WGS of sorted chromosomes of WI-38 cells
Five chromosomes were sorted per well of a 384 well plate, with NERL Blood Bank Saline (8504, Thermo Scientific)serving as the sheath fluid,Prior to library preparation, 20nl of Proteinase K (AM2546, Ambion) was dispensed into each 384-well plate containing sorted chromosomes using the Echo555 Liquid Handler (Labcyte). Libraries were prepared with a 0.25X scale-down of the Nextera XT Library Kit (FC-131-1096, Illumina) using Bravo Liquid Handling (Agilent Technologies), and 20 cycles of amplification. Equal volumes of each library were pooled andcleaned with either Zymo Clean and Concentrator -5, or with a modified 0.8X AmpureXP (A63881, Beckman Coulter) SPRI. We modified the SPRI cleanup by using a home-made SPRI bead binding buffer (https://openwetware.org/wiki/SPRI_bead_binding_buffer) to reduce the volume of beads required, and improve elution efficiency. Volume of beads = elution volume of sample, and home-made SPRI bead binding buffer = (0.8x sample volume  volume of beads). In both cases, pools were concentrated 16x during elution. Libraries were quantified on HS DNABioAnalyzer chips (Agilent Technologies), and size-selected 150-2000bp with Pippin HT (Sage Sciences)if primer dimers were visible. Clean libraries were diluted to 3nM in EB, and sequenced on HiSeq4000 (Illumina)using paired-end 150bp reads with 8bp dual-indexing.