Supporting data for “Transfer RNA Abundance and Modification Shape Codon-Dependent Translational Adaptation in Hepatocellular Carcinoma”

Abstract

This dataset was generated as part of a research project investigating how transfer RNA (tRNA) abundance and tRNA modification regulate codon-dependent translation in hepatocellular carcinoma (HCC). The data cover two complementary aspects of tRNA-mediated translational regulation.The first project examines the relationship between transcriptome-derived codon demand and mature tRNA abundance using RNA sequencing and dedicated mature-tRNA sequencing data from HCC models and paired tumor and adjacent non-tumor specimens. It also includes data from a pooled CRISPR interference screen designed to assess the functional requirement of individual tRNA genes in HCC cells. The second project investigates adenosine-to-inosine editing at tRNA anticodon position 34 and the role of the ADAT2-dependent editing pathway in translation. These datasets include measurements of tRNA inosine editing, ribosome profiling, nascent protein synthesis assays, polysome-associated RNA analyses, and quantitative proteomics under different experimental conditions, including normoxia and hypoxia.Together, the data enable integrated analysis of codon usage, mature tRNA availability, tRNA-gene dependency, modification-dependent codon decoding, translational efficiency, and protein expression in HCC. The deposited files contain experimental and processed data used for these analyses and do not include personally identifiable or confidential clinical information.