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Sample GSM252342 Query DataSets for GSM252342
Status Public on Dec 01, 2008
Title Human Prostate 643
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 643 treated with Neoadjuvant hormone suppression for 3-6 mo
Organism Homo sapiens
Characteristics Human Prostate 643. #: 643; 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 643 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 0.898230027 1 1 1 1 gi|220150|gb|D90427|D90427 3150 10010 120 2329 2500 749 29 1098 1098 1111 190 17 98 95 0 2581 2689 797 29 1496 1496 1511 206 13 91 84 0 1.135 1.175 1.267 1.252 1.955 1.064 0.604 120 676 100 2316 2595 0.182 1231 1085 1402 1193 299975 322721 7.311 5.718 0 0 0
237242 -3.82378039 1 1 2 1 gi|179280|gb|M27132.1|HUMATPSYB 3350 10010 100 22694 26451 12704 48 1103 1103 1120 190 16 100 100 0 3523 4043 1464 36 1497 1497 1512 218 14 97 97 0 10.657 9.956 9.204 10.578 1.719 10.778 0.725 80 473 100 23617 27894 3.414 21591 2026 25348 2546 2116075 323435 133.321 11.610 0 0 0
237243 1 1 3 1 gi|12420723|gb|BG030944|BG030944 3540 10000 140 1043 1048 180 17 1070 1070 1080 188 17 14 0 0 1416 1400 191 13 1435 1435 1444 200 13 12 1 0 1.421 0.629 1.050 1.142 4.347 0.087 0.000 156 862 100 -46 -57 0.507 -27 -19 -22 -35 163486 218340 -0.170 -0.220 -50 0 0
237244 -1.103297031 1 1 4 1 gi|21536438|ref|NM_012161.2| 3730 10010 100 4148 4641 1651 35 1087 1087 1080 175 16 100 100 0 2024 2249 669 29 1404 1404 1421 212 14 90 66 0 4.937 4.206 5.320 5.127 2.125 4.496 0.476 80 476 100 3681 4399 2.304 3061 620 3554 845 371296 179928 20.349 3.906 0 0 0
237245 -0.937132536 1 1 5 1 gi|21536438|ref|NM_012161.2| 3920 10010 100 3937 4493 1758 39 991 991 994 436 43 100 98 0 2037 2274 730 32 1347 1347 1433 1622 113 18 0 0 4.270 3.778 4.292 4.654 2.636 0.700 0.098 80 489 100 3636 4429 2.094 2946 690 3502 927 359479 181955 8.025 0.518 0 0 0
237246 1 1 6 1 gi|14065685|gb|BG755019|BG755019 4120 10000 140 899 897 145 16 928 928 942 358 38 0 0 0 1308 1289 194 15 1299 1299 1373 1296 94 0 0 0 -3.222 3.100 0.532 0.753 4.391 0.159 0.334 156 780 100 -20 -41 Error -29 9 -31 -10 139868 201144 -0.126 -0.065 -50 0 0
237247 1 1 7 1 gi|15996756|gb|BI856009|BI856009 4320 10000 140 901 915 164 17 953 953 997 266 26 4 0 0 1283 1305 229 17 1311 1311 1340 247 18 10 3 0 1.857 6.333 0.894 1.071 4.577 0.091 0.002 156 751 100 -80 -44 0.893 -52 -28 -38 -6 142669 203570 -0.308 -0.142 -50 0 0
237248 1 1 8 1 gi|19586973|gb|BM969386|BM969386 4510 10000 140 918 968 297 30 953 953 1041 1316 126 1 0 0 1307 1316 201 15 1303 1303 1327 383 28 5 0 0 -8.750 1.154 0.851 0.766 4.280 1.471 0.047 156 819 100 -31 28 Error -35 4 15 13 151077 205327 -0.055 -0.029 -50 0 0
237249 -2.620251918 1 1 9 1 gi|7703647|gb|AW771590| 4710 10010 100 14772 15773 6587 41 955 955 958 178 18 100 100 0 4146 4422 1265 28 1319 1319 1321 209 15 100 100 0 4.888 4.775 4.927 4.682 1.786 5.804 0.614 80 453 100 16644 17921 2.289 13817 2827 14818 3103 1261807 353729 83.230 14.837 0 0 0
237250 1 1 10 1 gi|20408448|gb|BQ227048|BQ227048 4900 10000 140 933 999 496 49 944 944 949 171 18 11 4 0 1289 1297 230 17 1267 1267 1279 202 15 15 3 0 -0.500 1.833 0.913 1.060 3.999 3.132 0.064 156 868 100 11 85 Error -11 22 55 30 155778 202383 0.292 0.089 -50 0 0
237251 -2.651921356 1 1 11 1 gi|11012215|gb|AU150694|AU150694 5090 10000 90 2318 2542 907 35 941 941 1000 509 50 94 65 0 1341 1472 472 32 1244 1244 1279 271 21 32 17 0 14.196 7.022 5.960 6.423 2.542 6.069 0.325 52 382 100 1474 1829 3.827 1377 97 1601 228 132168 76560 3.029 0.712 0 0 0
237252 1 1 12 1 gi|17298590|gb|AC009167.8| 5290 10000 140 867 872 142 16 898 898 934 360 38 0 0 0 1200 1235 275 22 1208 1208 1233 228 18 12 3 0 3.875 -0.963 1.000 0.941 3.789 0.573 0.112 156 880 100 -39 1 1.954 -31 -8 -26 27 135981 192584 -0.172 0.009 -50 0 0
237253 -1.571671652 1 1 13 1 gi|13477360|gb|BC005157|BC005157 5470 10000 110 2120 2245 662 29 880 880 889 166 18 100 100 0 1428 1538 393 25 1158 1158 1174 186 15 65 38 0 4.593 3.592 3.837 4.278 2.781 3.390 0.332 80 518 100 1510 1745 2.199 1240 270 1365 380 179576 123076 8.169 1.957 0 0 0
237254 1 1 14 1 UNKNOWN_4 5680 10000 140 820 830 166 20 835 835 856 348 40 2 0 0 1116 1134 226 19 1136 1136 1150 174 15 17 4 0 0.750 2.500 0.730 0.812 4.970 0.064 0.001 156 905 100 -35 -7 -0.415 -15 -20 -5 -2 129499 176938 -0.075 -0.092 -50 0 0
237255 -3.314092208 1 1 15 1 gi|5031976|ref|NM_005746.1| 5880 10010 80 12486 11852 5571 47 755 755 773 177 22 100 100 0 2413 2542 1047 41 1089 1089 1096 177 16 86 82 0 8.860 7.637 7.934 9.478 2.007 7.495 0.712 52 328 100 13055 12550 3.147 11731 1324 11097 1453 616303 132196 62.593 8.169 0 0 0
237256 0.350249761 1 1 16 1 gi|4827043|ref|NM_005121.1| 6120 10040 70 5552 5810 3805 65 313 313 330 120 36 93 90 0 9002 9508 6209 65 654 654 649 174 26 87 87 0 0.628 0.621 0.547 0.610 3.405 0.574 0.753 32 207 100 13587 14351 -0.672 5239 8348 5497 8854 185906 304267 45.667 50.914 0 0 0
237257 1 1 17 1 BLANK 6270 10000 140 525 577 348 60 607 607 600 218 36 5 3 0 832 860 221 25 937 937 939 359 38 3 1 0 0.781 0.390 0.967 1.006 3.325 0.436 0.418 156 832 100 -187 -107 -0.357 -82 -105 -30 -77 90001 134145 -0.106 -0.220 -50 0 0
237258 1 1 18 1 UNKNOWN_6 6460 10000 140 705 726 173 23 758 758 762 166 21 12 2 0 1020 1031 175 16 1044 1044 1066 277 25 4 1 0 2.208 2.462 1.011 1.234 3.951 0.154 0.034 156 796 100 -77 -45 1.143 -53 -24 -32 -13 113272 160893 -0.217 -0.126 -50 0 0
237259 -1.84754122 1 1 19 1 gi|14042897|gb|AK027893|AK027893 6650 10000 110 2259 2419 830 34 824 824 830 167 20 100 100 0 1343 1492 391 26 1089 1089 1106 209 18 56 35 0 5.650 3.958 4.786 4.969 2.663 3.529 0.401 80 520 100 1689 1998 2.498 1435 254 1595 403 193550 119389 9.515 1.847 0 0 0
237260 1 1 20 1 gi|5901981|ref|NM_006899.1| 6850 10000 140 828 838 184 21 797 797 817 207 25 14 3 0 1093 1099 197 17 1059 1059 1086 241 22 14 2 0 0.912 1.025 0.833 0.977 3.809 0.548 0.036 156 847 100 65 81 -0.133 31 34 41 40 130677 171472 0.101 0.054 -50 0 0

Total number of rows: 15488

Table truncated, full table size 4226 Kbytes.




Supplementary file Size Download File type/resource
GSM252342.gpr.gz 1.6 Mb (ftp)(http) GPR
Processed data included within Sample table
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