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Sample GSM120914 Query DataSets for GSM120914
Status Public on Nov 08, 2006
Title Case_33_2005090106
Sample type genomic
 
Channel 1
Source name 82/F Stomach
Organism Homo sapiens
Characteristics Age: 82, Gender: female, tissue : stomach
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from a frozen fragment of the tumor, using a microdissection technique to reduce contamination with non-neoplastic tissue. DNA was extracted using a standard proteinase K digestion followed by phenol/chloroform extraction and ethanol precipitation.
Label Cy5
Label protocol The gDNA was labeled by a random prime labeling system (Bioprime DNA labeling System; Invitrogen) using Cy5-labeled dCTPs (Amersham Biociences). See also Vermeesch et al: Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2005, 53:413-22.
 
Channel 2
Source name control DNA
Organism Homo sapiens
Characteristics normal individual, Tissue : lymphocyte
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from lymphocytes of normal individuals.
Label Cy3
Label protocol The gDNA was labeled by a random prime labeling system (Bioprime DNA labeling System; Invitrogen) using Cy3-labeled dCTPs (Amersham Biociences). See also Vermeesch et al: Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2005, 53:413-22.
 
 
Hybridization protocol Probe preparation and preblocking of the slide were performed as described by Fiegler et al. (2003). Equal amounts (200 pmol) of Cy5- and Cy3-labeled probe were combined with 100 ug Cot-1 DNA followed by an ethanol precipitation. Resuspension of the pellet was done in hybridization buffer (50% formamide, 10% dextran sulfate, 0.1% Tween 20, 2 x SSC, and 10 mM Tris HCl, pH 7.5) containing 400 ug yeast tRNA to hybridize a spotting area of 24 x 60 mm. The slide was blocked with 50 ug Cot-1 DNA and 300 ug salmon sperm DNA dissolved in 60 ul hybridization buffer. Blocking solution and probe mixture were denaturated for 10 min in a water bath at 75C. Blocking solution was then placed on the slide covered with a coverslip (24 x 60 mm) and placed in a humid chamber. Meanwhile, the probe was placed at 37C for preannealing. After 1 hr of blocking, the coverslip was removed and probe was placed on the slide. After placing a coverslip (24 x 60 mm), the slide was placed in a humid chamber saturated with 20% formamide and 2 x SSC. Hybridization was allowed to take place for two nights at 37C. Posthybridization washes were performed as described by Fiegler et al. (2003). The coverslip was removed by placing the slide in PBS with 0.05% Tween 20, followed by a 10- min wash in a fresh solution of PBS/Tween 20 at room temperature, 30 min in 50% formamide/2 x SSC at 42C, and 10 min in PBS/0.05% Tween 20 at room temperature. Slides were spin dried at 1000 rpm for 5 min. See also Vermeesch et al: Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2005, 53:413-22.
Scan protocol Array slides were scanned with a GenePix 4000B scanner and hybridization signals were evaluated using GenePixPro 3.0 image analysis software.
Description Comparison between individual with Gastrointestinal stromal tumor (GIST) vs normal individual
Data processing All data analysis was performed with Excel. Spot intensities were corrected for local background, and only spots with signal intensities at least two fold above background signal intensities were included in the final analysis. For each clone, a ratio of Cy5 to Cy3 fluorescent intensity was calculated. Normalization of the data was achieved by dividing the fluorescent intensity ratio of each spot by the mean of the ratios of the autosomes followed by the 2D normalization. Normalized ratios of the duplicates were averaged and a log2 value was calculated. Precise localizations of clones spotted on the array were obtained from the Ensemble database (www.ensembl.org/Homo_sapiens). The Normalized ratio is not included in the submitted raw data.
 
Submission date Jul 18, 2006
Last update date Nov 08, 2006
Contact name Rekin's Janky
E-mail(s) Nucleomics.Bioinformatics@vib.be
Organization name VIB
Department Nucleomics Core
Street address Herestraat 49 Box 816
City Leuven
ZIP/Postal code B-3000
Country Belgium
 
Platform ID GPL3892
Series (1)
GSE5336 Array CGH Analysis in primary gastrointestinal stromal tumors

Data table header descriptions
ID_REF
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 - Cy5).
F635 Mean mean feature pixel intensity at wavelength #1 (635 nm - Cy5).
F635 SD the standard deviation of the feature pixel intensity at wavelength #1 (635 nm - Cy5).
B635 Median the median feature background intensity at wavelength #1 (635 nm - Cy5).
B635 Mean the mean feature background intensity at wavelength #1 (635 nm - Cy5).
B635 SD the standard deviation of the feature background intensity at wavelength #1 (635 nm - Cy5).
% > B635+1SD
% > B635+2SD
F635 % Sat. the percentage of feature pixels at wavelength #1 that are saturated.
F532 Median median feature pixel intensity at wavelength #2 (532 nm - Cy3).
F532 Mean mean feature pixel intensity at wavelength #2 (532 nm - Cy3).
F532 SD the standard deviation of the feature intensity at wavelength #2 (532 nm - Cy3).
B532 Median the median feature background intensity at wavelength #2 (532 nm - Cy3).
B532 Mean the mean feature background intensity at wavelength #2 (532 nm - Cy3).
B532 SD the standard deviation of the feature background intensity at wavelength #2 (532 nm - Cy3).
% > B532+1SD
% > B532+2SD
F532 % Sat. the percentage of feature pixels at wavelength #2 that are saturated.
Ratio of Medians the ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
Ratio of Means the ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.
Median of Ratios the median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Mean of Ratios the geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Ratios SD the geometric standard deviation of the pixel intensity ratios.
Rgn Ratio the regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.
Rgn R? 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.
VALUE Log Ratio = log (base 2) transform of the ratio of the medians.
F635 Median - B635 the median feature pixel intensity at wavelength #1 with the median background subtracted.
F532 Median - B532 the median feature pixel intensity at wavelength #2 with the median background subtracted.
F635 Mean - B635 the mean feature pixel intensity at wavelength #1 with the median background subtracted.
F532 Mean - B532 the mean feature pixel intensity at wavelength #2 with the median background subtracted.
Flags the type of flag associated with a feature.

Data table
ID_REF 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 Ratio of Means Median of Ratios Mean of Ratios Ratios SD Rgn Ratio Rgn R? F Pixels B Pixels Sum of Medians Sum of Means VALUE F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 Flags
1 2145 2430 80 6652 6622 2057 660 810 727 96 95 0 4559 4853 2162 795 913 549 97 94 0 0.628 0.681 0.633 0.653 1.61 0.702 0.721 208 1512 9756 10020 null 5992 3764 5962 4058 0
2 2490 2430 155 1618 1914 3124 629 679 382 72 59 0 1453 1959 5146 794 858 527 57 25 0 0.666 0.907 0.677 0.654 2.703 1.864 0.567 716 5480 1648 2450 null 989 659 1285 1165 0
3 2910 2430 95 1913 2007 751 649 828 1326 44 3 0 1429 1513 880 782 987 2514 0 0 0 0.512 0.538 0.49 0.491 2.435 1.767 0.503 256 2088 1911 2089 null 1264 647 1358 731 0
4 3315 2425 80 6858 6692 2161 668 941 1076 97 95 0 4181 4175 1301 832 1008 679 95 94 0 0.541 0.555 0.543 0.545 1.655 0.539 0.782 208 1512 9539 9367 null 6190 3349 6024 3343 0
5 3695 2425 110 2419 2344 1293 628 689 418 78 71 0 1883 1852 802 841 907 472 71 54 0 0.582 0.589 0.621 0.61 2.452 0.594 0.513 392 2896 2833 2727 null 1791 1042 1716 1011 0
6 4105 2415 105 2609 2751 1696 656 1359 5676 2 0 0 2034 2144 1126 841 1446 5275 1 0 0 0.611 0.622 0.617 0.606 2.605 0.927 0.901 316 2572 3146 3398 null 1953 1193 2095 1303 0
7 4495 2425 75 2661 2771 980 672 754 439 98 92 0 1838 2143 1075 792 839 299 98 86 0 0.526 0.644 0.573 0.598 2.273 0.73 0.443 156 1272 3035 3450 null 1989 1046 2099 1351 0
8 4895 2410 100 1124 1191 630 630 683 363 58 34 0 1034 1130 559 773 822 352 38 13 0 0.528 0.636 0.506 0.482 3.819 0.714 0.126 316 2384 755 918 null 494 261 561 357 0
9 5285 2420 180 723 820 549 624 747 1496 2 0 0 781 940 935 767 955 2549 2 0 0 0.141 0.883 0.649 0.662 4.101 1.845 0.755 1028 5984 113 369 null 99 14 196 173 -50
10 5690 2425 100 2427 2354 1133 658 709 396 84 76 0 1630 1604 560 763 855 576 69 28 0 0.49 0.496 0.523 0.478 2.334 0.461 0.42 316 2384 2636 2537 null 1769 867 1696 841 0
41 2090 2830 75 4374 4411 1253 641 900 1009 100 92 0 2895 2989 847 754 891 571 99 91 0 0.574 0.593 0.567 0.583 1.612 0.55 0.7 156 1272 5874 6005 null 3733 2141 3770 2235 0
42 2520 2825 85 6907 6673 2051 666 896 993 94 93 0 4154 4092 1214 820 983 767 98 91 0 0.534 0.545 0.529 0.584 2.293 0.535 0.788 208 1660 9575 9279 null 6241 3334 6007 3272 0
43 2905 2825 105 1984 2038 909 639 696 387 86 75 0 1688 1693 580 806 884 513 73 40 0 0.656 0.634 0.634 0.675 2.307 0.789 0.339 316 2572 2227 2286 null 1345 882 1399 887 0
44 3295 2835 100 1302 1366 677 624 677 387 65 43 0 1147 1189 440 796 865 536 32 5 0 0.518 0.53 0.595 0.547 3.502 0.956 0.188 316 2384 1029 1135 null 678 351 742 393 0
45 3695 2840 125 3848 5825 10686 677 1396 5747 12 5 1 2527 4328 10678 780 1139 4266 4 3 1 0.551 0.689 0.58 0.518 2.707 0.778 0.705 460 3704 4918 8696 null 3171 1747 5148 3548 0
46 4100 2820 115 2705 2749 1689 648 689 354 77 72 0 2696 2677 1513 767 818 371 74 69 0 0.938 0.909 0.865 0.901 2.579 0.883 0.69 392 3108 3986 4011 null 2057 1929 2101 1910 0
47 4490 2825 160 5745 5792 3757 630 675 352 84 79 0 3435 3519 2130 755 799 359 77 74 0 0.524 0.535 0.547 0.532 2.138 0.519 0.802 812 5648 7795 7926 null 5115 2680 5162 2764 0
48 4885 2825 140 5651 5914 2141 633 698 511 100 99 0 3242 3449 1197 748 790 332 99 98 0 0.497 0.511 0.508 0.506 1.567 0.483 0.786 624 4756 7512 7982 null 5018 2494 5281 2701 0
49 5290 2820 145 3091 3307 1520 625 707 585 96 84 0 1972 2215 987 736 798 447 90 68 0 0.501 0.551 0.538 0.529 2.013 0.511 0.694 624 5012 3702 4161 null 2466 1236 2682 1479 0
50 5685 2825 155 9888 10378 3286 621 684 543 100 100 0 5945 6401 2116 738 774 329 99 99 0 0.562 0.58 0.584 0.575 1.377 0.577 0.874 716 5480 14474 15420 null 9267 5207 9757 5663 0

Total number of rows: 3840

Table truncated, full table size 664 Kbytes.




Supplementary data files not provided
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