|
Status |
Public on Jan 06, 2011 |
Title |
MDA231-CTRL_MeDIP |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
5-methylcytosine immunoprecipitation (MeDIP) in MDA231-CTRL cells
|
Organism |
Homo sapiens |
Characteristics |
antibody: MAb-5MECYT (against 5-methylcytidine) from Diagenode
|
Growth protocol |
Cells were grown in DMEM or RPMI supplemented with 10% FBS.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Cells were cross-linked with 1% formaldehyde and processed as in Carroll et al. 2005 for ChIP-chip, or genomic DNA was directly prepared for MeDIP-chip as in Weber et al. 2005.
|
Label |
Biotin
|
Label protocol |
Standard Affymetrix protocol
|
|
|
Channel 2 |
Source name |
Input from MDA231-CTRL cells
|
Organism |
Homo sapiens |
Characteristics |
antibody: None (input control)
|
Growth protocol |
Cells were grown in DMEM or RPMI supplemented with 10% FBS.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Cells were cross-linked with 1% formaldehyde and processed as in Carroll et al. 2005 for ChIP-chip, or genomic DNA was directly prepared for MeDIP-chip as in Weber et al. 2005.
|
Label |
Biotin
|
Label protocol |
Standard Affymetrix protocol
|
|
|
|
Hybridization protocol |
Standard Affymetrix protocol
|
Scan protocol |
Scanned at the Nantes microarray core facility
|
Description |
5-methylcytosine immunoprecipitation (MeDIP) in MDA231-CTRL cells
|
Data processing |
Model-based analysis of tiling array (MAT) (chip.dfci.harvard.edu/~wli/MAT/). Bar files provide individual probe signal level after MAT normalization (MAT score) (Johnson WE et al. PNAS 2006)
|
|
|
Submission date |
Apr 26, 2010 |
Last update date |
Jun 05, 2012 |
Contact name |
Jérôme Eeckhoute |
E-mail(s) |
jerome.eeckhoute@inserm.fr
|
Organization name |
CNRS
|
Lab |
INSERM UMR 1011, Université Lille-Nord de France
|
Street address |
Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc
|
City |
Lille |
ZIP/Postal code |
59045 |
Country |
France |
|
|
Platform ID |
GPL4915 |
Series (1) |
GSE21513 |
Role of DNA methylation in FOXA1 cell type-specific recruitment to chromatin |
|