title: AR-ChIP-LNCaP
design: Treatment protocol :  LNCaP cells were seqentially transfected twice every 24 hours with 5nM of DsiRNA (IDT technologies) targetting LINC00844 or non-specic control (NC). Androgen-deprived cells were treated with DHT to a final concentration of 100 nM for 2 hrs prior to the ChIP procedure. Cells treated with an equal volume of vehicle, Et, for 2 hrs, served as controls. Growth protocol: Human LNCaP prostate cancer cells were maintained in RPMI Medium 1640 (Gibco) supplemented with 10% fetal bovine serum (FBS) in a 37°C incubator with 5% CO2. Prior to vehicle/drug stimulation, ~4 millions cells were seeded into 100 mm dish and starved with phenol red-free RPMI Medium 1640 containing 10% charcoal-dextran treated FBS (Hyclone)  as mentioned earlier for at least 72 hrs to ~80% confluence. Extraction method:  DNA library was constructed using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB) according to manufacturer's protocol. The libraries were amplified for 12 cycles of PCR with NEB indexing primers  and purified using AMPure XP beads (Backman Coulter).  The barcoded libraries were mixed in equimolar ratio and sequenced using Illumina HiSeq-2000