alias: GSM4715689
title: GSM4715689: OE: Human multiple myeloma cells with NAT10 overexpression for Ribo-seq; Homo sapiens; OTHER
library_construction_protocol: After the cells are treated with cycloheximide, they are treated with nuclease to degrade the unprotected nuclease and recover the ribosomes Adapter sequences were removed from raw sequencing data using cutadapt1 software. Meanwhile, reads with length between 25 and 35 bp were kept for downstream analysis. Then reads were aligned to rRNA and tRNA sequences so as to remove rRNA and tRNA reads using bowtie2 software, remaining reads were used to align to human reference genome and transcriptome (Ensembl GRCh38 Version 91) using hisat23 and bowtie2 software separately. The trinucleotide periodicity of ribosomes and codon usage frequency were estimated using revised riboWaltz4 package. ORF identification was performed using Price5 software. Read counts were calculated using featureCounts6 software. Raw counts were further normalized as RPKM values using fpkm function in DESeq27 package. Translational efficiencies were determined as the ratio of (normalized abundance determined by ribosome profiling)/(normalized abundance determined by RNA-seq) as previously repored8. Different   translational efficiencies were estimated using DESeq27 package, genes with fold changes > 2 and FDR < 0.05 were regarded as significant. GO and KEGG analysis were performed using clusterProfiler9 package in R software. Heatmap was drawn using pheatmap package in R software.
identifiers.namespace: GEO
identifiers.id: GSM4715689
attributes.tag: GEO Accession
attributes.value: GSM4715689