Tagmentation enzyme

ATAC-seq was performed on 50,000 viable sorted myeloma cells similar to previously described^{43 (link),61 (link),62 (link)}. Briefly, cells were pelleted at 500 × g for 10 min at 4 °C and resuspend in ice-cold nuclei-lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% IGEPAL) and centrifuged at 500 × g for 30 min at 4 °C. Nuclei were resuspended in 22.5 μl of tagmentation DNA buffer (Illumina) with 2 μl tagmentation enzyme (Illumina) at 37 °C for 60 min. Proteins were digested with 2 μg of proteinase K at 40 °C for 60 min. Tagmented DNA was isolated with two rounds of negative (0.6×) and positive (1.2×) size selection with SPRI beads (PureBeads, Kapa Biosystems). ATAC-seq libraries were amplified 12 times with Hifi Polymerase (Kapa Biosystems) and quantitated by qPCR (Kapa Biosystems) and high sensitivity bioanalyzer (Agilent). Sequencing was performed on a NovaSeq 6000 (Illumina) using 150 bp paired-end at the New York Genome Center.

Whole-genome sequencing libraries were generated using a modified version of the Illumina Nextera protocol based on (Baym et al. 2015 (link)). Briefly, genomic DNA is fragmented using an Illumina Tagmentation enzyme that adds Illumina adaptor sequences to ends. “Tagmented” samples are then PCR amplified using oligonucleotide primers that add unique barcodes to each sample so that samples can be multiplexed on a single Illumina sequencing run. Coverage of all clones described can be found in Supplementary Table 5 in Supplementary File 1. Sequencing reads are deposited in the NCBI Sequence Read Archive (SRA) under BioProject PRJNA742704.