|
| 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 |
|
