SRA

Wild-type zebrafish larvae and our prp1ua5003/ua5003;prp2ua5001/ua5001 mutant zebrafish larvae at 3 days post fertilisation were pooled into three biological replicates each of 50 larvae. Each replicate underwent paired end 100-125 and Illumina HiSeq2500 sequencing to a depth of 40 million reads, carried out by Otogenetics (Atlanta, GA). Samples were subsequently processed using the TopHat/Cufflinks bioinformatics pipeline. Alignments were mapped to the zebrafish reference genome, GRCz10. A small amount of wild-type reads were found to contaminate two of the pooled mutant samples and were not included in subsequent analysis. In total there were 1249 genes showing at least a 50% increase (745) in transcript abundance or 50% decrease (504) decrease in transcript abundance in wild-type zebrafish larvae compared to double mutant zebrafish larvae. Subsequent gene ontology analysis shows the biological process showing genes with the biggest decrease in transcript abundance was cell adhesion, and the process with the most genes showing an increase in transcript abundance was Oxidation/Reduction. Our study finds the processes affected by prion knockdown in zebrafish is remarkably similar to other studies in early mice embryos, suggesting a conserved function of the cellular prion protein in the early development of organisms. Overall design: RNA-Sequencing analysis of 3 days post fertlisation whole wild-type and prp1-/-;prp2-/- zebrafish larvae