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Sample GSM171108 Query DataSets for GSM171108
Status Public on Mar 01, 2007
Title CTCF K562 RenLab ENCODE PCR tiling array replicate 3 ENC1880
Sample type genomic
 
Channel 1
Source name Chromatin immunoprecipitated DNA from K562 cells using CTCF antibody
Organism Homo sapiens
Characteristics Chromatin immunoprecipitated DNA from K562 cells using CTCF 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 -0.839 1.22 3.178e-01 275.00 224.84 330 336 176 55 62 47 630 637 261 138 141 54 0 -0.839
2 -1.176 0.97 5.326e-01 235.00 242.66 291 317 158 56 62 48 673 681 173 142 145 57 0 -1.176
3 -1.189 0.96 5.407e-01 544.00 566.67 601 614 288 57 64 50 1382 1410 513 142 148 73 0 -1.189
4 -1.377 0.84 6.653e-01 365.00 433.23 421 420 223 56 62 49 1089 1089 357 141 145 56 0 -1.377
5 -1.246 0.92 5.805e-01 352.00 381.59 404 417 191 52 59 46 977 981 327 142 143 53 0 -1.246
6 -0.623 1.42 1.691e-01 1317.00 926.77 1370 1338 451 53 61 47 2167 2128 469 139 142 55 0 -0.623
7 -1.504 0.77 7.358e-01 540.00 700.11 595 626 349 55 62 47 1670 1661 606 138 141 54 0 -1.504
8 -1.376 0.84 6.620e-01 205.00 243.12 261 276 130 56 63 48 672 674 214 140 143 54 0 -1.376
9 -1.284 0.90 6.107e-01 329.00 366.05 385 404 181 56 62 49 940 961 231 139 142 54 0 -1.284
10 -1.525 0.76 7.598e-01 239.00 314.41 295 310 144 56 61 46 824 809 202 136 140 54 0 -1.525
11 -1.335 0.87 6.375e-01 482.00 555.70 537 569 273 55 62 49 1352 1330 495 136 138 55 0 -1.335
12 1.079 4.62 1.102e-03 3908.00 845.43 3964 4115 1216 56 64 53 1988 2002 755 138 140 56 0 1.079
13 -1.134 1.00 5.029e-01 562.00 563.47 618 599 252 56 60 50 1370 1369 256 137 139 55 0 -1.134
14 -0.581 1.46 1.444e-01 3317.00 2267.58 3374 3378 889 57 63 51 5099 5042 692 137 139 55 0 -0.581
15 -0.599 1.45 1.636e-01 766.00 530.11 823 795 343 57 64 48 1300 1281 292 140 142 55 0 -0.599
16 -1.451 0.80 7.205e-01 637.00 796.08 695 706 361 58 65 60 1883 1834 478 141 143 56 0 -1.451
17 1.786 7.54 2.175e-04 6912.00 916.26 6970 6838 1615 58 68 60 2148 2130 384 143 146 57 0 1.786
18 -1.525 0.76 7.452e-01 673.00 885.19 729 782 404 56 65 57 2079 2074 806 142 145 57 0 -1.525
19 2.19 3.640e-01 10.00 4.57 60 65 47 58 67 62 148 151 61 144 158 267 -50 -1.000
20 0.045 2.26 1.996e-02 3259.00 1443.63 3317 3157 936 58 65 49 3301 3181 621 142 144 57 0 0.045

Total number of rows: 25246

Table truncated, full table size 2350 Kbytes.




Supplementary file Size Download File type/resource
GSM171108.gpr.gz 2.0 Mb (ftp)(http) GPR

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