GBS data for23 populations of Icelandic stickleback from both geothermal and ambient habitats
A total of 100 ng of genomic DNA was digested with ApeKI and custom adapters ligated to the resulting sequence overhang. The custom adapters were designed using a dual indexing approach to control for index hopping. Samples were pooled and a double sided size selection step was performed with AMPure AP beads using a bead:sample ration of 0.7:1 followed by a 1:1 ratio for an insert size range of 100  400 basepairs (bp). Polymerase chain reaction (PCR) was performed in a 50 l reaction with 25 l NEBNNext Ultra II mastermix, 25 M of each primer, and 20 l of pooled library. The PCR profile was 30 seconds at 98 degrees Celsius followed by 5 cycles of 10 seconds at 98 degrees Celsius, 30 seconds at 70 degrees Celsius, 45 seconds at 65 degrees Celsius, with a final extension of 5 minutes at 65 degrees Celsius. Following protocol in: Elshire, R. J. et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6, 110 (2011).