Zebrafish RNA-seq transcriptome analysis

RNA-sequencing was performed by the Nucleomics Core Facility (VIB, Leuven, Belgium). RNA was isolated using the RNeasy kit (Qiagen). From extracted RNA, libraries were made using the Illumina TruSeq Stranded mRNA Library protocol. These libraries were sequenced on an Illumina NextSeq 500 paired-end 75 bp and yield an average of 37.5 million reads per sample (range 35.1–40.5). To estimate the expression of the transcript of every sample, reads were counted using Salmon (v0.14.0) [55 (link)] against ensemble transcript for the zebrafish reference genome GRCz11. Transcript level expression from the protein coding genes was summarized to the gene level expression using the R-package tximport (v1.12.0). Differential expression was performed with edgeR (v3.24.3) [43 (link)]. Genes with a FDR-adjusted P value smaller than 0.05 and with an altered expression of 30% were deemed significantly differentially expressed. Datasets are deposited and available in ENA (project accession PRJEB50765).