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Sample GSM252340 Query DataSets for GSM252340
Status Public on Dec 01, 2008
Title Human Prostate 514
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 514 treated with Neoadjuvant hormone suppression for 3-6 mo
Organism Homo sapiens
Characteristics Human Prostate 514. #: 514; Treatment: Neoadjuvant hormone suppression for 3-6 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 514 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 -0.462118723 1 1 1 1 gi|220150|gb|D90427|D90427 3370 9600 120 1628 1741 560 32 352 352 431 560 129 95 64 0 1128 1154 487 42 221 221 305 658 215 71 22 0 1.407 1.489 1.426 1.753 2.851 1.029 0.646 120 676 100 2183 2322 0.492 1276 907 1389 933 208925 138518 2.339 1.290 0 0 0
237242 -2.919132366 1 1 2 1 gi|179280|gb|M27132.1|HUMATPSYB 3570 9600 110 18628 23737 12979 54 363 363 466 637 136 100 100 0 3382 3882 1933 49 215 215 324 751 231 97 92 0 5.767 6.374 5.727 6.468 1.879 7.530 0.570 80 518 100 21432 27041 2.528 18265 3167 23374 3667 1898946 310556 36.532 4.738 0 0 0
237243 1 1 3 1 gi|12420723|gb|BG030944|BG030944 3750 9590 140 343 357 109 30 359 359 369 117 31 11 3 0 222 223 43 19 216 216 220 48 21 16 2 0 -2.667 -0.286 2.661 2.974 4.932 -81371.953 0.000 156 839 100 -10 5 Error -16 6 -2 7 55687 34722 -0.103 0.063 -50 0 0
237244 -1.187529278 1 1 4 1 gi|21536438|ref|NM_012161.2| 3950 9600 110 1595 1648 537 32 337 337 346 100 28 100 100 0 710 762 313 41 210 210 213 49 23 96 93 0 2.516 2.375 2.204 2.510 2.013 2.468 0.611 80 536 100 1758 1863 1.331 1258 500 1311 552 131863 60955 13.020 11.204 0 0 0
237245 -0.702577771 1 1 5 1 gi|21536438|ref|NM_012161.2| 4150 9610 110 1344 1523 599 39 315 315 325 97 29 100 100 0 759 790 273 34 201 201 205 41 20 100 100 0 1.844 2.051 2.013 2.034 1.669 2.362 0.647 80 522 100 1587 1797 0.883 1029 558 1208 589 121824 63226 12.351 14.268 0 0 0
237246 1 1 6 1 gi|14065685|gb|BG755019|BG755019 4340 9590 140 295 316 112 35 295 295 304 92 30 22 6 0 196 207 80 38 192 192 196 41 20 17 9 0 0.000 1.400 2.385 2.217 4.625 13.479 0.008 156 789 100 4 36 Error 0 4 21 15 49306 32229 0.130 0.268 -50 0 0
237247 1 1 7 1 gi|15996756|gb|BI856009|BI856009 4530 9590 140 267 281 84 29 285 285 292 88 30 17 1 0 191 194 36 18 188 188 192 43 22 14 1 0 -6.000 -0.667 2.886 3.481 5.008 -22.241 0.004 156 762 100 -15 2 Error -18 3 -4 6 43812 30314 -0.125 0.047 -50 0 0
237248 1 1 8 1 gi|19586973|gb|BM969386|BM969386 4730 9590 140 282 294 86 29 285 285 298 124 41 8 1 0 194 196 46 23 185 185 195 103 52 3 0 0 -0.333 0.818 1.595 1.834 3.870 -99.750 0.000 156 814 100 6 20 Error -3 9 9 11 45877 30586 -0.032 0.010 -50 0 0
237249 -2.133323156 1 1 9 1 gi|7703647|gb|AW771590| 4920 9600 110 13794 14052 5904 42 290 290 334 333 99 100 100 0 4279 3718 1865 50 189 189 219 472 215 88 87 0 3.302 3.900 3.811 5.348 3.343 4.417 0.633 80 510 100 17594 17291 1.723 13504 4090 13762 3529 1124195 297477 41.195 7.413 0 0 0
237250 1 1 10 1 gi|20408448|gb|BQ227048|BQ227048 5120 9600 140 257 272 84 30 279 279 308 266 86 0 0 0 188 187 39 20 184 184 206 366 177 0 0 0 -5.500 -2.333 2.182 2.245 3.796 4.204 0.280 156 857 100 -18 -4 Error -22 4 -7 3 42500 29147 -0.135 -0.052 -50 0 0
237251 -0.628160822 1 1 11 1 gi|11012215|gb|AU150694|AU150694 5320 9600 100 1715 1731 642 37 265 265 285 157 55 100 100 0 1296 1422 650 45 182 182 213 260 122 100 95 0 1.302 1.182 1.222 1.206 1.489 1.123 0.454 80 452 100 2564 2706 0.380 1450 1114 1466 1240 138443 113744 9.210 4.650 0 0 0
237252 1 1 12 1 gi|17298590|gb|AC009167.8| 5510 9600 140 262 265 75 28 265 265 287 152 52 3 0 0 176 183 38 20 183 183 201 198 98 0 0 0 0.429 0.000 2.000 1.764 3.676 0.379 0.231 156 809 100 -10 0 -1.222 -3 -7 0 0 41328 28567 -0.145 -0.091 -50 0 0
237253 -1.034012303 1 1 13 1 gi|13477360|gb|BC005157|BC005157 5700 9600 120 1130 1211 410 33 259 259 267 82 30 100 99 0 549 572 260 45 180 180 184 41 22 91 87 0 2.360 2.429 2.491 2.733 1.954 2.360 0.655 120 595 100 1240 1344 1.239 871 369 952 392 145319 68615 11.512 9.463 0 0 0
237254 1 1 14 1 UNKNOWN_4 5900 9600 140 247 256 80 31 258 258 266 82 30 14 1 0 181 185 38 20 180 180 182 38 20 17 3 0 -11.000 -0.400 2.500 2.560 3.875 24.015 0.004 156 832 100 -10 3 Error -11 1 -2 5 39990 28860 -0.122 0.079 -50 0 0
237255 -3.204546889 1 1 15 1 gi|5031976|ref|NM_005746.1| 6100 9610 110 10828 11071 5032 45 264 264 271 87 32 100 100 0 2015 2479 1589 64 181 181 183 36 19 98 96 0 5.760 4.703 4.665 5.785 2.658 4.560 0.633 80 495 100 12398 13105 2.526 10564 1834 10807 2298 885671 198343 124.138 63.778 0 0 0
237256 1 1 16 1 gi|4827043|ref|NM_005121.1| 6290 9600 140 257 262 79 30 263 263 270 89 32 11 1 0 176 182 54 29 180 180 182 38 20 12 3 0 1.500 -0.500 2.292 2.186 3.494 18.328 0.004 156 792 100 -10 1 0.585 -6 -4 -1 2 40895 28335 -0.090 0.000 -50 0 0
237257 1 1 17 1 BLANK 6490 9600 140 269 267 81 30 255 255 271 94 34 15 1 0 174 180 36 20 178 178 187 130 69 0 0 0 -3.500 6.000 2.304 1.985 4.200 -533.442 0.000 156 776 100 10 14 Error 14 -4 12 2 41592 28077 -0.043 -0.054 -50 0 0
237258 1 1 18 1 UNKNOWN_6 6680 9600 140 268 281 99 35 276 276 282 91 32 14 5 0 185 189 51 26 182 182 188 47 25 10 1 0 -2.667 0.714 2.083 1.878 4.056 30.944 0.002 156 753 100 -5 12 Error -8 3 5 7 43855 29509 -0.011 0.021 -50 0 0
237259 1.038189273 1 1 19 1 gi|14042897|gb|AK027893|AK027893 6860 9610 120 1787 1820 529 29 290 290 299 91 30 100 100 0 3103 3281 1537 46 190 190 197 49 24 100 100 0 0.514 0.495 0.520 0.531 2.040 0.364 0.574 120 575 100 4410 4621 -0.960 1497 2913 1530 3091 218341 393728 16.714 62.939 0 0 0
237260 1 1 20 1 gi|5901981|ref|NM_006899.1| 7070 9600 140 298 316 95 30 302 302 311 92 29 19 5 0 205 212 53 25 199 199 207 51 24 16 6 0 -0.667 1.077 1.926 1.973 4.223 26.093 0.003 156 836 100 2 27 Error -4 6 14 13 49303 33100 0.054 0.098 -50 0 0

Total number of rows: 15488

Table truncated, full table size 4216 Kbytes.




Supplementary file Size Download File type/resource
GSM252340.gpr.gz 1.6 Mb (ftp)(http) GPR
Processed data included within Sample table
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