RADSeq raw data of Nautilus macromphalus: sample NC_AM09
DNA was extracted from ethanol preserved tissue using the DNAeasy Kit (Qiagen) following optimized manufacturer's instruction. Library preparation was conducted following Peterson et al. (2012) with the following modifications: Genomic DNA was digested using high-fidelity restriction enzymes Sbf1 and EcoR1 (New England Biolabs). Resulting fragments were ligated to custom-made P1 and P2 adapters containing sample-specific barcodes and primer annealing sites. Individually barcoded samples were then pooled into libraries and size-selected (320 to 720bp) using a Pippin prep (Sage Science). Each library was then PCR-amplified using Phusion Polymerase, and 14-18 PCR cycles. Resulting libraries were cleaned and size-selected to remove remaining adapters and primers using Agilent beads (ratio 1:0.8). Libraries were multiplexed with more diverse RNA-Seq libraries and paired-end sequenced (150 bp) on an Illumina HiSeq 2500 at the Center for Systems Biology - Harvard University (Cambridge, MA).