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Series GSE78262 Query DataSets for GSE78262
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
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).
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
Contributor(s) Nettersheim D, Schorle H
Citation(s) 27572311
Submission date Feb 24, 2016
Last update date May 15, 2019
Contact name Daniel Nettersheim
Organization name University Hospital Düsseldorf
Department Urology
Lab Urological Research Lab, Translational Urooncology
Street address Universitätsstr. 1
City Düsseldorf
State/province NRW
ZIP/Postal code 40225
Country Germany
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (3)
GSM2070584 TCam-2 Solvent 16h
GSM2070585 TCam-2 Romidepsin 16h
GSM2070586 Pooled (human+Drosophila) input control
BioProject PRJNA313057
SRA SRP070758

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Supplementary file Size Download File type/resource
GSE78262_Normalized_data_active_regions.txt.gz 1.0 Mb (ftp)(http) TXT
GSE78262_Romidepsin_study_ChIP-seq_bigWig.txt.gz 354 b (ftp)(http) TXT
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