 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 16, 2015 |
| Title |
Dam_Dil10_Rep2_Neuro-2a |
| Sample type |
SRA |
| |
|
| Source name |
Mouse neuroblastoma cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Neuro-2a
virus dilution used to infect cells with dam or tox-dam: 1:10
triggered expression: DAM only
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated and prepared as described in Vogel et al. 2006 (Vogel, M.J., Peric-Hupkes, D., and van Steensel, B. (2007). Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nat. Protoc. 2, 1467–1478.)
Sequencing libraries were prepared as described in Aprea et al. 2013
DamID-Seq - is an alternative to ChIP-Seq Sequencing for investigating DNA-Protein Interactions if no antibody is available. DamID is based on the expression of a fusion protein consisting of a protein of interest and DNA adenine methyltransferase (Dam). This leads to methylation of adenines near sites where the protein of interest interacts with the DNA. These methylated sequences are subsequently amplified by a methylation-specific enrichment protocol and identified by NGS. (Vogel, M.J., Peric-Hupkes, D., and van Steensel, B. (2007). Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nat. Protoc. 2, 1467–1478.)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
library strategy: DamID-Seq
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads from each condition were merged, and then mapped to mm9 or hg19 whole genome using bowtie1 with parameters -M 1
Peaks were called using SICER1.1 with the parameters: window size 50, gap size 250 and FDR 0.01
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: Sicer peaks [chrom, start, end, ChIP_island_read_count, CONTROL_island_read_count, p_value, fold_change, FDR_threshold]
|
| |
|
| Submission date |
Dec 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Federico Calegari |
| E-mail(s) |
federico.calegari@tu-dresden.de
|
| Organization name |
TU Dresden
|
| Department |
Center for Molecular and Cellular Bioengineering (CMCB)
|
| Lab |
Calegari Lab
|
| Street address |
Fetscherstr. 105
|
| City |
Dresden |
| ZIP/Postal code |
01307 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE64240 |
Identification of Tox chromatin binding properties and of its downstream targets by DamID |
|
| Relations |
| BioSample |
SAMN03267492 |
| SRA |
SRX814805 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
