|
| Status |
Public on Jun 17, 2015 |
| Title |
80-test-NIPP1-RATA-rep2 |
| Sample type |
genomic |
| |
|
| Source name |
HeLa cells, integrated Dam-NIPP1-RATA cassette
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
transgene: integrated Dam-NIPP1-RATA cassette
|
| Treatment protocol |
No additional treatment
|
| Growth protocol |
Polyclonal stable HeLa cell lines with integrated Dam 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 |
Samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Double-Stranded DNA Terminal Labeling Kit.
|
| |
|
| Hybridization protocol |
A mixture of fragmented biotinylated DNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix GeneChip Human Promoter 1.0 R Arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
|
| Scan protocol |
To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
|
| Description |
NIPP1-RATA.wig
NIPP1-RATA.bed
NIPP1-RATA samples compared to Dam controls
|
| Data processing |
MAT (Model-based Analysis for Tiling Arrays) analysis algorithm used to detect regions enriched by immunoprecipitation on Affymetrix tiling array. Bed-files are text files containing the enriched genomic regions. MAT algorithm settings: Bandwidth = 300, MaxGap = 300, MinProbes = 5, p-value = 1.00E-04
|
| |
|
| Submission date |
Jan 16, 2014 |
| Last update date |
Jun 17, 2015 |
| 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 |
GPL5082 |
| Series (1) |
| GSE54170 |
Mapping and characterization of promoter-binding sites of protein phosphatase 1 |
|
