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Sample GSM144660 Query DataSets for GSM144660
Status Public on Jan 01, 2007
Title H3K4me3 IMR90 replicate 2
Sample type genomic
 
Channel 1
Source name Chromatin immunoprecipitated DNA from IMR90 cells using H3K4me3 antibody
Organism Homo sapiens
Characteristics Chromatin immunoprecipitated DNA from IMR90 cells using H3K4me3 antibody
Extracted molecule genomic DNA
Extraction protocol NimbleGen
Label Cy5
Label protocol Cy3 input Cy5 sample NimbleGen
 
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 sample NimbleGen
 
 
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 Nov 15, 2006
Last update date Nov 17, 2006
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)
GSE6292 Ludwig Institute/UCSD ENCODE project

Data table header descriptions
ID_REF ID_REF
VALUE log ratio (F635/F532) (useful values only)
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 0.080 0.90 6.763e-01 7448.00 8292.40 7869 8066 2832 421 560 579 7731 7995 2140 684 716 319 0 0.080
2 -0.149 0.77 8.646e-01 4765.00 6219.00 5186 5574 2398 421 630 1296 5940 6050 1938 655 676 289 0 -0.149
3 -0.248 0.72 9.171e-01 15186.00 21222.27 15626 14983 5770 440 645 1724 18692 18199 7157 657 685 281 0 -0.248
4 0.85 5.086e-01 10.00 11.77 404 552 551 408 560 581 687 725 274 681 699 267 -50 0
5 -0.115 0.78 8.465e-01 9670.00 12325.04 10109 10422 3949 439 603 674 11151 11050 3230 677 686 258 0 -0.115
6 -0.107 0.79 8.441e-01 17419.00 22071.87 17853 18051 5326 434 587 656 19422 18442 4625 665 686 272 0 -0.107
7 -0.376 0.65 9.604e-01 11887.00 18158.08 12326 12733 4665 439 586 564 16106 15634 4136 675 700 268 0 -0.376
8 -0.441 0.63 9.720e-01 5062.00 8087.64 5484 5523 2357 422 596 903 7543 7262 2027 670 697 273 0 -0.441
9 -0.549 0.58 9.867e-01 6405.00 11024.76 6835 7217 2238 430 582 609 10035 9974 2088 666 692 268 0 -0.549
10 -0.549 0.58 9.851e-01 4933.00 8492.44 5343 5468 2418 410 575 633 7877 7575 2432 660 676 252 0 -0.549
11 -0.357 0.66 9.463e-01 7973.00 12014.38 8411 8535 4719 438 588 693 10872 10479 5658 662 686 263 0 -0.357
12 -0.381 0.65 9.586e-01 5951.00 9118.46 6396 6867 2963 445 600 762 8404 8855 2802 655 679 266 0 -0.381
13 -0.417 0.64 9.706e-01 8242.00 12947.53 8664 8757 2557 422 573 654 11662 11849 1556 659 679 271 0 -0.417
14 -0.385 0.65 9.651e-01 24280.00 37316.37 24709 24616 5232 429 583 996 32393 31729 4809 681 706 278 0 -0.385
15 -0.512 0.60 9.836e-01 7142.00 11986.14 7584 7698 2539 442 592 683 10882 10877 1611 696 717 274 0 -0.512
16 -0.723 0.51 9.962e-01 9102.00 17685.03 9538 9682 2538 436 751 2960 15725 15668 2065 696 825 2059 0 -0.723
17 -0.697 0.52 9.950e-01 5040.00 9612.68 5425 5538 2127 385 537 587 8861 8759 1583 692 707 267 0 -0.697
18 -0.825 0.48 9.978e-01 9108.00 18986.49 9509 10023 3929 401 553 602 16827 17048 5001 692 711 278 0 -0.825
19 -0.937 0.44 9.990e-01 3860.00 8697.19 4278 4281 1922 418 566 670 8134 8017 1825 743 765 291 0 -0.937
20 -0.287 0.70 9.389e-01 21962.00 31531.58 22402 22281 4307 440 608 637 27548 27304 2893 752 778 300 0 -0.287

Total number of rows: 25246

Table truncated, full table size 2609 Kbytes.




Supplementary data files not provided
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