title: crosslinked undigested control
description: Sample preparation. Haloferax volcanii DS2 cells (obtained from the ATCC) were grown to mid-log phase at 42*C in ATCC 974 Halobacterium medium supplemented with 2M NaCl. Cells were fixed with 2% formaldehyde for 30 min then quenched with 125mM of glycine for 5 min. Cells were pelleted and snap frozen prior to MNase digestion and DNA extraction. Frozen cells were processed according to a modified protocol from Rizzo et al.(Rizzo et al., 2011, Tsui et al., 2012). Samples were digested with increasing concentrations of MNase and a no MNase control. After digestion, fragments 50-60bp in length were size-selected using an Agilent Bioanalyzer High Sensitivity chip (Agilent, part# 5067-4626) and further processed for Illumina deep sequencing. This size-selection was critical, as the formaldehyde crosslinking causes both histones as well as other DNA-binding proteins to crosslink with bound DNA. Nucleosomal and genomic libraries were pooled equally according to qPCR quantitation, and sequenced using v3 chemistry on one single-read HiSeq2000 lane (50x8). Samples were demultiplexed using an 8bp index read at the end of read 1.