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Series GSE46613 Query DataSets for GSE46613
Status Public on Feb 09, 2016
Title Genome-wide and experimental resolution of relative translation elongation speed at individual gene level in human cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary In the process of translation, ribosomes first bind to mRNAs (translation initiation) and then move along the mRNA (elongation) to synthesize proteins. Elongation pausing is deemed highly relevant to co-translational folding of nascent peptides and the functionality of protein products, which positioned the evaluation of elongation speed as one of the central questions in the field of translational control. By employing three types of RNA-seq methods, we experimentally and computationally resolved elongation speed at individual gene level and under physiological condition in human cells. We proposed the elongation velocity index (EVI) as a relative measure and successfully distinguished slow-translating genes from the background translatome. The proteins encoded by the low-EVI genes are more stable than the proteome background. In normal cell and lung cancer cell comparisons, we found that the relatively slow-translating genes are relevant to the maintenance of malignant phenotypes. In addition, we identified cell-specific slow-translating codons, which may serve as a causal factor of elongation deceleration.
Overall design We sequenced mRNA, translating mRNA (RNC-mRNA) and ribosome footprints in normally growing HeLa cells.
Contributor(s) Lian X, Guo J, Gu W, Cui Y, Jin J, Zhong J, Zhang G, Wang T
Citation(s) 26926465
Submission date May 03, 2013
Last update date May 15, 2019
Contact name Gong Zhang
Organization name Jinan University
Department Institute of Life and Health Engineering
Lab Translatomics Lab
Street address Huang-Pu Avenue West 601
City Guangzhou
ZIP/Postal code 510632
Country China
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (7)
GSM1133259 HeLa mRNA
GSM1133260 HeLa RNC-mRNA
GSM1133261 HeLa Ribosome footprints
BioProject PRJNA201228
SRA SRP022049

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Supplementary file Size Download File type/resource
GSE46613_HeLa_rpkM_all.txt.gz 227.6 Kb (ftp)(http) TXT
GSE46613_HelaRFP_replicate2_rpkM.txt.gz 185.4 Kb (ftp)(http) TXT
GSE46613_rpkM-RFP-zhanggong.xlsx.gz 1016.8 Kb (ftp)(http) XLSX
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Processed data are available on Series record
Raw data are available in SRA

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