Genome-wide quantification of ribosome-protected mRNA fragments using RNA sequencing (RNA-seq) and ribosome profiling (Ribo-seq).

(A) Workflow of differential analysis and filtering prior to DESeq2 analysis to determine translation efficiency at genomic features. (B) Scatter plots of reads aligning to annotated genomic features at the transcript or gene level as indicated. Log2 fold-change values represent the average of biological replicates for DUX4 pulse+IFNγ condition relative to IFNγ treatment alone in MB135iDUX4 myoblasts, n = 3. Translationally up-regulated mRNAs (red) and translationally down-regulated mRNAs (blue) are highlighted (|log2FC>1|, p-adj<0.05, n = 3). DUX4, double homeobox protein 4; IFNγ, interferon gamma; RNA-seq, RNA sequencing.

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