The role of DNA methylation in regulation of transcriptional response to anoxia and re-oxygenation in crucian carp

In this study we used whole-genome bisulfite sequencing to investigate whether there are changes in methylation patterns of specific genes in response to anoxia and re-oxygenation in the brain of crucian carp (Carassius carassius). Crucian carp were exposed to either 6 days of normoxia (4 individuals), 6 days of anoxia (4 individuals) or 6 days of anoxia followed by 1 day of reoxygenation (4 individuals). We extracted DNA and used the Pico Methyl-Seq Library Prep Kit (Zymo Research) for bisulfite conversion and library preparation, and also extracted RNA from the same brain samples, to perform RNAseq, and thus look at both changes in gene expression and methylation patterns in the same individuals. DNA libraries were sequenced on 2/4 Illumina Novaseq6000 S4 flowcells (300 cycles; 150 bp paired-end reads) while RNA was sequenced on 1/2 Illumina Novaseq6000 SP flowcells (300 cycles; 150 bp paired-end reads).