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Sample GSM171089 Query DataSets for GSM171089
Status Public on Mar 01, 2007
Title H3K4me2 K562 RenLab ENCODE PCR tiling array replicate 1 ENC1808
Sample type genomic
 
Channel 1
Source name Chromatin immunoprecipitated DNA from K562 cells using H3K4me2 antibody
Organism Homo sapiens
Characteristics Chromatin immunoprecipitated DNA from K562 cells using H3K4me2 antibody
Extracted molecule genomic DNA
Extraction protocol NimbleGen
Label Cy5
Label protocol Cy3 input Cy5 ChIP sample
 
Channel 2
Source name Input DNA from K562 cells
Organism Homo sapiens
Characteristics Input DNA from K562 cells
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 Feb 26, 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 -1.446 0.51 9.959e-01 963.00 1872.42 1055 1092 505 92 122 227 3153 2945 1007 530 549 248 0 -1.446
2 -1.449 0.51 9.959e-01 1120.00 2182.23 1217 1243 515 97 126 223 3560 3298 1219 503 522 247 0 -1.449
3 -1.345 0.55 9.943e-01 3384.00 6136.95 3475 3419 953 91 116 99 9093 8802 2212 496 502 153 0 -1.345
4 -1.368 0.54 9.957e-01 2111.00 3889.05 2205 2189 516 94 113 93 5937 5982 1012 489 502 150 0 -1.368
5 -1.213 0.60 9.853e-01 2802.00 4637.16 2893 2870 731 91 111 91 6989 6653 1733 493 498 146 0 -1.213
6 -0.911 0.74 9.060e-01 3820.00 5129.00 3912 3733 1084 92 117 101 7681 7280 1945 496 504 149 0 -0.911
7 -1.296 0.57 9.927e-01 2426.00 4251.68 2523 2475 717 97 115 91 6456 6421 1012 500 507 152 0 -1.296
8 -1.438 0.52 9.972e-01 1315.00 2542.73 1411 1416 504 96 114 89 4067 4039 802 505 515 153 0 -1.438
9 -1.051 0.68 9.555e-01 2386.00 3528.55 2478 2390 799 92 112 92 5440 5120 1542 497 505 148 0 -1.051
10 -1.395 0.53 9.965e-01 1562.00 2931.78 1648 1702 519 86 109 93 4590 4636 725 483 490 147 0 -1.395
11 -1.308 0.57 9.933e-01 2497.00 4414.44 2576 2638 694 79 106 94 6672 6635 1123 488 500 151 0 -1.308
12 -0.115 1.29 1.168e-01 7703.00 5953.50 7792 7708 1353 89 110 91 8828 8840 995 488 495 149 0 -0.115
13 -1.140 0.64 9.764e-01 1802.00 2835.41 1891 1856 599 89 111 94 4461 4345 947 489 495 152 0 -1.140
14 -0.262 1.17 2.350e-01 11943.00 10220.88 12036 11657 2487 93 115 94 14807 14654 2219 489 498 149 0 -0.262
15 -1.345 0.55 9.951e-01 1594.00 2891.09 1692 1696 456 98 117 92 4556 4624 638 506 516 153 0 -1.345
16 -1.222 0.60 9.663e-01 2880.00 4796.35 2978 3233 2217 98 117 94 7210 7617 4576 491 496 149 0 -1.222
17 -0.792 0.81 8.362e-01 3018.00 3729.14 3113 3163 660 95 116 90 5723 5762 695 499 508 179 0 -0.792
18 -0.960 0.72 9.326e-01 5131.00 7124.21 5223 5205 979 92 111 89 10481 10351 1655 501 506 151 0 -0.960
19 1.40 4.514e-01 10.00 7.14 95 114 93 98 118 97 536 541 163 530 536 158 -50 0
20 0.650 2.20 5.388e-04 26467.00 12041.20 26565 25588 4804 98 121 102 17396 16254 4046 528 537 153 0 0.650

Total number of rows: 25246

Table truncated, full table size 2509 Kbytes.




Supplementary file Size Download File type/resource
GSM171089.gpr.gz 2.1 Mb (ftp)(http) GPR

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