tRF-seq of DUS1L knockout and wild-type A375 human melanoma cells
Small RNA sequencing (tRF-seq) was performed on A375 human melanoma cells with CRISPR/Cas9-mediated knockout of DUS1L and wild-type control cells, with three biological replicates per group. Small RNA libraries were prepared using the NEBNext Small RNA Library Prep Set for Illumina and sequenced on an Illumina NextSeq 500 platform to generate single-end FASTQ files. Sequencing quality was assessed using FastQC, and 3' adaptor sequences were trimmed with cutadapt. Clean reads were aligned to the human tRNA genome using MINTmap to obtain read count-based expression profiles of tRNA-derived fragments (tRFs). Overall design: Six small RNA-seq libraries were generated from A375 cells: three biological replicates of wild-type cells (WT1–WT3) and three biological replicates of DUS1L knockout cells (DUS1LKO1–DUS1LKO3). Small RNA libraries were prepared with the NEBNext Small RNA Library Prep Set and sequenced as single-end reads on an Illumina NextSeq 500 platform. MINTmap-based mapping to the human tRNA genome was used to quantify tRNA-derived fragments (tRFs), followed by DESeq2-based differential expression analysis between DUS1L knockout and wild-type samples.