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Sample GSM171036 Query DataSets for GSM171036
Status Public on Mar 01, 2007
Title TAFII p250 (6B3) GM06990 RenLab ENCODE PCR tiling array replicate 3 ENC1529
Sample type genomic
 
Channel 1
Source name Chromatin immunoprecipitated DNA from GM06990 cells using TAFII p250 (6B3) antibody
Organism Homo sapiens
Characteristics Chromatin immunoprecipitated DNA from GM06990 cells using TAFII p250 (6B3) antibody
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM06990
Extracted molecule genomic DNA
Extraction protocol NimbleGen
Label Cy5
Label protocol Cy3 input Cy5 ChIP sample
 
Channel 2
Source name Input DNA from GM06990 cells
Organism Homo sapiens
Characteristics Input DNA from GM06990 cells
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM06990
Extracted molecule genomic DNA
Extraction protocol NimbleGen
Label Cy3
Label protocol Cy3 input Cy5 ChIP sample
 
 
Hybridization protocol NimbleGen
Scan protocol NimbleGen
Description ChIP-chip analyses were performed for various transcription factors and chromatin modifications in various cell types. Details to be described in publications.
Data processing raw data
 
Submission date Feb 23, 2007
Last update date Aug 28, 2007
Contact name Bing Ren
E-mail(s) biren@ucsd.edu
Organization name Ludwig Institute for Cancer Research
Department Department of Cellular and Molecular Medicine
Lab Laboratory of Gene Regulation
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093-0653
Country USA
 
Platform ID GPL1454
Series (1)
GSE7118 Ludwig Institute/UCSD ENCODE project March 2007 Release

Data table header descriptions
ID_REF ID_REF
VALUE same as UNF_VALUE but with flagged values removed
STATISTICS statistics
PVAL p-value
F635_INT F635 intensity with background intensity subtracted (normalized)
F532_INT F532 intensity with background intensity subtracted (normalized)
F635_MEDIAN F635 mdian 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 F532standard deviation
B532_MEDIAN B532 median intensity
B532_MEAN B532 mean intensity
B532_SD B532 standard deviation
FLAG flag from GenePro, 0 is useful
UNF_VALUE log ratio (F635/F532)

Data table
ID_REF VALUE STATISTICS PVAL 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 FLAG UNF_VALUE
1 -0.157 1.21 2.218e-01 842.00 694.66 919 932 369 77 92 73 1160 1156 325 221 224 72 0 -0.157
2 -0.263 1.13 3.185e-01 764.00 678.39 836 874 349 72 86 67 1137 1130 343 220 224 74 0 -0.263
3 -0.581 0.90 6.604e-01 1917.00 2120.97 1988 2036 662 71 86 70 3097 3049 818 230 231 71 0 -0.581
4 -0.524 0.94 5.997e-01 1255.00 1334.58 1327 1344 445 72 87 70 2031 2034 472 227 230 70 0 -0.524
5 -0.519 0.94 5.948e-01 1208.00 1280.57 1279 1287 386 71 87 71 1957 1916 482 226 230 77 0 -0.519
6 -0.142 1.22 2.019e-01 2500.00 2041.07 2570 2476 745 70 86 73 2984 2851 665 225 226 72 0 -0.142
7 -0.562 0.92 6.415e-01 1415.00 1545.42 1486 1487 530 71 86 72 2312 2286 502 223 226 68 0 -0.562
8 -0.720 0.82 7.901e-01 638.00 777.52 708 721 254 70 85 68 1270 1260 250 219 223 82 0 -0.720
9 -0.702 0.83 7.741e-01 862.00 1037.18 933 973 332 71 87 72 1623 1575 375 221 225 85 0 -0.702
10 -0.738 0.81 8.058e-01 752.00 927.69 823 840 274 71 86 74 1475 1483 260 221 225 70 0 -0.738
11 -0.731 0.81 7.973e-01 1076.00 1321.26 1145 1151 417 69 85 71 2007 1980 495 221 226 71 0 -0.731
12 -0.511 0.95 5.866e-01 1781.00 1877.58 1851 1846 573 70 87 78 2763 2684 580 225 230 131 0 -0.511
13 -0.370 1.05 4.263e-01 1111.00 1062.34 1181 1167 373 70 89 82 1661 1635 297 225 232 135 0 -0.370
14 -0.063 1.29 1.400e-01 4922.00 3802.51 4995 5015 875 73 90 77 5366 5300 625 226 230 71 0 -0.063
15 -0.359 1.05 4.144e-01 1066.00 1011.29 1136 1116 420 70 87 73 1593 1571 315 226 228 70 0 -0.359
16 -0.486 0.97 5.588e-01 1243.00 1287.97 1313 1303 424 70 84 68 1967 1965 303 226 230 70 0 -0.486
17 -0.756 0.80 8.167e-01 721.00 901.06 792 798 315 71 86 70 1442 1411 298 224 228 71 0 -0.756
18 -0.766 0.79 8.283e-01 1721.00 2165.36 1794 1815 538 73 89 70 3154 3130 578 227 233 72 0 -0.766
19 1.35 4.223e-01 10.00 7.40 80 90 66 73 89 73 239 238 69 232 236 72 -50 0.000
20 0.013 1.36 9.935e-02 6539.00 4793.08 6612 6341 1413 73 90 74 6713 6543 1014 234 237 69 0 0.013

Total number of rows: 25246

Table truncated, full table size 2396 Kbytes.




Supplementary file Size Download File type/resource
GSM171036.gpr.gz 2.0 Mb (ftp)(http) GPR

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