Transcriptome Analysis of Acrylamide Exposure

Salmon (v0.9.1)^{48 (link)} generated transcript expression estimates for each library by mapping the raw Illumina RNA-seq data to the D. rerio transcriptome (vGRCz11)^{49 (link)}. Gene expression estimates were produced by combining all transcript estimates from the same gene⁵⁰ . Genes with low expression (an average log2 transformed count per million less or equal to one) were removed from further analysis^{51 (link)}. The gene expression estimates were normalized based on the sequencing depth of each library. EdgeR (v3.12.1)^{52 (link)} was used to find differentially expressed genes. Generalized linear models were used to test for differential expression based on contrasting the acrylamide treatment against the control. Genes with an FDR adjusted p-value ≤ 0.05 were considered differentially expressed. The sequencing data have been archived in the NCBI Short Read Archive with the BioProject accession number PRJNA515927.