title: Mate-pair Sequencing of homo sapiens: adult male bone marrow
design: DNA extraction and mate pair library preparation methods have been previously described. Briefly, DNA was isolated from CD138+ plasma cells using either the Qiagen Puregene extraction kit (for samples < 2 mL), Autopure LS Automated high quality DNA extraction (for samples >2 mL) or the QIAmp Tissue kit for fixed cell pellet samples. DNA is first sheered into large fragments (2-5kb). After shearing, biotin end-labeling and size selection, the 25kb DNA fragments are circularized by joining two ends of a single fragment. Before sequencing, the circularized DNA is randomly sheared into 500-bp fragments, and the biotin-containing fragments are isolated for sequencing. DNA was processed using the Illumina Nextera Mate Pair library preparation kit (Illumina) and sequenced on the Illumina HiSeq 2500 or Illumina NovaSeq 6000 in rapid run mode. Pooled libraries were hybridized onto a flow cell and sequenced using 101 or 151-basepair reads and paired end sequencing.