Zou et al. 2019 (PRJNA448763)

General Details

Title Landscapes of gene translation in hepatocellular carcinoma tumors revealed by ribosome profiling
Organism
Number of Samples 20
Release Date 2018/04/04 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP137150
ENA SRP137150
GEO GSE112705
BioProject PRJNA448763

Publication

Title
Authors Zou Q,Xiao Z,Huang R,Wang X,Wang X,Zhao H,Yang X
Journal Theranostics
Publication Date 2019
Abstract Despite the critical position of translation in the multilevel gene expression regulation program, high-resolution and genome-wide view of the landscape of RNA translation in solid tumors is still limited. Methods : With a ribosome profiling procedure optimized for solid tissue samples, we profiled the translatomes of liver tumors and their adjacent noncancerous normal liver tissues from 10 patients with hepatocellular carcinoma (HCC). A set of bioinformatics tools was then applied to these data for the mining of novel insights into the translation shifts in HCC. Results : This is the first translatome data resource for dissecting dysregulated translation in HCC at the sub-codon resolution. Based on our data, quantitative comparisons of mRNA translation rates yielded the genes and processes that were subjected to patient specific or universal dysregulations of translation efficiencies in tumors. For example, multiple proteins involved in extracellular matrix organization exhibited significant translational upregulation in tumors. We then experimentally validated the tumor-promoting functions of two such genes as examples: AGRN and VWA1. In addition, the data was also used for de novo annotation of the translatomes in tumors and normal tissues, including multiple types of novel non-canonical small ORFs, which would be a resource for further functional studies. Conclusions : The present study generates the first survey of the HCC translatome with ribosome profiling, which is an insightful data resource for dissecting the translatome shift in liver cancer, at sub-codon resolution.
PMC PMC6592166
PMID 31281537
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR6939924 PRJNA448763 Homo sapiens Ribo-Seq Cycloheximide
SRR6939926 PRJNA448763 Homo sapiens Ribo-Seq Cycloheximide
SRR6939928 PRJNA448763 Homo sapiens Ribo-Seq Cycloheximide
SRR6939930 PRJNA448763 Homo sapiens Ribo-Seq Cycloheximide
SRR6939932 PRJNA448763 Homo sapiens Ribo-Seq Cycloheximide
SRR6939934 PRJNA448763 Homo sapiens Ribo-Seq Cycloheximide
SRR6939936 PRJNA448763 Homo sapiens Ribo-Seq Cycloheximide
SRR6939938 PRJNA448763 Homo sapiens Ribo-Seq Cycloheximide
SRR6939940 PRJNA448763 Homo sapiens Ribo-Seq Cycloheximide
SRR6939942 PRJNA448763 Homo sapiens Ribo-Seq Cycloheximide
SRR6939944 PRJNA448763 Homo sapiens Ribo-Seq Cycloheximide
SRR6939946 PRJNA448763 Homo sapiens Ribo-Seq Cycloheximide
SRR6939948 PRJNA448763 Homo sapiens Ribo-Seq Cycloheximide
SRR6939950 PRJNA448763 Homo sapiens Ribo-Seq Cycloheximide
SRR6939952 PRJNA448763 Homo sapiens Ribo-Seq Cycloheximide
SRR6939955 PRJNA448763 Homo sapiens Ribo-Seq Cycloheximide
SRR6939957 PRJNA448763 Homo sapiens Ribo-Seq Cycloheximide
SRR6939959 PRJNA448763 Homo sapiens Ribo-Seq Cycloheximide
SRR6939961 PRJNA448763 Homo sapiens Ribo-Seq Cycloheximide
SRR6939963 PRJNA448763 Homo sapiens Ribo-Seq Cycloheximide
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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