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Sample GSM253462 Query DataSets for GSM253462
Status Public on Dec 01, 2008
Title Time: at Radical Prostatectomy, Treatment: Low-fat/lowglycemic load, Type: Needle (030107_PL)
Sample type RNA
 
Channel 1
Source name Reference
Organism Homo sapiens
Characteristics Reference
Extracted molecule total RNA
Extraction protocol Biopsy cores were embedded individually in polyethylene glycol freezing media (Tissue-Tek OCT Compound, Sakura Finetek, Torrance, CA) and placed in isopentane that was precooled in liquid nitrogen. Specimens were then placed at 80°C until laser-capture microdissection (LCM). At time of LCM, 8-um frozen sections were obtained and immediately fixed in cold 95% ethanol. Sections were briefly (5 to 10 seconds) stained with hematoxylin using the Arcturus HistoGene Staining Solution (Arcturus Bioscience, Mountain View, CA) and dehydrated in 100% ethanol followed by xylenes (described in the Arcturus HistoGene LCM Frozen Section Staining Kit protocol). Five thousand epithelial cells from histologically benign glands were obtained by LCM using the Arcturus PixCell II instrument (modified from Emmert-Buck as described in Moore S, Knudsen B, True LD, et al: Loss of stearoyl-CoA desaturase expression is a frequent event in prostate carcinoma. Int J Cancer 114:563-571, 2005). Digital photos were taken of tissue sections before, during, and after LCM and assessed by an experienced genitourinary pathologist (B.S.K.) to confirm the histology of the laser captured cells. Each slide capture session lasted no longer than 20 minutes to minimize RNA degradation. The laser capture settings were 55mWbeam, 1.5 ms pulse, and 15um spot size. Cells were lysed in Arcturus RNA Extraction Buffer, RNA was isolated using the Arcturus PicoPure RNA Isolation Kit, and the samples were treated with DNAse using the Qiagen RNase-Free DNAse Set (Qiagen Inc, Valencia, CA). RNA was amplified for two rounds using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), and sample quality and quantity were assessed by agarose gel electrophoresis and absorbance at A260. To provide a reference standard RNA for use on cDNA microarrays, we isolated total RNA from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640-1640 medium supplemented with 10% fetal bovine serum (FBS; Life Technologies, Rockville, MD). RNA was purified using Trizol (Life Technologies) following the manufacturer’s protocol.
Label Cy5
Label protocol We prepared and hybridized spotted cDNA microarrays as previously described (Moore S, Knudsen B, True LD, et al: Loss of stearoyl-CoA desaturase expression is a frequent event in prostate carcinoma. Int J Cancer 114:563- 571, 2005) using RNA from a single batch of reference standard for each hybridization.
 
Channel 2
Source name Human Prostate 030107_PL treated with Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100
Organism Homo sapiens
Characteristics Human Prostate 030107_PL. Specimen_ID: 030107_PL; Age (years): 60; Race/Ethnicity: White; PSA (ng/dL): 3.5; Total Operative Time (minutes) : 210; Treatment: Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100; Gleason Sum: 6; pStage: T2aN0; Prostate Volume (mL): 50; Nerve Sparing: Bilateral; Patient Number: 8; Type: Needle; Ischemia Time (minutes): 30; Estimated Blood Loss (mL): "1,600";
Extracted molecule total RNA
Extraction protocol Biopsy cores were embedded individually in polyethylene glycol freezing media (Tissue-Tek OCT Compound, Sakura Finetek, Torrance, CA) and placed in isopentane that was precooled in liquid nitrogen. Specimens were then placed at 80°C until laser-capture microdissection (LCM). At time of LCM, 8-um frozen sections were obtained and immediately fixed in cold 95% ethanol. Sections were briefly (5 to 10 seconds) stained with hematoxylin using the Arcturus HistoGene Staining Solution (Arcturus Bioscience, Mountain View, CA) and dehydrated in 100% ethanol followed by xylenes (described in the Arcturus HistoGene LCM Frozen Section Staining Kit protocol). Five thousand epithelial cells from histologically benign glands were obtained by LCM using the Arcturus PixCell II instrument (modified from Emmert-Buck as described in Moore S, Knudsen B, True LD, et al: Loss of stearoyl-CoA desaturase expression is a frequent event in prostate carcinoma. Int J Cancer 114:563-571, 2005). Digital photos were taken of tissue sections before, during, and after LCM and assessed by an experienced genitourinary pathologist (B.S.K.) to confirm the histology of the laser captured cells. Each slide capture session lasted no longer than 20 minutes to minimize RNA degradation. The laser capture settings were 55mWbeam, 1.5 ms pulse, and 15um spot size. Cells were lysed in Arcturus RNA Extraction Buffer, RNA was isolated using the Arcturus PicoPure RNA Isolation Kit, and the samples were treated with DNAse using the Qiagen RNase-Free DNAse Set (Qiagen Inc, Valencia, CA). RNA was amplified for two rounds using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), and sample quality and quantity were assessed by agarose gel electrophoresis and absorbance at A260. To provide a reference standard RNA for use on cDNA microarrays, we isolated total RNA from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640-1640 medium supplemented with 10% fetal bovine serum (FBS; Life Technologies, Rockville, MD). RNA was purified using Trizol (Life Technologies) following the manufacturer’s protocol.
Label Cy3
Label protocol We prepared and hybridized spotted cDNA microarrays as previously described (Moore S, Knudsen B, True LD, et al: Loss of stearoyl-CoA desaturase expression is a frequent event in prostate carcinoma. Int J Cancer 114:563- 571, 2005) using RNA from a single batch of reference standard for each hybridization.
 
 
Hybridization protocol We prepared and hybridized spotted cDNA microarrays as previously described (Moore S, Knudsen B, True LD, et al: Loss of stearoyl-CoA desaturase expression is a frequent event in prostate carcinoma. Int J Cancer 114:563- 571, 2005) using RNA from a single batch of reference standard for each hybridization.
Scan protocol Fluorescence array images were collected for both Cy3 and Cy5 using a GenePix 4000B fluorescent scanner (Axon Instruments, Foster City, CA), and GenePix Pro 4.1 software was used to grid and extract image intensity data.
Description Human Prostate 030107_PL from Human hybridized against Reference
Data processing Spots of poor quality, as determined by visual inspection, were removed from further analysis. To normalize log-ratio data, a print-tip specific Lowess curve was fit to the log-intensity versus log-ratio plot, using 20.0% of the data to calculate the fit at each point. This curve was used to center the log-ratio for each spot. Data were filtered to exclude poorly hybridized cDNAs by removing values with average foreground-minus-background intensity levels less than 300. We used the average of the two duplicatecDNAsspotsoneach microarray chip in subsequent analyses. Data were filtered to include clones returning data for at least 75% of the samples in both presurgery and postsurgery groups, which reduced the initial list of 6,751 clones to 5,753 clones.
 
Submission date Dec 26, 2007
Last update date Dec 27, 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 GPL4766
Series (1)
GSE10028 Low-Fat, Low-Glycemic Load Diet, Surgical Manipulation and Prostate Gene Expression

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
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 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
206241 1.977490771 2330 16540 130 706 766 382 66 76 67 95 93 0 2900 2996 1421 130 147 115 99 97 0 0.231 0.244 0.239 0.240 1.638 0.242 0.856 120 670 3410 3566 -2.114 640 2770 700 2866 91958 359497 10.299 24.774 0 0
206242 -2.340300008 2520 16540 120 6917 7866 3368 63 96 210 100 100 0 1897 2233 1026 129 135 54 98 98 0 3.877 3.709 3.666 3.838 1.535 3.654 0.882 120 569 8622 9907 1.955 6854 1768 7803 2104 943894 268000 37.000 38.852 0 0
206243 -2.502426669 2720 16540 140 2985 2897 1418 65 96 197 93 92 0 704 720 294 129 135 53 91 89 0 5.078 4.792 4.582 4.516 1.769 4.974 0.874 156 714 3495 3423 2.344 2920 575 2832 591 451854 112339 14.218 11.038 0 0
206244 0.283369828 2930 16530 130 546 551 254 63 76 68 93 90 0 906 958 396 126 143 108 97 97 0 0.619 0.587 0.619 0.535 1.847 0.593 0.737 120 615 1263 1320 -0.691 483 780 488 832 66069 115003 6.985 7.546 0 0
206245 0.73897047 3120 16530 140 379 401 229 62 75 66 87 81 0 835 822 437 127 143 105 89 84 0 0.448 0.488 0.511 0.496 1.825 0.487 0.813 156 664 1025 1034 -1.159 317 708 339 695 62489 128240 4.939 6.467 0 0
206246 3.757506874 3310 16530 130 338 373 203 61 65 35 97 95 0 4904 4939 2242 127 129 29 100 99 0 0.058 0.065 0.064 0.062 1.901 0.059 0.620 120 640 5054 5124 -4.108 277 4777 312 4812 44762 592712 8.800 165.862 0 0
206247 -2.113424819 3510 16530 120 15788 15014 5480 61 66 36 100 100 0 3572 3444 1045 128 130 30 99 99 0 4.566 4.509 4.567 4.324 1.463 4.775 0.910 120 612 19171 18269 2.191 15727 3444 14953 3316 1801705 413305 415.222 110.467 0 0
206248 0.054965554 3710 16530 120 681 633 201 62 66 24 99 99 0 941 928 267 126 129 29 100 100 0 0.760 0.712 0.722 0.693 1.537 0.682 0.822 120 542 1434 1373 -0.397 619 815 571 802 75968 111310 23.625 27.552 0 0
206249 -1.576820988 3890 16530 140 15379 17214 13161 62 66 25 100 100 0 4835 5214 3747 124 127 28 95 94 0 3.251 3.370 3.348 3.352 1.633 3.545 0.927 156 634 20028 22242 1.701 15317 4711 17152 5090 2685405 813355 685.920 181.679 0 0
206250 -2.023241278 4080 16520 120 7748 7537 3245 61 64 24 100 100 0 2680 2937 1343 123 126 29 99 98 0 3.006 2.657 2.639 2.763 1.524 2.673 0.861 120 563 10244 10290 1.588 7687 2557 7476 2814 904452 352494 311.375 96.931 0 0
206251 0.151930106 4280 16520 120 838 847 294 62 67 28 100 100 0 1304 1334 632 124 129 34 100 100 0 0.658 0.649 0.681 0.700 1.484 0.577 0.849 120 581 1956 1995 -0.605 776 1180 785 1210 101605 160136 27.857 35.441 0 0
206252 0.838915553 4480 16520 130 223 228 78 63 78 166 43 3 0 527 540 164 126 132 69 99 97 0 0.399 0.399 0.396 0.384 1.602 0.361 0.664 120 605 561 579 -1.326 160 401 165 414 27328 64824 0.904 5.913 0 0
206253 -0.423517044 4670 16520 120 1007 972 284 64 72 44 100 100 0 1073 1048 305 124 127 31 100 100 0 0.994 0.983 0.980 0.993 1.418 0.963 0.883 120 619 1892 1832 -0.009 943 949 908 924 116637 125734 20.455 29.710 0 0
206254 -0.331055734 4870 16530 110 657 643 196 66 70 34 100 100 0 747 735 197 124 127 30 100 98 0 0.949 0.944 0.882 0.948 1.510 0.946 0.826 80 535 1214 1188 -0.076 591 623 577 611 51408 58783 16.853 20.267 0 0
206255 0.216915585 5070 16520 120 818 825 226 66 74 43 100 100 0 1288 1305 357 122 127 32 100 100 0 0.645 0.642 0.625 0.644 1.429 0.633 0.809 120 633 1918 1942 -0.633 752 1166 759 1183 98982 156603 17.465 36.813 0 0
206256 1.311863337 5270 16510 120 770 726 298 66 74 49 97 95 0 2193 2323 1126 124 131 55 98 98 0 0.340 0.300 0.316 0.302 1.603 0.267 0.821 120 620 2773 2859 -1.555 704 2069 660 2199 87150 278739 13.306 39.855 0 0
206257 1.070157104 5460 16520 100 333 343 125 65 123 333 26 1 0 882 852 278 128 148 134 97 91 0 0.355 0.384 0.365 0.388 1.781 0.341 0.559 80 452 1022 1002 -1.492 268 754 278 724 27406 68168 0.661 5.254 0 0
206258 -1.303544883 5650 16510 130 2861 2724 1072 65 108 280 100 97 0 1479 1365 588 130 144 114 99 94 0 2.073 2.153 2.246 2.305 1.502 2.174 0.900 120 646 4145 3894 1.051 2796 1349 2659 1235 326828 163790 9.343 10.711 0 0
206259 -0.004148658 5840 16520 120 516 532 145 65 69 25 100 100 0 730 727 214 127 131 33 98 98 0 0.748 0.778 0.760 0.800 1.608 0.736 0.816 120 605 1054 1067 -0.419 451 603 467 600 63856 87217 18.520 18.061 0 0
206260 -0.505280982 6050 16520 120 854 802 295 63 67 24 98 98 0 815 788 240 124 128 30 97 96 0 1.145 1.113 1.105 1.022 1.756 1.143 0.875 120 606 1482 1403 0.195 791 691 739 664 96238 94543 30.625 22.000 0 0

Total number of rows: 15488

Table truncated, full table size 3259 Kbytes.




Supplementary file Size Download File type/resource
GSM253462.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table

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