Ingolia et al. 2011 (PRJNA144149)
General Details
| Title | Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes |
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| Number of Samples | 31 |
| Release Date | 2011/11/03 00:00 |
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Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP007567 |
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| ENA | SRP007567 |
| GEO | GSE30839 |
| BioProject | PRJNA144149 |
Publication
| Title | |
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| Authors | Ingolia NT, Lareau LF, Weissman JS |
| Journal | Cell |
| Publication Date | 2011 Nov 11 |
| Abstract | The ability to sequence genomes has far outstripped approaches for deciphering the information they encode. Here we present a suite of techniques, based on ribosome profiling (the deep sequencing of ribosome-protected mRNA fragments), to provide genome-wide maps of protein synthesis as well as a pulse-chase strategy for determining rates of translation elongation. We exploit the propensity of harringtonine to cause ribosomes to accumulate at sites of translation initiation together with a machine learning algorithm to define protein products systematically. Analysis of translation in mouse embryonic stem cells reveals thousands of strong pause sites and unannotated translation products. These include amino-terminal extensions and truncations and upstream open reading frames with regulatory potential, initiated at both AUG and non-AUG codons, whose translation changes after differentiation. We also define a class of short, polycistronic ribosome-associated coding RNAs (sprcRNAs) that encode small proteins. Our studies reveal an unanticipated complexity to mammalian proteomes. Copyright © 2011 Elsevier Inc. All rights reserved. |
| PMC | PMC3225288 |
| PMID | 22056041 |
| 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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| SRR315597 | PRJNA144149 | Mus musculus | E14 | 0.0 | Cycloheximide |  |
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| SRR315598 | PRJNA144149 | Mus musculus | E14 | 0.0 | Cycloheximide | |
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| SRR315599 | PRJNA144149 | Mus musculus | E14 | 0.0 | Cycloheximide | |
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| SRR315600 | PRJNA144149 | Mus musculus | E14 | 0.0 | Cycloheximide | |
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| SRR315601 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315602 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315603 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315604 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Harringtonine | |
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| SRR315605 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315606 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315607 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315608 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315609 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315610 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315611 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315612 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315613 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315614 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315615 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315616 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315617 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Frozen | |
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| SRR315618 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Frozen | |
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| SRR315619 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Frozen | |
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| SRR315620 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315621 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315622 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315623 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315624 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315625 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315626 | PRJNA144149 | Mus musculus | E14 | Ribo-Seq | Cycloheximide | |
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| SRR315627 | PRJNA144149 | Mus musculus | E14 | 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) |
ⓘ For more Information on the columns shown here see: About