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Sample GSM171088 Query DataSets for GSM171088
Status Public on Mar 01, 2007
Title H3K4me3 K562 RenLab ENCODE PCR tiling array replicate 2 ENC1807
Sample type genomic
 
Channel 1
Source name Chromatin immunoprecipitated DNA from K562 cells using H3K4me3 antibody
Organism Homo sapiens
Characteristics Chromatin immunoprecipitated DNA from K562 cells using H3K4me3 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 -0.925 0.83 9.001e-01 1728.00 2081.72 1816 1919 584 88 144 829 4148 4211 865 866 1047 3167 0 -0.925
2 -1.068 0.75 9.656e-01 1545.00 2055.08 1631 1715 808 86 106 90 4058 3950 1354 818 829 221 0 -1.068
3 -0.980 0.80 9.413e-01 4934.00 6172.84 5018 5116 1336 84 106 110 10551 10254 2002 819 836 227 0 -0.980
4 -0.900 0.84 8.816e-01 3305.00 3912.89 3389 3359 820 84 112 124 7001 7018 1380 832 842 219 0 -0.900
5 -0.823 0.89 7.896e-01 3911.00 4387.97 3997 3871 952 86 105 86 7742 7506 1731 824 834 212 0 -0.823
6 -0.573 1.06 3.396e-01 8074.00 7616.47 8158 7826 1908 84 106 91 12833 12264 2436 825 840 220 0 -0.573
7 -0.669 0.99 5.245e-01 4138.00 4174.21 4225 4205 823 87 110 99 7423 7284 1579 842 847 224 0 -0.669
8 -0.917 0.84 8.946e-01 2140.00 2562.50 2225 2233 577 85 105 95 4886 4788 1019 846 859 255 0 -0.917
9 -0.734 0.95 6.457e-01 3116.00 3288.12 3202 3026 1018 86 107 99 6004 5862 1350 820 835 250 0 -0.734
10 -1.039 0.77 9.669e-01 2336.00 3043.92 2427 2403 686 91 111 90 5613 5595 1011 814 838 227 0 -1.039
11 -0.913 0.84 8.952e-01 3964.00 4733.65 4047 4060 996 83 106 93 8283 8156 1283 820 842 227 0 -0.913
12 -0.810 0.90 7.775e-01 4732.00 5263.28 4816 4836 847 84 104 86 9113 9282 1037 815 826 222 0 -0.810
13 -0.856 0.87 8.376e-01 3099.00 3557.69 3185 3207 580 86 105 86 6434 6433 884 825 837 229 0 -0.856
14 -0.912 0.84 8.986e-01 10373.00 12383.73 10460 10431 1200 87 108 95 20368 20308 1930 844 853 240 0 -0.912
15 -0.930 0.83 9.061e-01 2735.00 3305.88 2822 2744 794 87 110 90 6065 5948 1260 853 860 220 0 -0.930
16 -0.853 0.87 8.331e-01 4287.00 4911.88 4370 4281 865 83 105 89 8586 8347 1400 842 851 228 0 -0.853
17 -0.973 0.80 9.406e-01 3154.00 3928.11 3248 3288 658 94 119 119 7041 7023 831 848 868 276 0 -0.973
18 -0.709 0.96 6.017e-01 7087.00 7345.63 7174 7211 1135 87 110 91 12422 12342 1642 841 841 225 0 -0.709
19 1.58 4.331e-01 10.00 6.34 90 114 117 88 108 90 879 885 241 883 891 234 -50 0
20 -0.100 1.47 3.703e-03 23654.00 16075.26 23742 23145 3781 88 109 96 26222 24767 5663 878 890 240 0 -0.100

Total number of rows: 25246

Table truncated, full table size 2521 Kbytes.




Supplementary file Size Download File type/resource
GSM171088.gpr.gz 2.1 Mb (ftp)(http) GPR

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