|
| Status |
Public on Jul 19, 2010 |
| Title |
RATA.vs.Ctrl |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
RATA DamID DNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HeLa
|
| Treatment protocol |
no additional treatment
|
| Growth protocol |
Polyclonal stable HeLa cell lines with integrated Dam, Dam-NIPP1 and Dam-NIPP-RATA transgenes were generated and grown following standard cell culture procedures, using G418 as selective agent (also: see Vogel et al. 2007 as cited below)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from cells (Sigma GeneElute Mammalian Genomic DNA Minprep kit) and processed according to the DamID protocol published in (Vogel, M.J., Peric-Hupkes, D., and van Steensel, B. 2007. Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nature protocols 2(6): 1467-1478.)
|
| Label |
biotin
|
| Label protocol |
For each sample 10-30 ng of genomic DNA was amplified using the Sigma WGA2 kit and subsequently fragmented and labeled according the the Affymetrix Chromatin Immunoprecipitation Assay Protocol.
|
| |
|
| Channel 2 |
| Source name |
unfused DamID (control)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HeLa
|
| Treatment protocol |
no additional treatment
|
| Growth protocol |
Polyclonal stable HeLa cell lines with integrated Dam, Dam-NIPP1 and Dam-NIPP-RATA transgenes were generated and grown following standard cell culture procedures, using G418 as selective agent (also: see Vogel et al. 2007 as cited below)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from cells (Sigma GeneElute Mammalian Genomic DNA Minprep kit) and processed according to the DamID protocol published in (Vogel, M.J., Peric-Hupkes, D., and van Steensel, B. 2007. Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nature protocols 2(6): 1467-1478.)
|
| Label |
biotin
|
| Label protocol |
For each sample 10-30 ng of genomic DNA was amplified using the Sigma WGA2 kit and subsequently fragmented and labeled according the the Affymetrix Chromatin Immunoprecipitation Assay Protocol.
|
| |
|
| |
| Hybridization protocol |
Fragmented biotinylated DNA was hybridized on Affymetrix GeneChip® ENCODE 2.0R Arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
|
| Scan protocol |
To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
|
| Description |
DamID for RATA (FDN mutant) versus Control (unfused DamID)
|
| Data processing |
Raw data were processed and analysed using Model-based Analysis of Tiling arrays (MAT) (Johnson, et al. 2006)
*.bar files and *.bed files were generated by MAT and represent the MAT scores for each probe and the putative enriched genomic regions respectively.
|
| |
|
| Submission date |
Jun 03, 2010 |
| Last update date |
Jul 19, 2010 |
| Contact name |
Rekin's Janky |
| E-mail(s) |
Nucleomics.Bioinformatics@vib.be
|
| Organization name |
VIB
|
| Department |
Nucleomics Core
|
| Street address |
Herestraat 49 Box 816
|
| City |
Leuven |
| ZIP/Postal code |
B-3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL6129 |
| Series (1) |
| GSE22123 |
Mapping of NIPP1-WT and NIPP-RATA binding sites to ENCODE regions |
|
