Andreev et al. 2015 (PRJNA259424)
General Details
| Title | Time resolved ribosome profiling study of oxygen and glucose deprivation of rat pheochromocytoma cells |
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| Organism | |
| Number of Samples | 8 |
| Release Date | 2014/08/26 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 | SRP045777 |
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| ENA | SRP045777 |
| GEO | |
| BioProject | PRJNA259424 |
Publication
| Title | |
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| Authors | Andreev DE,O'Connor PB,Zhdanov AV,Dmitriev RI,Shatsky IN,Papkovsky DB,Baranov PV |
| Journal | Genome biology |
| Publication Date | 2015 May 6 |
| Abstract | Oxygen and glucose metabolism play pivotal roles in many (patho)physiological conditions. In particular, oxygen and glucose deprivation (OGD) during ischemia and stroke results in extensive tissue injury and cell death. Using time-resolved ribosome profiling, we assess gene expression levels in a neural cell line, PC12, during the first hour of OGD. The most substantial alterations are seen to occur within the first 20 minutes of OGD. While transcription of only 100 genes is significantly altered during one hour of OGD, the translation response affects approximately 3,000 genes. This response involves reprogramming of initiation and elongation rates, as well as the stringency of start codon recognition. Genes involved in oxidative phosphorylation are most affected. Detailed analysis of ribosome profiles reveals salient alterations of ribosome densities on individual mRNAs. The mRNA-specific alterations include increased translation of upstream open reading frames, site-specific ribosome pauses, and production of alternative protein isoforms with amino-terminal extensions. Detailed analysis of ribosomal profiles also reveals six mRNAs with translated ORFs occurring downstream of annotated coding regions and two examples of dual coding mRNAs, where two protein products are translated from the same long segment of mRNA, but in two different frames. These findings uncover novel regulatory mechanisms of translational response to OGD in mammalian cells that are different from the classical pathways such as hypoxia inducible factor (HIF) signaling, while also revealing sophisticated organization of protein coding information in certain genes. |
| PMC | PMC4419486 |
| PMID | 25943107 |
| 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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| SRR1557705 | PRJNA259424 | Rattus norvegicus | PC12 | Ribo-Seq |  |
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| SRR1557707 | PRJNA259424 | Rattus norvegicus | PC12 | Ribo-Seq | |
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| SRR1557709 | PRJNA259424 | Rattus norvegicus | PC12 | Ribo-Seq | |
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| SRR1557711 | PRJNA259424 | Rattus norvegicus | PC12 | Ribo-Seq | |
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| SRR1557713 | PRJNA259424 | Rattus norvegicus | PC12 | Ribo-Seq | |
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| SRR1557715 | PRJNA259424 | Rattus norvegicus | PC12 | Ribo-Seq | |
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| SRR1557717 | PRJNA259424 | Rattus norvegicus | PC12 | Ribo-Seq | |
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| SRR1557719 | PRJNA259424 | Rattus norvegicus | PC12 | Ribo-Seq | |
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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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