Male germ cell-specific deletion of eukaryotic translation initiation factor 5 causes the apoptosis of mouse progenitor spermatogonia by excessive endoplasmic reticulum stress and defective DNA repair

Meanwhile, reads with lengths between 25 and 35 bp were kept for downstream analysis. Then, reads were aligned to rRNA sequences to remove rRNA reads using Bowtie software, and the remaining reads were used to align to GRCm38 using STAR. The trinucleotide periodicity of ribosomes and codon usage frequency were estimated using the revised riboWaltz package.

Read counts were calculated using the featureCounts software. Raw counts were further normalized in the DESeq2 package. Translational efficiencies were determined by the ratio (normalized abundance determined by ribosome profiling/normalized abundance determined by RNA-seq) as previously reported (Duan et al., 2022; Su et al., 2022).

Different translational efficiencies were estimated using the DESeq2 package, and genes with fold changes≥1.5 and P-value<0.05 were considered significant. GO and KEGG analyses were performed using the cluster Profiler package in R software.