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Sample GSM272855 Query DataSets for GSM272855
Status Public on Jun 04, 2008
Title Normal Liver, Patient 2, me3K27 Promoter 2 Array, array 81470
Sample type genomic
 
Channel 1
Source name Normal Liver
Organism Homo sapiens
Characteristics me3K27 antibody-immunoprecipitated fraction
Extracted molecule genomic DNA
Extraction protocol Performed following the 'Chromatin Immunoprecipitation Assay (ChIPs)' protocol provided at http://genomics.ucdavis.edu/farnham
Label Cy5
Label protocol The labeling of DNA samples for ChIP-ChIP analysis was performed by NimbleGen Systems, Inc. Briefly, each DNA sample (1 ug) was denatured in the presence of 5'-Cy3- or Cy5-labeled random nonamers (TriLink Biotechnologies) and incubated with 100 units (exo-) Klenow fragment (NEB) and dNTP mix [6 mM each in TE buffer (10 mM Tris/1 mM EDTA, pH 7.4; Invitrogen)] for 2 h at 37°C. Reactions were terminated by addition of 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water.
 
Channel 2
Source name Normal Liver
Organism Homo sapiens
Characteristics control total input
Extracted molecule genomic DNA
Extraction protocol see extract protocol for channel 1
Label Cy3
Label protocol see labeling protocol for channel 1
 
 
Hybridization protocol The hybridization of DNA samples for ChIP-ChIP analysis was performed by NimbleGen Systems, Inc. Briefly, 13ug of the Cy5-labeled ChIP sample and 13ug of the Cy3-labeled total sample were mixed, dried down, and resuspended in 40 ul of NimbleGen Hybridization Buffer (NimbleGen Systems) plus 1.5 ug of human COT1 DNA. After denaturation, hybridization was carried out in a MAUI Hybridization System (BioMicro Systems) for 18 h at 42°C. The arrays were washed using NimbleGen Wash Buffer System (NimbleGen Systems), dried by centrifugation.
Scan protocol The arrays were scanned at 5-um resolution using the GenePix 4000B scanner (Axon Instruments).
Description Normal Liver. Note array 2 of 2 5 kb promoter array; complement is 88819; see Acevedo et al., 2008 Cancer Res in press
Data processing raw, log base 2 ratios
 
Submission date Mar 12, 2008
Last update date Jun 04, 2008
Contact name Mark Bieda
E-mail(s) markb7002000@yahoo.com
Organization name University of Calgary
Department Biochemistry and Molecular Biology
Lab Bieda
Street address 3330 Hospital Dr NW
City Calgary
State/province AB
ZIP/Postal code T2N4N1
Country Canada
 
Platform ID GPL3930
Series (1)
GSE10842 Tumor Liver vs Normal Liver: ChIP-chip and RNA expression

Data table header descriptions
ID_REF each probe NimbelGen ID
Rval ch1 signal, Cy5 ChIP DNA
Gval ch2 signal, Cy3 input DNA
VALUE log2(Rval/Gval)

Data table
ID_REF Rval Gval VALUE
HG17PR0406S09891_CHR6HH1P00000246 6083.33 4724.44 0.364719
HG17PR0406S09891_CHR6HH1P00000374 3082.78 2065.11 0.578015
HG17PR0406S09891_CHR6HH1P00000500 5060.56 3430.67 0.560809
HG17PR0406S09891_CHR6HH1P00000612 1635.33 1719.00 -0.071988
HG17PR0406S09891_CHR6HH1P00000722 8465.78 6365.00 0.411484
HG17PR0406S09891_CHR6HH1P00000848 3275.11 2252.67 0.539909
HG17PR0406S09891_CHR6HH1P00000958 2836.78 2426.11 0.22561
HG17PR0406S09891_CHR6HH1P00001068 1381.78 2120.78 -0.618069
HG17PR0406S09891_CHR6HH1P00001182 3129.00 1771.44 0.820782
HG17PR0406S09891_CHR6HH1P00001325 3162.22 2024.11 0.643652
HG17PR0406S09891_CHR6HH1P00001435 1380.56 936.89 0.559304
HG17PR0406S09891_CHR6HH1P00001545 1589.33 1807.22 -0.185354
HG17PR0406S09891_CHR6HH1P00001685 2707.56 1963.78 0.463362
HG17PR0406S09891_CHR6HH1P00001803 4014.56 3694.78 0.119754
HG17PR0406S09891_CHR6HH1P00001930 1505.33 1960.44 -0.381099
HG17PR0406S09891_CHR6HH1P00002040 2164.89 1670.89 0.373678
HG17PR0406S09891_CHR6HH1P00002150 3406.89 3093.33 0.139295
HG17PR0406S09891_CHR6HH1P00002260 1056.11 951.44 0.150576
HG17PR0406S09891_CHR6HH1P00002370 2952.00 2409.67 0.292858
HG17PR0406S09891_CHR6HH1P00002799 1560.56 1289.11 0.275689

Total number of rows: 364132

Table truncated, full table size 20293 Kbytes.




Supplementary file Size Download File type/resource
GSM272855_81470_532_pair.txt.gz 6.4 Mb (ftp)(http) TXT
GSM272855_81470_635_pair.txt.gz 6.4 Mb (ftp)(http) TXT
Processed data not applicable for this record

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