NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM235386 Query DataSets for GSM235386
Status Public on Jan 01, 2008
Title methylated DNA Immunoprecipitation/INPUT HCT116 wild type - array 1 of 2
Sample type genomic
 
Channel 1
Source name methylated DNA immunoprecipitated
Organism Homo sapiens
Characteristics methylated DNA immunoprecipitated from the HCT116 wild type
Extracted molecule genomic DNA
Extraction protocol DNA from the Methylated DNA Immunoprecipitation (MeDIP) as previously described (Weber et al. Nat Genet 2005)
Label Cy5
Label protocol 2 µg of genomic DNA were primed with 20 µl of 2.5x Random Primers at 95°C for 5 min and then labeled with 5µl of 10x dUTP mix, 3 µl of Cy3 or Cy5 dUTP (1.0mM) and 1 µl of Exp-Klenow at 37ºC for 3 hours.
 
Channel 2
Source name Total Genomic DNA (INPUT)
Organism Homo sapiens
Characteristics Total genomic DNA from HCT116 wild type
Extracted molecule genomic DNA
Extraction protocol DNA from the Methylated DNA Immunoprecipitation (MeDIP) as previously described (Weber et al. Nat Genet 2005)
Label Cy3
Label protocol 2 µg of genomic DNA were primed with 20 µl of 2.5x Random Primers at 95°C for 5 min and then labeled with 5µl of 10x dUTP mix, 3 µl of Cy3 or Cy5 dUTP (1.0mM) and 1 µl of Exp-Klenow at 37ºC for 3 hours.
 
 
Hybridization protocol Human cot-1 DNA, Agilent 10x blocking agent and Agilent 2x hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
Scan protocol Scanned on an Agilent G2565AA scanner.
Images were quantified using Agilent Feature Extraction Software (version v:8.1).
Description none
Data processing LINEAR normalized, background subtracted data obtained from log10 of processed Red signal/processed Green signal. Agilent feature extraction software (version v8.1) was used.
 
Submission date Oct 09, 2007
Last update date Aug 14, 2011
Contact name Filipe Vicente Jacinto
E-mail(s) fvjacinto@cnio.es
Phone + (34) 912 246 964
Fax + (34) 912 246 980
Organization name CNIO
Department Molecular Pathology
Lab Cancer Epigenetics
Street address C/ Melchor Fernández Almagro, 3,
City Madrid
State/province Madrid
ZIP/Postal code E-28029
Country Spain
 
Platform ID GPL4089
Series (1)
GSE9267 Epigenetically Silenced Genes Found Using Methylated DNA Immunoprecipitation in Colon Cancer Cells Deficient in DNMTs

Data table header descriptions
ID_REF
VALUE normalized log10 ratio (Cy5/Cy3)

Data table
ID_REF VALUE
23216 0.00252697
456 -0.039958815
42570 -0.021919031
42140 0.067994701
41710 0.024305331
40850 -0.138018718
40420 -0.156801917
39990 -0.007357455
39560 0.104144401
38270 -0.031816314
37840 0.042279134
37410 -0.013850511
36980 -0.061723044
36550 -0.029151569
36120 -0.082492357
35690 -0.089167935
34830 -0.03042099
34400 -0.069547651
33970 -0.056814716
33540 -0.12346751

Total number of rows: 37621

Table truncated, full table size 662 Kbytes.




Supplementary file Size Download File type/resource
GSM235386.txt.gz 10.3 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap