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Sample GSM60773 Query DataSets for GSM60773
Status Public on Jun 12, 2005
Title TriMeH3K27 in HeLa cell - rep3 of 3
Sample type genomic
 
Channel 1
Source name Chromatin immunoprecipiated DNA using trimethyl-K27 histone H3 antibody, HeLa cells
Organism Homo sapiens
Characteristics Human cervix epithelial adenocarcinoma cells, HeLa cells, trimethyl-K27 histone H3 antibody
Extracted molecule genomic DNA
Label Cy5
 
Channel 2
Source name Input DNA from HeLa cells
Organism Homo sapiens
Characteristics Human cervix epithelial adenocarcinoma cells, HeLa cells
Extracted molecule genomic DNA
Label Cy3
 
 
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.
Description Genome-wide location analysis of TriMeH3K27 binding in HeLa cells using RenLab ENCODE PCR tiling array. Array ID is ENC854. Replicate 3 of 3.
Data processing The two channels in each array are normalized using printtip loess with normexp background correction using R. The replicate arrays are then quantile normalized using reference channel intensity. The normalized intensities are then used for p-value calculation using single array error model, and log2 ratio calculation.
 
Submission date Jun 09, 2005
Last update date Jun 10, 2005
Contact name Chunxu Qu
E-mail(s) qchunxu@ucsd.edu
Phone (858)822-5767
Organization name Ludwig Institute for Cancer Research
Department Gene Regulation
Lab RenLab
Street address
City San Diego
State/province CA
ZIP/Postal code 92093
Country USA
 
Platform ID GPL1454
Series (1)
GSE2801 ENCODE: GWLA analysis of SUZ12 and triMeH3K27 binding in HeLa cells

Data table header descriptions
ID_REF
VALUE log2 ratio or normalized intensities
STATISTICS X-statistics
P-VAL p-value calculated using single array error model
F635_INT normalized F635 intensity
F532_INT normalized F532 intensity
F635_MEDIAN F635 median intensity
F635_MEAN F635 mean intensity
F635_SD F635 standard deviation
B635_MEDIAN B635 median intensity
B635_MEAN B635 mean intensity
B635_SD B635 standard deviation
F532_MEDIAN F532 median intensity
F532_MEAN F532 mean intensity
F532_SD F532 standard deviation
B532_MEDIAN B532 median intensity
B532_MEAN B532 mean intensity
B532_SD B532 standard deviation

Data table
ID_REF VALUE STATISTICS P-VAL F635_INT F532_INT F635_MEDIAN F635_MEAN F635_SD B635_MEDIAN B635_MEAN B635_SD F532_MEDIAN F532_MEAN F532_SD B532_MEDIAN B532_MEAN B532_SD
1 0.074434 2.87103261e-02 3.67443207e-01 1011.70534 960.83129 1705 1679 396 59 63 31 1770 1778 424 277 281 69
2 -0.038825 -1.51344956e-02 5.70838156e-01 1203.01332 1235.82760 2057 1987 456 58 64 45 2202 2147 458 278 282 67
3 -0.037138 -1.44347272e-02 5.67595128e-01 3278.82488 3364.32547 5967 5630 1290 57 65 45 5553 5263 1281 264 268 72
4 -0.114310 -4.47632996e-02 7.01241468e-01 1518.15977 1643.34339 2550 2555 566 59 63 35 2674 2697 541 271 273 70
5 -0.090203 -3.57010464e-02 6.63154199e-01 1333.18053 1419.19739 2269 2224 413 58 63 41 2422 2394 418 272 274 67
6 -0.012535 -4.88983405e-03 5.22996105e-01 978.65874 987.19927 1645 1639 373 59 64 45 1858 1806 359 268 270 69
7 0.074880 2.66617532e-02 3.76581965e-01 300.30336 285.11430 676 673 176 60 67 61 913 919 216 267 271 70
8 0.121973 4.85524123e-02 2.83435327e-01 1125.07614 1033.86600 1858 1848 257 61 67 48 1858 1859 318 262 266 66
9 0.400533 1.50923966e-01 3.75282451e-02 534.78653 405.14270 994 990 222 59 68 66 1069 1078 201 259 264 69
10 -0.058900 -1.88995808e-02 5.88199908e-01 136.61788 142.31093 357 368 124 60 66 37 602 613 139 256 258 67
11 -0.189153 -6.73006627e-02 7.86343567e-01 174.72329 199.20097 462 471 115 59 64 37 752 763 134 258 261 67
12 -0.097933 -3.88830120e-02 6.76745603e-01 1303.08405 1394.61164 2212 2179 375 59 64 37 2408 2356 393 263 265 67
13 0.386940 1.48212850e-01 4.02197305e-02 1122.57288 858.48757 1864 1827 379 59 66 37 1689 1638 394 265 267 67
14 -0.058698 -2.24637276e-02 6.04478060e-01 699.76699 728.82508 1251 1231 305 59 63 30 1497 1489 332 262 264 66
15 0.015472 5.74061531e-03 4.73008464e-01 512.58622 507.11858 948 965 251 59 66 39 1234 1215 309 267 268 66
16 -0.008110 -3.17704003e-03 5.14945896e-01 629.96374 633.51481 1120 1128 221 61 67 44 1387 1378 226 270 270 68
17 -0.176839 -6.94662788e-02 7.93704147e-01 728.99234 824.05641 1285 1279 247 61 66 33 1619 1604 262 264 268 65
18 0.033171 1.19979644e-02 4.43732081e-01 306.30443 299.34208 677 686 194 61 67 38 949 941 187 267 270 67
19 -0.180690 -6.96805888e-02 7.94424289e-01 1300.79125 1474.35086 2309 2184 565 62 66 32 2507 2458 564 265 267 67
20 -0.144115 -5.73102657e-02 7.50468089e-01 972.62144 1074.79799 1624 1642 278 61 66 32 1913 1927 275 273 273 67

Total number of rows: 25392

Table truncated, full table size 2775 Kbytes.




Supplementary file Size Download File type/resource
GSM60773.gpr.gz 2.1 Mb (ftp)(http) GPR

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