 369 142 38 5 1 0 9.500 -0.909 2.921 2.526 4.543 6.392 0.225 156 736 100 -21 1 3.248 -19 -2 -10 11 276497 57542 -0.048 0.000 -50 0 0
237248 1 1 8 1 gi|19586973|gb|BM969386|BM969386 4740 9960 140 1734 1755 213 12 1751 1751 1757 177 10 12 3 0 356 360 59 16 350 350 361 134 37 3 0 0 -2.833 0.400 4.629 4.755 4.179 18.556 0.024 156 829 100 -11 14 Error -17 6 4 10 273821 56171 -0.011 -0.007 -50 0 0
237249 -1.586255374 1 1 9 1 gi|7703647|gb|AW771590| 4940 9980 100 7465 7979 3760 47 1782 1782 1789 170 9 96 96 0 3166 3144 1703 54 356 356 362 62 17 97 96 0 2.022 2.223 2.185 2.259 1.894 2.434 0.751 80 455 100 8493 8985 1.016 5683 2810 6197 2788 638324 251554 36.412 44.871 0 0 0
237250 1 1 10 1 gi|20408448|gb|BQ227048|BQ227048 5130 9970 140 1666 1667 161 9 1742 1742 1748 164 9 8 0 0 335 336 57 16 341 341 350 67 19 7 0 0 12.667 15.000 2.838 2.989 4.554 29.473 0.008 156 848 100 -82 -80 3.663 -76 -6 -75 -5 260114 52344 -0.494 -0.209 -50 0 0
237251 -0.702054646 1 1 11 1 gi|11012215|gb|AU150694|AU150694 5320 9970 110 2521 2605 892 34 1651 1651 1654 172 10 72 67 0 1329 1399 757 54 330 330 343 145 42 90 85 0 0.871 0.892 0.835 0.888 4.422 1.005 0.493 80 529 100 1869 2023 -0.199 870 999 954 1069 208406 111897 5.529 7.283 0 0 0
237252 1 1 12 1 gi|17298590|gb|AC009167.8| 5520 9970 140 1598 1615 249 15 1642 1642 1651 177 10 11 2 0 322 336 119 35 329 329 340 119 35 3 2 0 6.286 -3.857 3.739 3.150 5.033 5.822 0.133 156 858 100 -51 -20 2.652 -44 -7 -27 7 252001 52453 -0.203 -0.034 -50 0 0
237253 1.181036825 1 1 13 1 gi|13477360|gb|BC005157|BC005157 5690 10010 110 1622 1651 376 22 1596 1596 1605 166 10 30 18 0 371 396 110 27 316 316 329 69 20 45 22 0 0.473 0.688 3.305 3.566 5.211 7.305 0.095 80 448 100 81 135 -1.081 26 55 55 80 132100 31663 0.277 0.971 0 0 0
237254 1 1 14 1 UNKNOWN_4 5900 9980 140 1536 1537 133 8 1556 1556 1570 176 11 5 1 0 308 315 51 16 310 310 330 96 29 3 0 0 10.000 -3.800 2.630 2.288 4.154 23.975 0.008 156 911 100 -22 -14 3.322 -20 -2 -19 5 239809 49078 -0.187 -0.156 -50 0 0
237255 1 1 15 1 gi|5031976|ref|NM_005746.1| 6100 9980 140 1467 1473 153 10 1531 1531 1538 158 10 8 1 0 284 293 58 19 302 302 318 214 67 0 0 0 3.556 6.444 3.014 2.847 4.591 0.017 0.000 156 753 100 -82 -67 1.830 -64 -18 -58 -9 229854 45708 -0.411 -0.117 -50 0 0
237256 1 1 16 1 gi|4827043|ref|NM_005121.1| 6290 9980 140 1461 1471 163 11 1515 1515 1512 153 10 12 1 0 298 308 91 29 300 300 314 210 66 0 0 0 27.000 -5.500 2.542 2.512 3.747 0.031 0.001 156 721 100 -56 -36 4.755 -54 -2 -44 8 229461 48080 -0.268 -0.029 -50 0 0
237257 1 1 17 1 BLANK 6490 9980 140 1441 1442 169 11 1451 1451 1457 156 10 15 3 0 305 304 52 17 292 292 296 47 15 23 3 0 -0.769 -0.750 2.969 3.017 4.645 26.858 0.013 156 746 100 3 3 Error -10 13 -9 12 224905 47408 -0.096 0.170 -50 0 0
237258 1 1 18 1 UNKNOWN_6 6680 9990 140 1365 1384 148 10 1425 1425 1426 143 10 11 1 0 291 300 76 25 289 289 294 50 17 20 5 0 -30.000 -3.727 2.906 2.856 4.634 10.414 0.041 156 796 100 -58 -30 Error -60 2 -41 11 215856 46836 -0.294 0.120 -50 0 0
237259 1.25591037 1 1 19 1 gi|14042897|gb|AK027893|AK027893 6880 10000 110 2190 2269 388 17 1422 1422 1422 152 10 98 92 0 3716 4617 2565 55 292 292 303 134 44 100 100 0 0.224 0.196 0.204 0.205 1.851 0.149 0.481 80 511 100 4192 5172 -2.157 768 3424 847 4325 181498 369348 5.572 32.194 0 0 0
237260 1 1 20 1 gi|5901981|ref|NM_006899.1| 7070 9990 140 1324 1328 131 9 1363 1363 1360 165 12 5 0 0 289 307 89 28 279 279 289 111 38 10 4 0 -3.900 -1.250 2.607 2.681 4.971 12.747 0.013 156 905 100 -29 -7 Error -39 10 -35 28 207208 47865 -0.194 0.162 -50 0 0

Total number of rows: 15488

Table truncated, full table size 4220 Kbytes.




Supplementary file Size Download File type/resource
GSM252347.gpr.gz 1.6 Mb (ftp)(http) GPR
Processed data included within Sample table
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