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Sample GSM251858 Query DataSets for GSM251858
Status Public on Dec 01, 2008
Title Human Prostate GSK-6
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-6 treated with Immediate Radical Prostatectomy
Organism Homo sapiens
Characteristics Human Prostate GSK-6. Specimen ID: GSK-6; 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-6 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) dmauldin@fhcrc.org
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 0.707498287 1 1 1 1 P:1 2140 9340 140 1783 1941 805 239 264 119 99 98 0 1661 1841 1060 83 91 39 98 96 0 0.978 0.968 0.947 1.112 1.911 0.881 0.818 156 761 3122 3460 -0.031 1544 1578 1702 1758 302837 287262 14.092 44.872 0 0
237242 -2.89218617 1 1 2 1 P:5 2340 9340 140 20995 23336 15363 251 275 123 100 100 1 2428 2840 2739 84 93 37 93 91 0 8.85 8.376 10.391 8.935 2.422 10.617 0.415 156 713 23088 25841 3.146 20744 2344 23085 2756 3640388 442990 187.488 74.243 0 0
237243 -2.648710541 1 1 3 1 P:9 2530 9340 110 7943 8154 2482 232 245 84 100 100 0 929 967 292 83 92 42 100 100 0 9.115 8.962 8.966 9.018 1.374 9.613 0.739 80 506 8557 8806 3.188 7711 846 7922 884 652318 77380 94.155 20.833 0 0
237244 -1.349023371 1 1 4 1 P:13 2720 9340 120 2356 2361 783 227 238 86 100 100 0 682 692 263 80 91 43 99 96 0 3.537 3.487 3.648 3.719 1.836 3.857 0.712 120 615 2731 2746 1.822 2129 602 2134 612 283261 83087 24.686 13.977 0 0
237245 -1.185571839 1 1 5 1 P:17 2910 9340 120 2392 2502 945 215 229 83 100 100 0 730 747 250 81 91 37 100 100 0 3.354 3.434 3.366 3.387 1.586 3.917 0.74 120 601 2826 2953 1.746 2177 649 2287 666 300252 89620 27.386 17.73 0 0
237246 3.647109432 1 1 6 1 P:21 3100 9330 110 778 838 288 212 227 84 100 98 0 4602 4963 1951 80 91 63 100 100 0 0.125 0.128 0.119 0.123 1.847 0.102 0.54 80 539 5088 5509 -2.998 566 4522 626 4883 67005 397065 7.274 77.333 0 0
237247 -2.222426517 1 1 7 1 P:97 3280 9330 90 33593 34934 10903 230 896 3907 100 100 0 4376 4433 1689 83 261 946 98 90 0 7.771 7.978 7.786 8.447 1.614 8.208 0.758 52 400 37656 39054 2.958 33363 4293 34704 4350 1816562 230521 8.712 4.41 0 0
237248 -1.818118178 1 1 8 1 P:101 3480 9340 100 3231 3156 1202 221 628 2861 51 0 0 620 586 259 83 213 849 8 0 0 5.605 5.835 6.219 6.499 1.922 5.977 0.777 80 481 3547 3438 2.487 3010 537 2935 503 252507 46840 0.884 0.439 0 0
237249 -1.92535822 1 1 9 1 P:105 3680 9330 120 26780 26713 6581 222 238 86 100 100 0 4511 4378 1441 83 91 40 100 99 0 5.998 6.168 6.22 6.44 1.582 6.323 0.802 120 604 30986 30786 2.584 26558 4428 26491 4295 3205569 525372 307.849 107.175 0 0
237250 -1.023841106 1 1 10 1 P:109 3870 9330 120 17260 18147 8286 220 233 87 100 100 0 5615 5241 2548 81 88 32 99 99 0 3.079 3.474 3.562 3.844 2.06 3.81 0.769 120 605 22574 23087 1.623 17040 5534 17927 5160 2177676 628861 205.908 161.031 0 0
237251 0.074772029 1 1 11 1 P:113 4070 9340 120 2159 2301 902 212 234 281 100 100 0 1399 1344 487 81 114 490 88 85 0 1.477 1.654 1.665 1.765 1.945 1.483 0.394 120 636 3265 3352 0.563 1947 1318 2089 1263 276083 161279 7.356 2.51 0 0
237252 1.783912755 1 1 12 1 P:117 4270 9320 110 1543 1668 686 203 228 300 100 96 0 3365 3746 1747 79 116 528 100 100 0 0.408 0.4 0.402 0.399 1.578 0.336 0.668 80 549 4626 5132 -1.294 1340 3286 1465 3667 133477 299717 4.8 6.875 0 0
237253 -1.139564096 1 1 13 1 P:193 4460 9320 130 1277 1299 322 200 211 74 100 100 0 464 467 143 75 81 30 99 99 0 2.769 2.804 2.777 2.866 1.616 3.084 0.708 120 684 1466 1491 1.469 1077 389 1099 392 155927 56088 14.703 12.867 0 0
237254 -0.757095433 1 1 14 1 P:197 4650 9320 110 639 648 212 203 212 71 98 92 0 223 258 240 75 82 32 100 97 0 2.946 2.432 2.662 2.553 1.971 2.497 0.25 80 534 584 628 1.559 436 148 445 183 51819 20667 6.141 5.5 0 0
237255 -2.777458436 1 1 15 1 P:201 4850 9320 120 8572 10129 6322 201 214 83 100 100 0 923 1021 527 78 85 34 98 95 0 9.907 10.528 9.97 10.298 1.948 13.402 0.67 120 652 9216 10871 3.308 8371 845 9928 943 1215491 122528 119.458 27.529 0 0
237256 0.130267077 1 1 16 1 P:205 5050 9330 110 3450 3607 1172 199 208 68 100 100 0 2916 3127 1435 78 84 30 100 100 0 1.146 1.118 1.245 1.226 1.839 1.038 0.715 80 538 6089 6457 0.196 3251 2838 3408 3049 288596 250134 49.985 101.433 0 0
237257 2.107456551 1 1 17 1 P:209 5240 9320 110 870 908 227 196 205 74 100 100 0 2112 2100 651 80 86 30 100 100 0 0.332 0.352 0.368 0.354 1.413 0.308 0.663 80 570 2706 2732 -1.592 674 2032 712 2020 72635 168005 9.5 67.133 0 0
237258 -1.114574231 1 1 18 1 P:213 5430 9330 110 5098 5481 1407 193 204 72 100 100 0 3051 3138 532 83 90 35 100 100 0 1.653 1.731 1.674 1.706 1.295 1.673 0.688 80 527 7873 8343 0.725 4905 2968 5288 3055 438497 251073 73.292 87.086 0 0
237259 1.444056893 1 1 19 1 P:289 5620 9310 130 1378 1455 507 192 199 67 100 100 0 2090 2337 1104 80 87 30 100 100 0 0.59 0.56 0.581 0.592 1.93 0.46 0.58 120 694 3196 3520 -0.761 1186 2010 1263 2257 174645 280426 18.746 75 0 0
237260 -0.131582458 1 1 20 1 P:293 5820 9320 120 3117 3672 2139 186 210 145 100 100 0 1961 1870 982 79 94 66 97 92 0 1.557 1.946 1.914 2.145 2.377 2.3 0.667 120 599 4813 5277 0.639 2931 1882 3486 1791 440663 224383 23.876 26.909 0 0

Total number of rows: 15488

Table truncated, full table size 3468 Kbytes.




Supplementary file Size Download File type/resource
GSM251858.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
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