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Sample GSM234792 Query DataSets for GSM234792
Status Public on Nov 01, 2007
Title Human Lung, me3K9 Promoter 1 Array, 99607
Sample type genomic
 
Channel 1
Source name Lung
Organism Homo sapiens
Characteristics me5K27 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 Lung
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 Lung
Data processing log base 2 ratios
 
Submission date Oct 05, 2007
Last update date Aug 14, 2011
Contact name Kimberly Rose Blahnik
E-mail(s) krblahnik@ucdavis.edu
Organization name University of California Davis
Department Genome and Biomedical Sciences
Lab Peggy Farnham
Street address GBSF 1 Shields Ave
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
 
Platform ID GPL4704
Series (1)
GSE8667 Genome-wide Analysis of KAP1 Binding Suggests Auto-regulation of KRAB-ZNFs

Data table header descriptions
ID_REF each probe NimbelGen ID
Rval ch1 signal
Gval ch2 signal
VALUE log2(Rval/Gval)

Data table
ID_REF Rval Gval VALUE
HG17PR0406S13400_CHR10P00084179 1402.78 2106.00 -1.00
HG17PR0406S13400_CHR10P00084289 951.33 353.11 1.02
HG17PR0406S13400_CHR10P00084399 799.78 384.78 0.64
HG17PR0406S13400_CHR10P00084509 1050.56 622.11 0.34
HG17PR0406S13400_CHR10P00084619 1074.78 548.22 0.56
HG17PR0406S13400_CHR10P00084729 1679.89 805.00 0.65
HG17PR0406S13400_CHR10P00084839 1382.44 892.67 0.22
HG17PR0406S13400_CHR10P00084949 1160.89 636.78 0.45
HG17PR0406S13400_CHR10P00085059 1277.89 1001.00 -0.06
HG17PR0406S13400_CHR10P00085169 1061.67 412.44 0.95
HG17PR0406S13400_CHR10P00087820 4035.78 5284.89 -0.80
HG17PR0406S13400_CHR10P00087930 2701.89 4862.67 -1.26
HG17PR0406S13400_CHR10P00088040 1330.22 1750.33 -0.81
HG17PR0406S13400_CHR10P00088150 3930.00 5223.11 -0.82
HG17PR0406S13400_CHR10P00088506 3887.11 7177.11 -1.30
HG17PR0406S13400_CHR10P00088616 4276.78 5923.22 -0.88
HG17PR0406S13400_CHR10P00088809 1114.67 1039.67 -0.31
HG17PR0406S13401_CHR10P00167069 2156.56 2892.56 -0.84
HG17PR0406S13401_CHR10P00167210 844.00 706.78 -0.16
HG17PR0406S13401_CHR10P00167320 1181.67 543.56 0.71

Total number of rows: 382661

Table truncated, full table size 19505 Kbytes.




Supplementary file Size Download File type/resource
GSM234792_99607_532_pair.txt.gz 6.5 Mb (ftp)(http) TXT
GSM234792_99607_635_pair.txt.gz 6.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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