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Sample GSM251871 Query DataSets for GSM251871
Status Public on Dec 01, 2008
Title Human Prostate GSK-12
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). Approximately 2000-3000 epithelial cells per sample were collected from 8µm sections using the Arcturus Veritas™ Laser Capture Microdissection System according to the Arcturus HistoGene LCM Frozen Section Staining Kit Protocol (Mountain View, CA). Total RNA was isolated 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 GSK-12 treated with Immediate Radical Prostatectomy
Organism Homo sapiens
Characteristics Human Prostate GSK-12. Specimen ID: GSK-12; Treatment: Immediate Radical Prostatectomy; Reference: HGSv5;
Extracted molecule total RNA
Extraction protocol Prostate samples embedded in OCT were used for laser capture microdissection (LCM). Approximately 2000-3000 epithelial cells per sample were collected from 8µm sections using the Arcturus Veritas™ Laser Capture Microdissection System according to the Arcturus HistoGene LCM Frozen Section Staining Kit Protocol (Mountain View, CA). Total RNA was isolated 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 GSK-12 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 18, 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)
GSE9972 Prostate Cancer Gene Expression Changes after Treatment with Neoadjuvant Dutasteride

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).
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+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).
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+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.
Sum of Medians the sum of the median intensities for each wavelength, with the median background subtracted.
Sum of Means 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).

Data table
ID_REF VALUE MetaCol MetaRow Column Row Name X Y Dia. F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD % > 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 Sum of Medians Sum of Means 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
237241 -0.012907858 1 1 1 1 P:1 3060 9340 130 1749 1932 778 261 317 722 94 53 0 951 1254 725 215 220 44 100 100 0 2.022 1.608 1.785 1.765 1.36 1.48 0.804 120 743 2224 2710 1.016 1488 736 1671 1039 231869 150533 2.237 23.5 0 0
237242 -3.713833281 1 1 2 1 P:5 3260 9350 120 24271 25379 10533 300 313 131 100 100 0 1489 1526 433 231 235 37 100 100 0 19.055 19.366 20.14 18.693 1.501 21.816 0.84 120 620 25229 26374 4.252 23971 1258 25079 1295 3045501 183126 191.344 34.892 0 0
237243 -2.591103051 1 1 3 1 P:9 3450 9360 100 7080 7857 2934 316 328 104 100 100 0 817 909 252 243 246 38 100 100 0 11.784 11.323 11.563 11.348 1.337 11.935 0.864 80 464 7338 8207 3.559 6764 574 7541 666 628559 72733 72.394 17.447 0 0
237244 -0.810064469 1 1 4 1 P:13 3650 9350 120 1848 1841 518 316 326 102 100 100 0 733 785 219 246 247 38 100 100 0 3.146 2.829 3.128 2.851 1.613 3.013 0.767 120 619 2019 2064 1.653 1532 487 1525 539 220936 94235 14.853 14.158 0 0
237245 -0.685114066 1 1 5 1 P:17 3840 9360 120 1792 1844 415 318 322 86 100 100 0 758 782 220 247 250 35 99 99 0 2.885 2.852 3.064 3.065 1.565 2.861 0.74 120 594 1985 2061 1.528 1474 511 1526 535 221327 93787 17.698 15.2 0 0
237246 3.027565458 1 1 6 1 P:21 4030 9350 120 900 942 190 311 314 87 100 100 0 2406 2408 818 250 257 55 100 100 0 0.273 0.292 0.303 0.304 1.627 0.244 0.703 120 552 2745 2789 -1.872 589 2156 631 2158 112987 288955 7.218 39.109 0 0
237247 1 1 7 1 P:97 4220 9350 140 220 227 71 251 284 243 0 0 0 200 201 40 211 219 76 1 0 0 2.818 2.4 1.809 1.742 2.937 3.324 0.103 156 743 -42 -34 1.495 -31 -11 -24 -10 35381 31348 -0.235 -0.237 -50 0
237248 -2.119691439 1 1 8 1 P:101 4430 9360 100 3823 3603 1033 221 246 198 100 98 0 600 561 152 172 175 32 100 93 0 8.416 8.694 8.333 9.308 1.504 8.626 0.884 80 450 4030 3771 3.073 3602 428 3382 389 288207 44865 16.955 12.063 0 0
237249 -2.580113652 1 1 9 1 P:105 4610 9360 120 23289 22346 5585 275 303 181 100 100 0 2328 2191 707 214 219 55 100 100 0 10.886 11.164 11.28 12.29 1.506 10.851 0.91 120 621 25128 24048 3.444 23014 2114 22071 1977 2681531 262869 121.785 35.855 0 0
237250 -1.123568788 1 1 10 1 P:109 4800 9360 110 17924 19505 6541 316 342 152 100 100 0 4313 4603 1682 241 248 70 100 100 0 4.324 4.399 4.395 4.515 1.369 4.567 0.771 80 525 21680 23551 2.112 17608 4072 19189 4362 1560434 368250 126.072 62.214 0 0
237251 -0.529906124 1 1 11 1 P:113 4990 9350 120 2467 2447 553 317 336 138 100 100 0 1172 1145 212 253 256 52 100 100 0 2.339 2.388 2.33 2.387 1.27 2.422 0.88 120 636 3069 3022 1.226 2150 919 2130 892 293644 137387 15.297 17.096 0 0
237252 1.920904972 1 1 12 1 P:117 5200 9360 120 1302 1310 370 322 334 159 98 95 0 2897 3145 1538 258 265 90 100 99 0 0.371 0.342 0.383 0.377 2.008 0.273 0.719 120 643 3619 3875 -1.429 980 2639 988 2887 157142 377377 6.138 32 0 0
237253 -1.158098933 1 1 13 1 P:193 5390 9360 130 1547 1602 344 330 346 167 100 100 0 535 544 108 256 262 80 100 90 0 4.362 4.417 4.617 4.569 1.461 4.739 0.736 120 676 1496 1560 2.125 1217 279 1272 288 192239 65244 7.521 3.525 0 0
237254 -0.661287161 1 1 14 1 P:197 5590 9350 110 918 946 154 317 330 103 100 100 0 338 340 49 247 249 39 86 61 0 6.604 6.763 6.513 7.665 2.024 7.065 0.424 80 526 692 722 2.723 601 91 629 93 75644 27160 5.981 2.333 0 0
237255 -0.89800189 1 1 15 1 P:201 5780 9360 110 4539 4745 1166 334 349 137 100 100 0 1909 1878 484 256 267 101 100 100 0 2.544 2.719 2.605 2.825 1.38 2.689 0.859 80 527 5858 6033 1.347 4205 1653 4411 1622 379621 150238 32.088 15.95 0 0
237256 1 1 16 1 P:205 5980 9350 140 322 329 88 334 348 125 7 0 0 257 255 32 262 272 100 0 0 0 2.4 0.714 2.76 2.702 4.33 28.981 0.005 156 780 -17 -12 1.263 -12 -5 -5 -7 51366 39832 -0.152 -0.17 -50 0
237257 1.463494555 1 1 17 1 P:209 6190 9340 110 1496 1547 376 346 349 84 100 100 0 2483 2496 614 267 273 53 100 100 0 0.519 0.539 0.53 0.541 1.366 0.811 0.304 80 553 3366 3430 -0.946 1150 2216 1201 2229 123766 199678 14.262 41.943 0 0
237258 -0.80085524 1 1 18 1 P:213 6370 9360 100 6471 6552 1180 359 367 105 100 100 0 3415 3389 898 272 282 79 100 100 0 1.945 1.987 1.993 2.112 1.527 1.913 0.873 80 468 9255 9310 0.96 6112 3143 6193 3117 524192 271113 58.905 39.329 0 0
237259 0.739074455 1 1 19 1 P:289 6570 9350 120 1748 1926 617 351 362 102 100 100 0 1647 1732 419 271 278 61 100 100 0 1.015 1.078 1.047 1.05 1.353 1.139 0.786 120 638 2773 3036 0.022 1397 1376 1575 1461 231128 207891 15.333 23.836 0 0
237260 -1.077321506 1 1 20 1 P:293 6770 9350 100 5027 5652 3006 352 388 224 100 100 0 2025 2329 1129 269 279 69 100 100 0 2.662 2.573 2.453 2.596 1.439 2.886 0.768 80 476 6431 7360 1.413 4675 1756 5300 2060 452124 186349 23.5 29.71 0 0

Total number of rows: 15488

Table truncated, full table size 3461 Kbytes.




Supplementary file Size Download File type/resource
GSM251871.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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