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Sample GSM159999 Query DataSets for GSM159999
Status Public on Sep 01, 2007
Title D1 NPF_cyclin D1_1
Sample type RNA
 
Channel 1
Source name NPF Control
Organism Homo sapiens
Characteristics NPF Control
Extracted molecule total RNA
Extraction protocol RNA was isolated from NPFs, CAFs, and NPF cyclin D1 cells using total RNA isolation kit (Qiagen).
Label Cy5
Label protocol Total RNA was amplified through one round of linear amplification using the MessageAmp aRNA kit (Ambion, Austin, TX). Sample quality and quantification was assessed by agarose gel electrophoresis and absorbance at A260. Cy3 and Cy5 labeled cDNA probes were made from 4 µg of amplified RNA.
 
Channel 2
Source name Human normal prostate fibroblasts overexpressing cyclin D1 NPF_cyclin D1_1
Organism Homo sapiens
Characteristics Human normal prostate fibroblasts overexpressing cyclin D1 NPF_cyclin D1_1. prostate cancer status: N; Specimen ID: NPF_cyclin D1_1; origin: primary prostate stromal cells from benign peripheral prostate from patient with bladder cancer; Tissue: normal prostate fibroblasts overexpressing cyclin D1;
Extracted molecule total RNA
Extraction protocol RNA was isolated from NPFs, CAFs, and NPF cyclin D1 cells using total RNA isolation kit (Qiagen).
Label Cy3
Label protocol Total RNA was amplified through one round of linear amplification using the MessageAmp aRNA kit (Ambion, Austin, TX). Sample quality and quantification was assessed by agarose gel electrophoresis and absorbance at A260. Cy3 and Cy5 labeled cDNA probes were made from 4 µg of amplified RNA.
 
 
Hybridization protocol Two NPF cyclin D1 and two CAF samples (labeled with Cy3) were hybridized head-to-head with an NPF control sample labeled with Cy5. Probes were hybridized competitively to microarrays under a coverslip for 16 h at 63oC.
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 by using a GenePix 4000B fluorescent scanner, and image intensity data were gridded and extracted using GenePix Pro 4.1 software.
Description Human normal prostate fibroblasts overexpressing cyclin D1 NPF_cyclin D1_1 from Human hybridized against NPF Control
Data processing Differences in gene expression between NPF cyclin D1/NPF and CAF/NPF groups were determined using a two-sample t-test with Significance Analysis of Microarrays (SAM) software (http://www-stat.stanford.edu/_tibs/SAM/) with a False Discovery Rate (FDR) of +/- 10% considered significant (Tusher, PNAS, 2001). Similarities in gene expression between NPF cyclin D1/NPF and CAF/NPF groups were determined using a one-sample t-test in SAM with an FDR of +/- 0.1% considered significant. These results were reduced to unique genes by eliminating all but the highest scoring clones for each gene. A Pearson correlation coefficient was calculated in Excel to assess the strength of the linear relationship between NPF cyclin D1/NPF and CAF/NPF average log2 ratios.
 
Submission date Feb 01, 2007
Last update date Jan 02, 2013
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)
GSE6936 Comparison of Normal Prostate Fibroblasts Overexpressing Cyclin D1 and Carcinoma Associated Fibroblasts

Data table header descriptions
ID_REF
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)
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
237241 0.237798642 2890 16720 140 779 818 342 79 83 38 96 95 0 1014 1035 449 93 95 24 98 97 0 0.76 0.785 0.803 0.799 2.27 0.737 0.538 156 700 1621 1681 -0.396 700 921 739 942 127596 161469 19.342 39.167 0 0
237242 0.233389042 3080 16720 140 14257 13717 5561 80 86 43 98 98 0 13109 12416 4324 94 97 24 100 100 0 1.089 1.107 1.12 0.978 3.153 1.147 0.824 156 620 27192 25959 0.123 14177 13015 13637 12322 2139896 1936964 317 513.292 0 0
237243 -0.44870863 3270 16720 130 13268 12101 3908 81 102 152 99 99 0 9042 9106 1948 97 100 24 100 100 0 1.474 1.334 1.393 1.253 1.747 1.487 0.787 120 599 22132 21029 0.56 13187 8945 12020 9009 1452146 1092769 78.941 375.25 0 0
237244 -0.244678429 3470 16710 130 5839 5494 1810 86 103 146 99 98 0 3963 3946 999 97 99 24 100 100 0 1.488 1.405 1.515 1.349 1.82 1.586 0.726 120 642 9619 9257 0.573 5753 3866 5408 3849 659331 473526 36.925 160.292 0 0
237245 -0.201633724 3670 16710 130 5735 5686 1568 86 95 55 99 99 0 4009 4181 1003 98 101 29 100 100 0 1.444 1.372 1.432 1.362 1.566 1.502 0.748 120 647 9560 9683 0.53 5649 3911 5600 4083 682372 501695 101.655 140.69 0 0
237246 -0.126497339 3870 16720 130 730 784 221 84 93 55 100 100 0 744 763 203 99 102 30 100 100 0 1.002 1.054 1.076 1.049 1.511 1.052 0.61 120 627 1291 1364 0.002 646 645 700 664 94032 91583 12.564 22.033 0 0
237247 -0.649733467 4070 16710 140 45932 44448 12771 85 91 51 100 100 1 23961 22251 7550 101 104 24 100 99 0 1.922 2.003 1.979 1.868 1.745 2.05 0.816 156 661 69707 66513 0.942 45847 23860 44363 22150 6933894 3471162 869.745 922.792 0 0
237248 -0.407616544 4250 16730 130 9410 9237 2389 92 118 209 100 100 0 6785 6665 1495 103 106 53 100 100 0 1.394 1.394 1.428 1.365 1.516 1.503 0.728 120 540 16000 15707 0.48 9318 6682 9145 6562 1108495 799767 43.632 123.755 0 0
237249 -0.38183052 4440 16710 150 27206 25823 9924 94 133 281 99 98 0 16054 15573 5215 103 107 48 100 100 0 1.7 1.663 1.74 1.549 1.866 1.84 0.795 156 707 43063 41199 0.765 27112 15951 25729 15470 4028367 2429328 91.423 322.208 0 0
237250 0.724285383 4660 16720 140 27552 27652 6869 93 112 112 100 100 0 36853 34742 13039 105 107 26 100 100 0 0.747 0.796 0.741 0.871 2.425 0.725 0.788 156 645 64207 62196 -0.42 27459 36748 27559 34637 4313740 5419724 245.893 1332.115 0 0
237251 -0.715563192 4850 16710 140 29948 28541 9692 90 112 156 100 100 0 13901 13578 4122 107 109 27 99 99 0 2.165 2.112 2.091 2.019 1.764 2.361 0.762 156 592 43652 41922 1.114 29858 13794 28451 13471 4452457 2118095 182.237 498.852 0 0
237252 -0.250748421 5030 16710 150 614 659 280 85 107 180 92 82 0 527 506 167 103 106 26 98 96 0 1.248 1.424 1.477 1.483 1.752 1.579 0.683 156 668 953 977 0.319 529 424 574 403 102747 78918 3.067 15.385 0 0
237253 -0.226280091 5240 16720 140 2387 2316 730 83 94 63 100 98 0 1966 1872 721 98 101 26 98 97 0 1.233 1.259 1.227 1.404 2.357 1.199 0.708 156 647 4172 4007 0.303 2304 1868 2233 1774 361356 292017 35.27 68.115 0 0
237254 -0.39221889 5440 16710 130 978 1094 453 87 89 37 100 100 0 853 889 305 97 99 23 100 100 0 1.179 1.271 1.219 1.222 1.701 1.387 0.712 120 574 1647 1799 0.237 891 756 1007 792 131290 106721 27.162 34.348 0 0
237255 -0.493829905 5630 16720 140 21312 19911 7060 84 90 39 98 98 0 11019 10856 3758 98 99 23 100 100 0 1.944 1.843 1.885 1.627 2.977 2.022 0.732 156 614 32149 30585 0.959 21228 10921 19827 10758 3106060 1693467 508.231 467.696 0 0
237256 -0.280413319 5820 16710 140 5153 4866 1731 84 92 44 98 97 0 3508 3449 1312 96 97 23 99 98 0 1.486 1.426 1.446 1.461 2.427 1.491 0.686 156 640 8481 8135 0.571 5069 3412 4782 3353 759070 537969 108.5 145.739 0 0
237257 0.626520907 6020 16690 130 1610 1511 598 87 100 103 96 95 0 2380 2306 779 94 98 27 100 100 0 0.666 0.644 0.694 0.613 2.124 0.635 0.723 120 621 3809 3636 -0.586 1523 2286 1424 2212 181274 276776 13.699 81.778 0 0
237258 0.59973997 6220 16700 140 4345 4346 1291 84 97 102 100 100 0 5236 5264 1912 95 99 30 99 99 0 0.829 0.825 0.821 0.854 1.551 0.803 0.755 156 632 9402 9431 -0.271 4261 5141 4262 5169 677939 821116 41.657 172.167 0 0
237259 -0.09502744 6420 16730 150 9585 9544 2220 81 86 41 100 100 0 8963 9035 2620 91 96 26 100 100 0 1.071 1.058 1.051 1.082 1.436 1.018 0.787 156 624 18376 18407 0.099 9504 8872 9463 8944 1488890 1409421 230.683 343.808 0 0
237260 -0.432435083 6610 16710 130 10007 9733 2248 84 96 68 100 100 0 7283 7107 1875 91 94 24 100 100 0 1.38 1.375 1.376 1.391 1.3 1.424 0.774 120 558 17115 16665 0.464 9923 7192 9649 7016 1167956 852837 141.721 292.208 0 0

Total number of rows: 15488

Table truncated, full table size 3279 Kbytes.




Supplementary file Size Download File type/resource
GSM159999.gpr.gz 1.4 Mb (ftp)(http) GPR

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