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| Status |
Public on Sep 01, 2016 |
| Title |
ChIP-seq. analysis of pan-histone 3 acetylation in Romidepsin treated TCam-2 |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
ChIP-seq. analysis of TCam-2 16 h after 10 nanomolar Romidepsin application. DMSO treated cells were used as controls. For ChIP, an antibody against histone H3 pan-acetylation was used. These data are part of the article 'The Histone Deacetylase Inhibitor Romidepsin Efficiently Targets Cisplatin-resistant Germ Cell Cancer Cells via Downregulation of the SWI/SNF-Complex Member ARID1A' (Nettersheim et al., 2016).
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| Overall design |
TCam-2 cells treated for 16h with romidepsin or the solvent were fixed by formaldehyde solution and further processed by Active Motif, including DNA shearing by sonication, chromatin-immunoprecipitaion, library generation and sequencing (NextSeq 500, Illumina). Pooled input DNA of each sample including spike-in Drosophila DNA was used as controls and for normalization. The 75-nt sequence reads were mapped against the genome using BWA algorithm. Duplicate reads were removed. Only peaks that align with no more than 2 mismatches and map uniquely to the genome were used for further analysis. Intervals / peaks were identified by the MACS peak finding algorithm (cutoff p-value 1x10-7) including ENCODE blacklist filtering
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| Contributor(s) |
Nettersheim D, Schorle H |
| Citation(s) |
27572311 |
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| Submission date |
Feb 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Nettersheim |
| E-mail(s) |
Daniel.nettersheim@med.uni-duesseldorf.de
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| Organization name |
University Hospital Düsseldorf
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| Department |
Urology
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| Lab |
Urological Research Lab, Translational Urooncology
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| Street address |
Universitätsstr. 1
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| City |
Düsseldorf |
| State/province |
NRW |
| ZIP/Postal code |
40225 |
| Country |
Germany |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA313057 |
| SRA |
SRP070758 |
