title: GSM5484690: SETDB1KO_Periphilin rep 1; Homo sapiens; RIP-Seq
library_construction_protocol: RIPseq:  Lysates from UV-treated cells were clarified from sonicated nuclei and RNA-protein complexes were isolated with anti-HA magnetic beads. ChIPseq: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K9me3 antibody. RIPseq: Immunoprecipitated RNA was subjected to DNA library preparation using SMARTer Stranded Total RNA-Seq Kit V3 – Pico Input Mammalian (Takara Bio, USA) kit according to the manufacturer's instructions and following conditions: initial fragmentation at 94°C for 3-4 min, ribosomal RNA depletion step included, 5 PCR cycles for PCR adding adapters and indexes and 12 for final library amplification). The library quality was determined using Bioanalyzer, and sequenced using Illumina MiniSeq System with the following specifications: 32 bp (R1) and 43 bp (R2), paired-end reads were sequenced using MiniSeq High-Output 75 cycles kit. ChIPseq: ChIP DNA and input DNA were subjected to library preparation with NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer's instructions. Libraries were purified, quantified, multiplexed (with NEBNext Multiplex Oligos for Illumina) and sequenced with 2× 50-bp pair-end reads on Illumina Novaseq platform (Genomics Core, Cancer Research UK Cambridge Institute).