RNA-Seq analysis of Wild Type and lrpap1-/- zebrafish eyes at three month

Zebrafish is a good model organism for studying eye diseases, but there is a lack of transcriptome information, especially as it related to myopia. The aim of this study was to compare transcriptome differences between lrpap1-/- mutant and wild-type zebrafish eyeballs. Eye tissue mRNA profiles of three-month-old wild-type (WT) and low-density lipoprotein receptor-related protein-associated protein 1 knockout (lrpap1-/-) zebrafishes were generated by deep sequencing using Illumina HiSeq2500. RNA-seq reads were aligned to the zebrafish genome(Ensembl, GRCz11) using HISAT2, TPM was used to further normalize gene expression counts between all samples. Differentially expressed genes (DEG) were determined by DESeq2, which was based on the Negative Binomial Generalize Linear Model. Finally, there are 1661 differentially expressed genes between the mutant and the wild-type zebrafish eyeballs using the criterion of p-value <0.05 and ׀Log (Fold Change)|>1 ,among which 1209 genes are up-regulated, and 452 genes are down-regulated in the mutants. Our study shows the first detailed analysis of zebrafish eyes transcriptomes by RNA-seq technology. The transcriptome information provided in this study may help to reveal the molecular mechanism of genetic myopia. mRNA profiles of three-month-old wild type (WT) and lrpap1-/- zebrafish eyes.