Nebnext multiplex oligos dual index primers set 1

Before library preparation and sequencing, all antibodies were first screened for ChIP-grade potential in SMARCB1-expressing cells by ChIP-qPCR. We considered antibodies suitable for ChIP-seq when target enrichment at positive control genes was 10-fold greater than IgG background signal at the same loci (Figure S4, IGV screenshot of antibodies used for ChIP-seq). ChIP-DNA was quantified using the Qubit^® 2.0 Fluorometer (Thermo Fisher Scientific). ChIP libraries were prepared from 10 ng DNA using the NEBNext^®Ultra-library preparation kit for Illumina (New England BioLabs, Ipswich, MA, USA) with Dual indexing NEBNext^® Multiplex Oligos (Dual Index Primers Set 1) following the manufacturer’s protocol. DNA libraries were purified and size selected (200–500 base pairs) by two rounds of AMPure bead purification. Library fragment length was validated using the High Sensitivity (HS) ScreenTape for 2200 TapeStation (Agilent, Santa Clara, CA, USA). ChIP library amplification was validated by qPCR at a set of known positive and negative control genes.