title: Androgen receptor DNA binding and chromatin accessibility profiling in prostate cancer.
abstract: Prostate cancer (PCa) is the second most common cancer in men. The Androgen Receptor (AR) is the major driver of PCa and the main target of therapy in the advanced setting. AR is a nuclear receptor that binds the chromatin and regulates transcription of genes involved in cancer cell proliferation and survival. In a study by Stelloo et al. (1) we explored prostate cancer on the level of transcriptional regulation by means of Formaldehyde-Assisted Isolation of Regulatory Elements and Chromatin Immunoprecipitation coupled with massive parallel sequencing (FAIRE-seq and ChIP-seq, respectively). We employed these data for the assessment of differences in transcriptional regulation at distinct stages of PCa progression and to construct a prognostic gene expression classifier. Genomics data includes FAIRE-seq data from normal prostate tissue as well as primary, hormone therapy resistant and metastatic PCa. Furthermore, ChIP-seq data from primary and resistant PCa were generated, along with multiple input controls. The data are publicly available through NCBI GEO database with accession number GSE65478. Here we describe the genomics and clinical data in detail and provide comparative analysis of FAIRE-seq and ChIP-seq data.
authors.affiliation: Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands; Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Nevedomskaya
authors.affiliation: Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Suzan
authors.initials: S
authors.lastname: Stelloo
authors.affiliation: Division of Urology, The Netherlands Cancer Institute, Amsterdam, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Henk G
authors.initials: HG
authors.lastname: van der Poel
authors.affiliation: Division of Pathology, The Netherlands Cancer Institute, Amsterdam, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Jeroen
authors.initials: J
authors.lastname: de Jong
authors.affiliation: Division of Urology, The Netherlands Cancer Institute, Amsterdam, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Lodewyk F A
authors.initials: LF
authors.lastname: Wessels
authors.affiliation: Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Andries M
authors.initials: AM
authors.lastname: Bergman
authors.affiliation: Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Wilbert
authors.initials: W
authors.lastname: Zwart
keywords: ChIP-seq; FAIRE-seq; Prostate cancer; androgen receptor