title: Genome-wide chromatin accessibility, DNA methylation and gene expression analysis of histone deacetylase inhibition in triple-negative breast cancer.
abstract: Triple-negative breast cancer (TNBC), especially the subset with a basal phenotype, represents the most aggressive subtype of breast cancer. Unlike other solid tumors, TNBCs harbor a low number of driver mutations. Conversely, we and others have demonstrated a significant impact of epigenetic alterations, including DNA methylation and histone post-translational modifications, affecting TNBCs. Due to the promising results in pre-clinical studies, histone deacetylase inhibitors (HDACi) are currently being tested in several clinical trials for breast cancer and other solid tumors. However, the genome-wide epigenetic and transcriptomic implications of HDAC inhibition are still poorly understood. Here, we provide detailed information about the design of a multi-platform dataset that describes the epigenomic and transcriptomic effects of HDACi. This dataset includes genome-wide chromatin accessibility (assessed by ATAC-Sequencing), DNA methylation (assessed by Illumina HM450K BeadChip) and gene expression (assessed by RNA-Sequencing) analyses before and after HDACi treatment of HCC1806 and MDA-MB-231, two human TNBC cell lines with basal-like phenotype.
authors.affiliation: Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA 90404, USA.
authors.forename: Matias A
authors.initials: MA
authors.lastname: Bustos
authors.affiliation: Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA 90404, USA.
authors.forename: Matthew P
authors.initials: MP
authors.lastname: Salomon
authors.affiliation: Sequencing Center, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA 90404, USA.
authors.forename: Nellie
authors.initials: N
authors.lastname: Nelson
authors.affiliation: Sequencing Center, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA 90404, USA.
authors.forename: Sandy C
authors.initials: SC
authors.lastname: Hsu
authors.affiliation: Department of Surgery, David Geffen School of Medicine, University of California Los Angeles (UCLA), CA, USA.
authors.forename: Maggie L
authors.initials: ML
authors.lastname: DiNome
authors.affiliation: Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA 90404, USA; Sequencing Center, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA 90404, USA.
authors.forename: Dave S B
authors.initials: DS
authors.lastname: Hoon
authors.affiliation: Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA 90404, USA.
authors.forename: Diego M
authors.initials: DM
authors.lastname: Marzese