title: GSM4066306: LNCaP R1881 0.7 Dox-3; Homo sapiens; RNA-Seq
library_construction_protocol: The ChIP assays were performed using HighCell ChIP kit with IPure 2.0 kit elution (Diagenode) according to manufacturer's protocol. The antibodies used for ChIP assay are AR_PG-21 (Millipore Cat. # 06-680); TBP (Abcam Cat. #ab63766), and Normal Rabbit IgG Control (Diagenode). LNCaP cells were grown in charcoal-stripped serum containing media for 48 hrs followed by 12 hrs of vehicle or 1 nM R1881 and dox treatment (0.1 µM for 'low,' 0.4 µM for 'medium,' and 0.7 µM for 'high') for all ChIP-qPCR and ChIP-seq conditions.  ChIP-seq sample preparation for sequencing was performed according to the manufacturer's instructions (Illumina). The ChIP-seq sample preparation for sequencing was performed according to the manufacturer's instructions (Illumina). ChIP-enriched DNA samples (1-10 ng) were converted to blunt-ended fragments using T4 DNA polymerase, E.coli DNA polymerase I large fragment (Klenow polymerase) and T4 polynuleotide kinase (New England BioLabs, NEB). A single A-base was added to fragment ends by Klenow fragment (3' to 5' exo minus; NEB) followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-modified DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (QIAGEN). Libraries were quantified with the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2000 Sequencer (100 nucleotide read length). RNA-seq using cDNA based on manufacturer's instructions (Illumina)
attributes.tag: GEO Accession
attributes.value: GSM4066306