Genome-wide DNA methylation data
All individuals were analysed at the same age (10 months old). Fish were
euthanized using an overdose of methane-sulfonate (MS-222) following UK
Home Office Schedule 1, their brains were dissected and stored in
molecular grade ethanol before DNA extraction using Qiagen DNeasy Blood
and tissue kit (Qiagen Ltd, Crawley, UK).
Bisulphite converted genomic DNA libraries were prepared using the
Diagenode Premium Reduced Representation Bisulphite Sequencing (RRBS)
kit (Diagenode, Liege, Belgium) according manufacturer’s indications.
For the first generation, 16 individuals (ten from enriched, six from
poor) were multiplexed into a single library, pooled samples were
bisulphite-converted, amplified by enrichment PCR and their quality
assessed using Agilent D1000 ScreenTape System (Agilent Technologies,
Inc. 2014). The library was then sequenced on an Illumina NextSeq 500
platform using a 1x75pb single-end run (Cardiff University, Genomics
Research Hub). Standard PCR fully methylated and unmethylated spike
controls were used to monitor bisulphite conversion efficiency.
A second library was created using fourteen individuals from the
offspring (five from enriched to enriched environments, three from
enriched to poor, three from poor to poor, and three from poor to
enriched). The library followed the same procedures and sequencing
conditions as the first library.