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Sample GSM171104 Query DataSets for GSM171104
Status Public on Mar 01, 2007
Title H3K4me2 GM06990 RenLab ENCODE PCR tiling array replicate 2 ENC1876
Sample type genomic
 
Channel 1
Source name Chromatin immunoprecipitated DNA from GM06990 cells using H3K4me2 antibody
Organism Homo sapiens
Characteristics Chromatin immunoprecipitated DNA from GM06990 cells using H3K4me2 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 0.501 1.19 2.342e-01 668.00 562.91 744 728 328 76 93 68 976 983 205 504 508 98 0 0.501
2 0.344 1.06 3.928e-01 485.00 455.57 574 560 185 89 105 77 882 880 155 500 499 109 0 0.344
3 -0.052 0.81 8.183e-01 1140.00 1409.65 1221 1324 576 81 102 72 1673 1621 406 491 494 105 0 -0.052
4 0.142 0.93 6.315e-01 888.00 960.04 977 976 452 89 107 74 1303 1305 256 498 501 103 0 0.142
5 -0.080 0.79 8.351e-01 578.00 728.68 661 699 303 83 96 66 1109 1023 289 498 499 102 0 -0.080
6 0.775 1.43 6.129e-02 1843.00 1284.43 1930 1892 530 87 108 102 1564 1412 478 487 495 103 0 0.775
7 0.336 1.06 4.017e-01 1198.00 1131.78 1288 1266 464 90 108 107 1431 1411 282 482 484 98 0 0.336
8 -0.120 0.77 8.635e-01 403.00 522.36 495 536 244 92 104 69 931 917 135 493 498 95 0 -0.120
9 -0.003 0.84 7.765e-01 459.00 548.60 543 610 239 84 107 80 941 923 177 481 482 94 0 -0.003
10 0.095 0.90 6.841e-01 520.00 580.80 610 624 204 90 107 79 983 997 199 496 490 106 0 0.095
11 0.349 1.07 3.864e-01 1299.00 1216.45 1378 1379 447 79 99 72 1510 1507 312 490 492 106 0 0.349
12 0.854 1.52 4.379e-02 1036.00 683.36 1118 1193 503 82 104 81 1047 1041 247 474 480 102 0 0.854
13 0.644 1.31 1.261e-01 1014.00 774.00 1098 1022 403 84 98 65 1134 1079 324 485 487 106 0 0.644
14 1.625 2.59 2.166e-04 3044.00 1177.10 3132 3314 1120 88 106 85 1464 1427 363 477 483 108 0 1.625
15 1.315 2.09 1.625e-03 1888.00 905.18 1974 1897 524 86 107 91 1239 1287 197 480 536 1031 0 1.315
16 0.313 1.04 4.285e-01 1117.00 1072.15 1200 1290 379 83 103 73 1375 1361 300 476 480 98 0 0.313
17 0.053 0.87 7.285e-01 665.00 764.46 754 711 289 89 103 68 1116 1115 164 475 480 108 0 0.053
18 -0.135 0.76 8.799e-01 1059.00 1386.99 1153 1216 382 94 112 81 1639 1615 321 476 479 104 0 -0.135
19 0.84 5.453e-01 10.00 11.93 84 110 79 82 102 75 483 494 102 480 487 97 -50 -0.585
20 2.581 5.02 7.194e-07 4082.00 813.35 4174 4022 1509 92 107 79 1166 1133 327 484 490 100 0 2.581

Total number of rows: 25246

Table truncated, full table size 2388 Kbytes.




Supplementary file Size Download File type/resource
GSM171104.gpr.gz 2.0 Mb (ftp)(http) GPR

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