title: GSM9178535: A-shAldh2-R1-m; Homo sapiens; RNA-Seq
library_name: GSM9178535
library_construction_protocol: Total RNA Extraction with TRIzol, Ribosome Isolation via Sucrose Density Gradient Centrifugation. Raw reads were adapter-trimmed (cutadapt) and size-filtered (25-35 bp). rRNA and tRNA reads were removed (bowtie alignment). Clean reads were aligned to the reference genome and transcriptome (Ensembl v91; HISAT2 and bowtie software). Ribosome periodicity and codon usage were assessed (riboWaltz package), ORFs identified (Price software), and gene-level counts obtained (featureCounts software). Counts were RPKM-normalized (DESeq2 package). Translational efficiency (TE) was calculated as (Ribo-RPKM)/(RNA-seq-RPKM) as previously reported.15 Differential TE was identified (DESeq2 package; fold change (FC)>2, p<0.05, regarded as significant) with GO/KEGG enrichment (clusterProfiler package) and heatmaps (pheatmap package) in R.
identifiers.namespace: GEO
identifiers.id: GSM9178535_r1