NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM171085 Query DataSets for GSM171085
Status Public on Mar 01, 2007
Title H3K27Ac K562 RenLab ENCODE PCR tiling array replicate 2 ENC1783
Sample type genomic
 
Channel 1
Source name Chromatin immunoprecipitated DNA from K562 cells using H3K27Ac antibody
Organism Homo sapiens
Characteristics Chromatin immunoprecipitated DNA from K562 cells using H3K27Ac 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 -1.354 0.58 9.688e-01 449.00 772.99 538 554 213 89 105 72 1294 1254 346 146 151 61 0 -1.354
2 -1.403 0.56 9.767e-01 400.00 712.39 489 493 178 89 102 70 1206 1198 282 148 157 69 0 -1.403
3 -1.661 0.47 9.936e-01 815.00 1735.85 903 913 344 88 99 67 2728 2568 733 150 154 63 0 -1.661
4 -1.576 0.50 9.911e-01 646.00 1296.84 735 746 232 89 103 75 2076 2066 457 150 159 75 0 -1.576
5 -1.558 0.50 9.894e-01 657.00 1302.90 753 755 234 96 109 73 2088 2082 548 153 159 72 0 -1.558
6 -1.085 0.70 9.082e-01 1428.00 2040.20 1533 1568 352 105 141 160 3184 3141 413 154 202 296 0 -1.085
7 -1.316 0.60 9.679e-01 965.00 1618.02 1083 1088 318 118 137 113 2555 2552 459 152 193 221 0 -1.316
8 -1.671 0.47 9.942e-01 414.00 887.45 527 546 208 113 124 82 1467 1454 328 149 155 62 0 -1.671
9 -1.598 0.49 9.912e-01 557.00 1135.24 669 693 253 112 122 78 1839 1858 461 153 157 59 0 -1.598
10 -1.828 0.42 9.977e-01 478.00 1142.65 590 600 223 112 123 83 1848 1800 372 151 154 59 0 -1.828
11 -1.635 0.48 9.920e-01 636.00 1330.51 747 764 292 111 122 80 2127 2091 639 151 156 67 0 -1.635
12 0.109 1.60 4.238e-02 4735.00 2955.26 4842 4747 898 107 120 78 4540 4391 862 151 156 66 0 0.109
13 -1.207 0.64 9.466e-01 771.00 1198.53 887 891 241 116 126 81 1933 1935 276 153 156 64 0 -1.207
14 -0.108 1.38 1.131e-01 7162.00 5198.81 7289 7248 1005 127 152 231 7874 7797 895 153 164 141 0 -0.108
15 -1.259 0.62 9.562e-01 646.00 1040.97 776 797 263 130 142 90 1702 1688 312 156 161 65 0 -1.259
16 -1.118 0.68 9.208e-01 1213.00 1772.21 1333 1357 269 120 134 86 2786 2799 358 154 159 80 0 -1.118
17 -2.151 0.33 9.997e-01 594.00 1776.93 711 720 231 117 131 86 2798 2790 418 159 162 62 0 -2.151
18 -1.523 0.52 9.877e-01 1607.00 3108.78 1725 1700 574 118 134 85 4771 4733 1207 154 158 60 0 -1.523
19 1.49 4.215e-01 10.00 6.73 123 140 89 120 136 87 165 170 61 159 164 60 -50 -1.000
20 -0.547 1.02 4.750e-01 7675.00 7550.76 7804 7856 1052 129 150 158 11384 11141 1506 170 202 396 0 -0.547

Total number of rows: 25246

Table truncated, full table size 2417 Kbytes.




Supplementary file Size Download File type/resource
GSM171085.gpr.gz 2.0 Mb (ftp)(http) GPR

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap