Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish

Tubingen zebrafish at 6-months of age were euthanized in icy water and dissected to separate testis or brain tissues. All tissues collected were washed in 1x PBS, then flash-frozen on dry ice. Tissue chunks from one fish were considered as one replicate. For RNA extraction, we lysed tissues in TRIzol reagent and separated out the aqueous phase following the manufacturer's protocol (Invitrogen). RNA was extracted from the aqueous phase using RNA Clean & Concentrator-5 (Zymo). Poly(A)+ RNAs were isolated from total RNA using Dynabeads mRNA Purification Kit. NanoCAGE library preparation was performed as previously described using 50ng of poly(A)+ RNAs for each replicate (Poulain et al. 2017). The shallow sequencing data is the subset of the deep sequencing data.