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Sample GSM160002 Query DataSets for GSM160002
Status Public on Sep 01, 2007
Title CAF_2
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 carcinoma associated fibroblasts CAF_2
Organism Homo sapiens
Characteristics Human carcinoma associated fibroblasts CAF_2. prostate cancer status: Y; Specimen ID: CAF_2; origin: primary prostate stromal cells from prostate with carcinoma; Tissue: carcinoma associated fibroblasts;
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 carcinoma associated fibroblasts CAF_2 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 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 ?m 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 ?m 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 ?m 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
237241 -0.649221936 2810 16610 120 567 792 595 83 88 37 95 95 0 449 591 348 94 96 24 99 98 0 1.363 1.427 1.313 1.232 2.296 1.634 0.752 120 624 839 1206 0.447 484 355 709 497 95095 70970 19.027 20.625 0 0
237242 -0.263482663 3000 16620 120 10774 10285 4087 83 89 42 99 99 0 7475 7586 2810 96 97 24 100 100 0 1.449 1.362 1.344 1.325 1.733 1.451 0.813 120 606 18070 17692 0.535 10691 7379 10202 7490 1234186 910346 242.762 312.042 0 0
237243 -0.250614193 3210 16620 120 7583 7280 3212 85 92 42 99 98 0 6000 5564 2671 98 98 23 98 98 0 1.27 1.316 1.257 1.277 2.538 1.345 0.762 120 608 13400 12661 0.345 7498 5902 7195 5466 873551 667690 171.143 237.652 0 0
237244 -1.48578541 3400 16620 120 3709 3758 1604 87 94 62 100 99 0 1586 1570 704 100 102 26 99 98 0 2.437 2.497 2.371 2.398 1.963 2.718 0.752 120 562 5108 5141 1.285 3622 1486 3671 1470 450944 188345 59.097 56.462 0 0
237245 -1.378241781 3590 16620 120 4428 4297 1441 90 95 40 100 100 0 1838 1797 643 103 106 28 99 99 0 2.5 2.483 2.366 2.463 1.878 2.743 0.731 120 594 6073 5901 1.322 4338 1735 4207 1694 515650 215606 105.05 60.393 0 0
237246 -0.118655886 3800 16620 130 485 489 132 97 219 866 0 0 0 513 508 156 105 194 695 3 0 0 0.951 0.973 0.909 0.9 1.475 0.932 0.626 120 666 796 795 -0.073 388 408 392 403 58725 60968 0.312 0.452 0 0
237247 0.821573897 3990 16620 120 19123 18096 5639 101 149 343 100 100 0 19573 18776 7653 105 109 36 100 100 0 0.977 0.964 0.923 1.066 2.317 0.917 0.754 120 578 38490 36666 -0.033 19022 19468 17995 18671 2171518 2253066 52.324 518.528 0 0
237248 -2.999811192 4190 16620 120 5261 5325 2019 101 130 236 100 100 0 902 876 401 106 110 38 91 91 0 6.482 6.784 6.169 6.384 1.691 8.359 0.531 120 594 5956 5994 2.697 5160 796 5224 770 638978 105111 22.013 20.158 0 0
237249 -0.174552845 4380 16620 130 11156 11070 3025 99 128 346 100 100 0 7878 7997 2542 108 149 572 99 98 0 1.423 1.391 1.379 1.438 1.684 1.401 0.77 120 634 18827 18860 0.509 11057 7770 10971 7889 1328408 959654 31.624 13.72 0 0
237250 0.876655792 4580 16610 130 18609 18213 6051 99 363 1802 100 100 0 19826 18905 7142 114 249 1355 99 98 0 0.939 0.964 0.933 1.019 1.844 0.919 0.74 120 638 38222 36905 -0.091 18510 19712 18114 18791 2185593 2268540 9.906 13.768 0 0
237251 -2.31354971 4770 16620 130 21729 22015 5062 101 368 1808 100 100 0 3725 3700 1084 115 252 1360 96 83 0 5.991 6.113 5.827 6.089 1.389 6.011 0.518 120 634 25238 25499 2.583 21628 3610 21914 3585 2641857 444037 11.973 2.535 0 0
237252 -0.321427567 4970 16600 130 427 428 131 104 109 48 99 96 0 407 406 94 112 116 30 100 100 0 1.095 1.102 1.109 1.088 1.676 1.235 0.579 120 639 618 618 0.131 323 295 324 294 51394 48669 6.646 9.667 0 0
237253 -0.794184375 5160 16610 130 1484 1687 841 106 108 41 100 100 0 1063 1157 631 113 116 29 97 97 0 1.451 1.514 1.372 1.564 2.037 1.571 0.614 120 667 2328 2625 0.537 1378 950 1581 1044 202396 138793 38.512 35.897 0 0
237254 -0.939913315 5370 16600 120 945 1382 1153 111 113 40 99 98 0 654 885 732 117 120 29 95 92 0 1.553 1.655 1.789 1.742 3.134 1.852 0.564 120 583 1371 2039 0.635 834 537 1271 768 165803 106235 31.725 26.379 0 0
237255 -0.575726061 5550 16610 120 16169 15470 3942 115 345 1635 100 99 0 7610 7424 1997 122 170 424 100 99 0 2.144 2.103 2.121 2.124 1.566 2.301 0.805 120 545 23542 22657 1.1 16054 7488 15355 7302 1856457 890915 9.251 17.108 0 0
237256 0.2316241 5730 16600 130 3127 3188 1267 117 328 1475 93 52 0 3582 3855 1458 124 165 386 99 99 0 0.87 0.823 0.88 0.847 1.925 1.233 0.496 120 655 6468 6802 -0.2 3010 3458 3071 3731 382535 462555 1.939 9.56 0 0
237257 0.994578638 5940 16600 130 1264 1256 511 112 151 310 95 83 0 2960 3003 1061 120 127 72 100 100 0 0.406 0.397 0.381 0.381 1.769 0.37 0.657 120 653 3992 4027 -1.302 1152 2840 1144 2883 150727 360312 3.565 39.944 0 0
237258 1.241264577 6140 16590 130 2091 2111 871 111 116 43 96 96 0 4809 4871 1731 120 125 33 100 100 0 0.422 0.421 0.424 0.411 1.705 0.402 0.752 120 615 6669 6751 -1.244 1980 4689 2000 4751 253316 584475 46.395 143.818 0 0
237259 -0.54172825 6340 16600 140 5603 5395 2349 114 120 47 97 96 0 3823 3747 1718 121 125 33 98 97 0 1.483 1.456 1.441 1.49 2.617 1.567 0.646 156 650 9191 8907 0.568 5489 3702 5281 3626 841559 584558 112.234 109.758 0 0
237260 0.454661589 6530 16590 130 6550 6169 2196 112 127 87 98 97 0 8157 8166 2465 119 122 32 100 100 0 0.801 0.753 0.831 0.693 2.145 0.778 0.713 120 576 14476 14104 -0.32 6438 8038 6057 8047 740329 979914 69.448 251.375 0 0

Total number of rows: 15488

Table truncated, full table size 3220 Kbytes.




Supplementary file Size Download File type/resource
GSM160002.gpr.gz 1.4 Mb (ftp)(http) GPR

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