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Sample GSM126429 Query DataSets for GSM126429
Status Public on Nov 01, 2006
Title H3K36Ac vs H3 ChIP chip replicate 4
Sample type genomic
 
Channel 1
Source name H3 ChIP DNA
Organism Saccharomyces cerevisiae
Characteristics ChIP DNA
Growth protocol BY4741 strain cells were grown to OD of 0.8-1, fixed and DNA was purified after reversing crosslinks
Extracted molecule genomic DNA
Label Cy3
Label protocol ChIP DNA was labeled using Cy3
 
Channel 2
Source name H3K36Ac ChIP DNA
Organism Saccharomyces cerevisiae
Characteristics ChIP DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.0 analysi
Description Replicate 4 _array 060
Data processing After background correction and removal of flagged values, log base 2 expression ratios were median normalized
 
Submission date Aug 09, 2006
Last update date Aug 23, 2006
Contact name Jason D Lieb
E-mail(s) jlieb@bio.unc.edu
Phone 919-843-3228
Organization name UNC-Chapel Hill
Street address 203 Fordham Hall CB# 3280
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
 
Platform ID GPL4075
Series (2)
GSE5487 H3K36Ac or H3K9K14 vs H3 ChIP chip
GSE5544 H3K36Ac ChIP chips

Data table header descriptions
ID_REF
F635 Median
F635 Mean
F635 SD standard deviation
F635 CV
B635
B635 Median
B635 Mean
B635 SD
B635 CV
% > B635+1SD
% > B635+2SD
F635 % Sat.
F532 Median
F532 Mean
F532 SD
F532 CV
B532
B532 Median
B532 Mean
B532 SD
B532 CV
% > 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
Circularity
Sum of Medians (635/532)
Sum of Means (635/532)
VALUE Median normalized Log2 Ratio (635/532)
F635 Median - B635
F532 Median - B532
F635 Mean - B635
F532 Mean - B532
F635 Total Intensity
F532 Total Intensity
SNR 635

Data table
ID_REF F635 Median F635 Mean F635 SD F635 CV B635 B635 Median B635 Mean B635 SD B635 CV % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD F532 CV B532 B532 Median B532 Mean B532 SD B532 CV % > 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 Circularity Sum of Medians (635/532) Sum of Means (635/532) VALUE F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 F635 Total Intensity F532 Total Intensity SNR 635
1 3863 3859 1491 38 497 497 531 289 54 99 98 0 2024 1984 595 29 430 430 445 145 32 100 97 0 2.112 2.163 2.138 2.108 1.372 2.279 0.927 156 1030 100 4960 4916 1.217 3366 1594 3362 1554 601998 309443 11.516
2 5544 5540 2139 38 501 501 526 268 50 99 99 0 2784 2659 855 32 427 427 442 138 31 100 100 0 2.14 2.258 2.243 2.177 1.458 2.333 0.953 156 836 100 7400 7271 1.191 5043 2357 5039 2232 864184 414835 18.709
3 2873 2859 1196 41 501 501 527 216 40 98 95 0 2786 2808 1052 37 427 427 452 214 47 98 96 0 1.006 0.99 0.971 0.987 1.407 1.02 0.932 156 917 100 4731 4739 0.143 2372 2359 2358 2381 446056 438118 10.796
4 2951 3028 1237 40 505 505 560 284 50 97 95 0 2357 2276 834 36 432 432 483 272 56 96 92 0 1.271 1.368 1.417 1.356 1.359 1.38 0.883 120 738 100 4371 4367 0.495 2446 1925 2523 1844 363397 273109 8.69
5 3627 3547 1427 40 508 508 608 542 89 94 88 0 3092 2977 1103 37 439 439 530 478 90 95 89 0 1.176 1.197 1.208 1.174 1.381 1.205 0.945 156 967 100 5772 5577 0.342 3119 2653 3039 2538 553319 464411 5.423
6 4448 4440 1859 41 501 501 604 574 95 96 94 0 4961 4898 1879 38 442 442 561 596 106 98 94 0 0.873 0.884 0.887 0.847 1.333 0.904 0.949 156 1000 100 8466 8395 -0.098 3947 4519 3939 4456 692677 764092 6.683
7 4057 4422 3177 71 510 510 563 366 65 85 81 0 11062 11356 8542 75 458 458 546 510 93 87 84 0 0.334 0.359 0.375 0.398 1.699 0.363 0.962 120 633 100 14151 14810 -1.421 3547 10604 3912 10898 530587 1362681 10.544
8 8054 8781 4102 46 502 502 643 897 139 98 97 0 7167 7469 2964 39 448 448 599 948 158 100 94 0 1.124 1.179 1.183 1.13 1.306 1.194 0.958 156 854 100 14271 15300 0.364 7552 6719 8279 7021 1369764 1165180 9.072
9 3436 3208 1183 36 516 516 721 967 134 89 74 0 2112 1941 633 32 449 449 643 958 148 75 25 0 1.756 1.804 1.802 1.77 1.389 1.363 0.8 156 906 100 4583 4184 0.959 2920 1663 2692 1492 500420 302804 2.572
10 8431 7798 2573 32 530 530 712 894 125 100 97 0 8667 7777 2536 32 455 455 646 1018 157 99 97 0 0.962 0.993 0.995 0.991 1.215 0.977 0.953 156 905 100 16113 14590 0.175 7901 8212 7268 7322 1216554 1213243 7.926
11 3279 3101 1113 35 533 533 657 781 118 93 78 0 2158 1991 625 31 454 454 596 914 153 81 37 0 1.612 1.671 1.642 1.61 1.548 1.245 0.786 208 1104 100 4450 4105 0.839 2746 1704 2568 1537 644987 414174 3.129
12 2376 2211 829 37 532 532 638 495 77 87 76 0 1651 1475 496 33 452 452 520 304 58 92 76 0 1.538 1.641 1.606 1.577 1.42 1.69 0.898 156 861 100 3043 2702 0.862 1844 1199 1679 1023 344991 230128 3.178
13 3418 3173 1207 38 528 528 613 460 75 94 89 0 4181 3773 1360 36 446 446 544 524 96 96 93 0 0.774 0.795 0.794 0.765 1.323 0.802 0.911 208 1119 100 6625 5972 -0.273 2890 3735 2645 3327 660081 784688 5.565
14 1774 1745 577 33 528 528 618 480 77 90 71 0 2257 2030 681 33 458 458 612 696 113 87 66 0 0.693 0.774 0.767 0.758 1.607 0.755 0.838 156 890 100 3045 2789 -0.291 1246 1799 1217 1572 272245 316704 2.348
15 2260 2240 926 41 516 516 571 302 52 95 87 0 2575 2496 854 34 458 458 534 330 61 98 94 0 0.824 0.846 0.824 0.791 1.438 0.888 0.89 156 918 100 3861 3762 -0.106 1744 2117 1724 2038 349482 389440 5.526
16 2975 3008 1284 42 518 518 584 404 69 95 88 0 2375 2284 887 38 447 447 509 314 61 94 91 0 1.274 1.355 1.312 1.305 1.279 1.391 0.927 156 938 100 4385 4327 0.499 2457 1928 2490 1837 469287 356341 6
17 1839 1918 872 45 553 553 626 409 65 85 68 0 2576 2468 947 38 458 458 528 333 63 95 92 0 0.607 0.679 0.677 0.608 1.639 0.782 0.833 156 902 100 3404 3375 -0.51 1286 2118 1365 2010 299205 384933 3.159
18 5899 5448 2166 39 534 534 569 229 40 98 97 0 3995 3650 1450 39 458 458 489 214 43 98 97 0 1.517 1.539 1.581 1.552 1.289 1.546 0.925 208 931 100 8902 8106 0.703 5365 3537 4914 3192 1133234 759104 21.306
19 1913 1960 706 36 542 542 583 272 46 97 86 0 1510 1539 449 29 458 458 494 213 43 98 91 0 1.303 1.312 1.308 1.24 1.569 1.388 0.842 156 856 100 2423 2499 0.682 1371 1052 1418 1081 305744 240161 5.063
20 5311 4918 1784 36 574 574 648 483 74 98 96 0 4289 3991 1369 34 475 475 549 419 76 99 96 0 1.242 1.235 1.247 1.213 1.236 1.254 0.957 156 1040 100 8551 7860 0.411 4737 3814 4344 3516 767268 622668 8.841

Total number of rows: 19200

Table truncated, full table size 3738 Kbytes.




Supplementary file Size Download File type/resource
GSM126429.gpr.gz 1.8 Mb (ftp)(http) GPR

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