Handout     NAR 2006 Paper     NAR 2002 Paper     FAQ     MIAME     Email GEO  
   NCBI > GEO > Accession Display Not logged in | Login
GEO help: Mouse over screen elements for information.
Scope:    Format:    Amount:   GEO accession:    Go
Sample GSM239739 Query DataSets for GSM239739
Status Public on Nov 01, 2007
Title Human Ntera, me3K27 Promoter 2 Array, 100189
Sample type genomic
 
Channel 1
Source Name Ntera2 cells
Organism(s) Homo sapiens
Characteristics me3K27 antibody immunoprecipitated DNA
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(s) 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 26, 2007
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 GPL3930
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
HG17PR0406S14537_CHR11P00120140 454.00 1040.33 0.19
HG17PR0406S14537_CHR11P00120250 705.00 1736.44 0.09
HG17PR0406S14537_CHR11P00120360 466.67 1244.78 -0.02
HG17PR0406S14537_CHR11P00120470 844.67 2213.89 0.00
HG17PR0406S14537_CHR11P00120580 676.00 2043.56 -0.21
HG17PR0406S14537_CHR11P00120690 513.78 1789.78 -0.41
HG17PR0406S14537_CHR11P00120800 676.00 1870.78 -0.08
HG17PR0406S14537_CHR11P00120910 1153.89 3340.33 -0.14
HG17PR0406S14537_CHR11P00121020 690.89 2314.33 -0.35
HG17PR0406S14537_CHR11P00121130 2676.00 11409.89 -0.70
HG17PR0406S14537_CHR11P00121240 945.89 2741.22 -0.14
HG17PR0406S14537_CHR11P00121806 6638.89 18598.11 -0.10
HG17PR0406S14537_CHR11P00121916 3629.11 10746.22 -0.18
HG17PR0406S14537_CHR11P00122026 716.11 2938.78 -0.65
HG17PR0406S14537_CHR11P00122869 4274.67 15012.33 -0.42
HG17PR0406S14537_CHR11P00123045 2916.33 9937.00 -0.38
HG17PR0406S14537_CHR11P00123974 4492.33 15082.00 -0.36
HG17PR0406S14537_CHR11P00124555 355.78 1107.33 -0.25
HG17PR0406S14537_CHR11P00124665 1847.89 5341.44 -0.14
HG17PR0406S14538_CHR11P00180988 7552.22 22823.55 -0.21

Total number of rows: 362249

Table truncated, full table size 18643 Kbytes.




Supplementary file Size Download File type/resource
GSM239739_100189_532_pair.txt.gz 6.4 Mb (ftp)(http) TXT
GSM239739_100189_635_pair.txt.gz 6.3 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Section 508 |
NCBI Home NCBI Search NCBI SiteMap