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Sample GSM171094 Query DataSets for GSM171094
Status Public on Mar 01, 2007
Title H3K4me2 GM06990 RenLab ENCODE PCR tiling array replicate 5 ENC1813
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 -0.729 1.13 3.314e-01 604.00 534.67 703 661 202 99 125 93 1283 1228 273 282 280 63 0 -0.729
2 -1.363 0.73 8.630e-01 473.00 650.04 583 609 238 110 136 114 1481 1450 320 264 263 62 0 -1.363
3 -1.506 0.66 8.934e-01 976.00 1481.15 1083 1145 585 107 129 89 3042 2883 1407 269 272 61 0 -1.506
4 -1.753 0.56 9.709e-01 548.00 986.55 662 682 281 114 130 85 2106 1972 565 259 261 60 0 -1.753
5 -1.238 0.79 7.920e-01 972.00 1224.77 1083 1044 315 111 127 87 2557 2390 631 264 264 58 0 -1.238
6 -1.028 0.92 6.248e-01 1494.00 1626.97 1607 1624 410 113 135 90 3312 3287 272 266 269 61 0 -1.028
7 -1.317 0.75 8.488e-01 912.00 1213.55 1023 1049 360 111 130 90 2548 2479 331 276 275 64 0 -1.317
8 -1.578 0.63 9.453e-01 412.00 656.98 514 572 246 102 132 99 1500 1510 218 270 272 65 0 -1.578
9 -1.269 0.78 8.047e-01 719.00 925.65 832 873 414 113 134 92 2001 1857 512 268 268 60 0 -1.269
10 -1.785 0.54 9.772e-01 413.00 760.07 524 557 269 111 125 84 1683 1659 324 260 261 53 0 -1.785
11 -1.633 0.60 9.584e-01 736.00 1218.89 847 942 348 111 126 87 2554 2464 439 272 268 58 0 -1.633
12 -0.786 1.09 3.834e-01 1515.00 1395.16 1633 1550 491 118 130 86 2878 2709 672 266 268 58 0 -0.786
13 -1.148 0.84 7.293e-01 709.00 839.12 817 816 247 108 126 89 1842 1781 301 271 267 59 0 -1.148
14 -0.430 1.39 1.122e-01 3770.00 2712.33 3878 3876 557 108 128 92 5349 5386 391 271 272 65 0 -0.430
15 -1.204 0.81 7.659e-01 634.00 780.37 731 732 278 97 116 83 1733 1564 402 272 277 60 0 -1.204
16 -1.039 0.91 6.338e-01 1299.00 1426.14 1412 1424 466 113 129 87 2950 2920 421 280 282 62 0 -1.039
17 -1.315 0.75 8.412e-01 472.00 627.07 588 647 254 116 127 81 1454 1424 225 280 281 64 0 -1.315
18 -0.994 0.94 5.884e-01 2199.00 2338.97 2316 2391 710 117 135 90 4646 4401 995 267 269 65 0 -0.994
19 1.87 3.774e-01 10.00 5.34 120 125 74 115 133 92 286 289 60 287 290 66 -50 0
20 -0.340 1.48 8.383e-02 5436.00 3675.91 5554 6207 2166 118 132 90 7173 6932 1004 291 295 67 0 -0.340

Total number of rows: 25246

Table truncated, full table size 2432 Kbytes.




Supplementary file Size Download File type/resource
GSM171094.gpr.gz 2.0 Mb (ftp)(http) GPR

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