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Sample GSM239641 Query DataSets for GSM239641
Status Public on Nov 01, 2007
Title Human Ntera2, me3K27 Promoter 1 Array, 91211
Sample type genomic
 
Channel 1
Source name Ntera2 cells
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 Ntera2 cells
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 Human Ntera2 cells
Data processing log base 2 ratios
 
Submission date Oct 25, 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 GPL5989
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
CHR1:6688-11364_CHR01P000006688 4164.33 7738.33 -0.34
CHR1:6688-11364_CHR01P000006788 1413.22 3032.89 -0.55
CHR1:6688-11364_CHR01P000006888 2417.33 4742.00 -0.42
CHR1:6688-11364_CHR01P000006988 1721.56 4030.11 -0.68
CHR1:6688-11364_CHR01P000007088 3017.67 8460.67 -0.94
CHR1:6688-11364_CHR01P000007188 1197.67 2360.11 -0.43
CHR1:6688-11364_CHR01P000007288 1407.44 4007.11 -0.96
CHR1:6688-11364_CHR01P000007388 1209.56 3138.22 -0.83
CHR1:6688-11364_CHR01P000007488 871.67 2047.00 -0.68
CHR1:6688-11364_CHR01P000007588 811.78 982.78 0.27
CHR1:6688-11364_CHR01P000007688 1478.00 2972.89 -0.46
CHR1:6688-11364_CHR01P000007788 1251.22 2049.11 -0.16
CHR1:6688-11364_CHR01P000007888 923.89 2025.11 -0.58
CHR1:6688-11364_CHR01P000007988 3590.56 13354.33 -1.35
CHR1:6688-11364_CHR01P000008088 2355.00 8072.00 -1.23
CHR1:6688-11364_CHR01P000008188 1731.67 3808.00 -0.59
CHR1:6688-11364_CHR01P000008288 869.89 1214.56 0.07
CHR1:6688-11364_CHR01P000008388 892.00 2349.78 -0.85
CHR1:6688-11364_CHR01P000008488 1497.56 4758.89 -1.12
CHR1:6688-11364_CHR01P000008588 1137.11 3106.67 -0.90

Total number of rows: 378943

Table truncated, full table size 22317 Kbytes.




Supplementary file Size Download File type/resource
GSM239641_91211_532_pair.txt.gz 6.9 Mb (ftp)(http) TXT
GSM239641_91211_635_pair.txt.gz 6.8 Mb (ftp)(http) TXT
Processed data included within Sample table
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