title: ddRADseq raw data of Ophiocomina nigra sample OC_TAR_23
design: DNA was extracted from ethanol preserved tube feet tissue samples following a CTAB protocol. Briefly, tube feet were digested overnight at 57C in CTAB buffer, 2-mercaptoethanol and Proteinase K; subsequently, DNA was isolated with 24:1 chloroform:isoamyl alcohol and precipitated with ice-cold ethanol. DNA integrity, purity and quantity were checked in agarose electrophoresis gels, Nanodrop, and using a Qubit DNA HS assay (Life Technologies), respectively. Genomic DNA was digested using high-fidelity restriction enzymes EcoRI and MseI (New England Biolabs). Resulting fragments were purified with Agencourt AMPure beads (Beckham Coulter) and ligated with barcoded adapters. Individually barcoded samples were then pooled into libraries and size-selected (200 to 400 bp) using a Blue Pippin (Sage Science). Each library was PCR-amplified using a Phusion high-fidelity DNA polymerase kit (New England Biolabs) using indexed primers. Libraries were multiplexed and pair-end sequenced (150 bp) on an Illumina NovaSeq 6000 at the Novogene Core Facility (Cambridgeshire, UK).