|
| Status |
Public on Jan 06, 2011 |
| Title |
LNCaP_CTCF |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
CTCF ChIP in LNCaP cells
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: 07-729 (against CTCF) from Millipore
|
| 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 LNCaP 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 |
CTCF ChIP in LNCaP 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 |
|
