title: GSM8947507: Chip-seq, H3K4Me3, PC3, OE C, rep#1; Homo sapiens; ChIP-Seq
library_construction_protocol: RNA sequencing (RNA-seq) was performed on PC3 cells transduced with control (Ctrl), DDC, or SLC6A4 constructs. Total RNA was extracted using TRIzol Reagent (Invitrogen) and treated with DNase I to remove genomic DNA contamination. mRNA was enriched using Oligo(dT)-modified magnetic beads and subsequently used for cDNA synthesis (Invitrogen). RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were prepared and quantified before sequencing on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA) in high-output mode. ChIP assays were performed using the SimpleChIP Plus Enzymatic Chromatin IP Kit (9005, Cell Signaling Technology) following the manufacturer's protocol. Briefly, cells were crosslinked with 1% formaldehyde and sonicated to obtain chromatin fragments averaging 250–1000 bp. Immunoprecipitated chromatin was subsequently reverse crosslinked. For ChIP-seq, the immunoprecipitated DNA and input DNA were subjected to library preparation using the NEBNext Ultra II DNA Library Prep Kit (E7645, New England Biolabs) according to the manufacturer's protocol.