Zhang et al. 2018 (PRJNA369756)
General Details
| Title | Ribosome profiling of HEK293 cells. |
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| Organism | |
| Number of Samples | 2 |
| Release Date | 2017/02/03 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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| Visit GWIPS-viz | Visit Trips-Viz |
Repository Details
| SRA | SRP098797 |
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| ENA | SRP098797 |
| GEO | |
| BioProject | PRJNA369756 |
Publication
| Title | |
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| Authors | Zhang P,He D,Xu Y,Hou J,Pan BF,Wang Y,Liu T,Davis CM,Ehli EA,Tan L,Zhou F,Hu J,Yu Y,Chen X,Nguyen TM,Rosen JM,Hawke DH,Ji Z,Chen Y |
| Journal | Nature communications |
| Publication Date | 2017 Nov 23 |
| Abstract | Translation is principally regulated at the initiation stage. The development of the translation initiation (TI) sequencing (TI-seq) technique has enabled the global mapping of TIs and revealed unanticipated complex translational landscapes in metazoans. Despite the wide adoption of TI-seq, there is no computational tool currently available for analyzing TI-seq data. To fill this gap, we develop a comprehensive toolkit named Ribo-TISH, which allows for detecting and quantitatively comparing TIs across conditions from TI-seq data. Ribo-TISH can also predict novel open reading frames (ORFs) from regular ribosome profiling (rRibo-seq) data and outperform several established methods in both computational efficiency and prediction accuracy. Applied to published TI-seq/rRibo-seq data sets, Ribo-TISH uncovers a novel signature of elevated mitochondrial translation during amino-acid deprivation and predicts novel ORFs in 5'UTRs, long noncoding RNAs, and introns. These successful applications demonstrate the power of Ribo-TISH in extracting biological insights from TI-seq/rRibo-seq data. |
| PMC | PMC5701008 |
| PMID | 29170441 |
| DOI |
| 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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| SRR5227448 | PRJNA369756 | Homo sapiens | HEK293 | Ribo-Seq | Cycloheximide |  |
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| SRR5227449 | PRJNA369756 | Homo sapiens | HEK293 | Ribo-Seq | Cycloheximide | |
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| 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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