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Sample GSM171018 Query DataSets for GSM171018
Status Public on Mar 01, 2007
Title H3K4me1 IMR90 RenLab ENCODE PCR tiling array replicate 3 slide ENC1681H3K4me1
Sample type genomic
 
Channel 1
Source name Chromatin immunoprecipitated DNA from IMR90 cells using H3K4me1 antibody
Organism Homo sapiens
Characteristics Chromatin immunoprecipitated DNA from IMR90 cells using H3K4me1 antibody
Extracted molecule genomic DNA
Extraction protocol NimbleGen
Label Cy5
Label protocol Cy3 input Cy5 ChIP sample
 
Channel 2
Source name Input DNA from IMR90 cells
Organism Homo sapiens
Characteristics Input DNA from IMR90 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 0.015 1.05 4.045e-01 6480.00 6158.94 6844 7054 2671 364 475 448 7205 7014 2103 792 813 286 0 0.015
2 -0.241 0.88 7.246e-01 6038.00 6852.34 6395 6425 2688 357 484 628 7883 7560 2543 748 758 269 0 -0.241
3 -0.153 0.94 6.238e-01 16113.00 17203.35 16489 16370 4704 376 477 457 18660 18301 5909 747 754 264 0 -0.153
4 1.04 4.980e-01 10.00 9.60 341 483 618 366 470 474 703 705 243 695 716 259 -50 0
5 -0.255 0.87 7.477e-01 14233.00 16316.92 14616 14964 3546 383 486 460 17654 17437 3550 664 687 250 0 -0.255
6 0.179 1.18 2.093e-01 20339.00 17251.37 20698 20829 3675 359 460 419 18625 18209 2938 662 677 248 0 0.179
7 -0.192 0.91 6.746e-01 15072.00 16537.81 15431 14871 4137 359 462 427 17869 17182 3794 649 665 243 0 -0.192
8 -0.296 0.85 7.880e-01 6742.00 7948.14 7099 7096 2178 357 449 416 8904 9010 1485 628 645 248 0 -0.296
9 -0.370 0.81 8.534e-01 8749.00 10859.06 9112 9311 2372 363 455 431 11917 11833 1903 610 628 233 0 -0.370
10 -0.650 0.66 9.725e-01 6603.00 9950.54 6954 6871 2125 351 449 423 10964 10372 2948 603 624 258 0 -0.650
11 -0.404 0.79 8.741e-01 10328.00 13122.68 10681 10426 3383 353 452 517 14257 13705 3742 593 610 227 0 -0.404
12 -0.035 1.02 4.685e-01 13954.00 13730.61 14328 14272 2904 374 473 507 14898 14637 3603 601 619 265 0 -0.035
13 0.003 1.04 4.177e-01 10354.00 9926.53 10729 10760 2301 375 480 539 10935 10936 1412 599 622 246 0 0.003
14 0.358 1.33 7.997e-02 42967.00 32194.95 43362 43032 6627 395 603 1196 34130 33677 4826 607 696 768 0 0.358
15 0.415 1.39 5.782e-02 12226.00 8808.64 12636 12246 3133 410 666 1203 9798 9865 1377 626 714 675 0 0.415
16 -0.160 0.93 6.363e-01 14100.00 15133.73 14471 14657 3163 371 498 523 16359 16033 2295 601 630 294 0 -0.160
17 1.138 2.29 1.601e-04 19798.00 8639.61 20152 20142 3857 354 507 599 9595 9408 1886 599 624 254 0 1.138
18 -0.486 0.74 9.241e-01 15259.00 20523.40 15660 15609 3656 401 563 727 21975 22076 3644 605 651 456 0 -0.486
19 -0.730 0.63 9.643e-01 3835.00 6109.96 4205 4712 2850 370 481 462 6998 7587 5584 636 700 475 0 -0.730
20 0.102 1.12 2.915e-01 26761.00 23941.41 27141 26959 5250 380 477 448 25569 25305 2907 640 653 242 0 0.102

Total number of rows: 25246

Table truncated, full table size 2616 Kbytes.




Supplementary file Size Download File type/resource
GSM171018.gpr.gz 2.4 Mb (ftp)(http) GPR

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