Liu et al. 2019 (PRJNA477831)
General Details
| Title | Optimization of Ribosome Profiling Using Brain Tissue from Fragile X Mice |
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| Organism | |
| Number of Samples | 37 |
| Release Date | 2018/06/25 00:00 |
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| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP151279 |
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| ENA | SRP151279 |
| GEO | GSE116233 |
| BioProject | PRJNA477831 |
Publication
| Title | |
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| Authors | Liu B,Molinaro G,Shu H,Stackpole EE,Huber KM,Richter JD |
| Journal | Nucleic acids research |
| Publication Date | 2019 Mar 18 |
| Abstract | Dysregulated protein synthesis is a major underlying cause of many neurodevelopmental diseases including fragile X syndrome. In order to capture subtle but biologically significant differences in translation in these disorders, a robust technique is required. One powerful tool to study translational control is ribosome profiling, which is based on deep sequencing of mRNA fragments protected from ribonuclease (RNase) digestion by ribosomes. However, this approach has been mainly applied to rapidly dividing cells where translation is active and large amounts of starting material are readily available. The application of ribosome profiling to low-input brain tissue where translation is modest and gene expression changes between genotypes are expected to be small has not been carefully evaluated. Using hippocampal tissue from wide type and fragile X mental retardation 1 (Fmr1) knockout mice, we show that variable RNase digestion can lead to significant sample batch effects. We also establish GC content and ribosome footprint length as quality control metrics for RNase digestion. We performed RNase titration experiments for low-input samples to identify optimal conditions for this critical step that is often improperly conducted. Our data reveal that optimal RNase digestion is essential to ensure high quality and reproducibility of ribosome profiling for low-input brain tissue. © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. |
| PMC | PMC6411937 |
| PMID | 30590705 |
| 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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| SRR7883717 | PRJNA477831 | Mus musculus | Ribo-Seq |  |
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| SRR7883718 | PRJNA477831 | Mus musculus | Ribo-Seq | |
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| SRR7883719 | PRJNA477831 | Mus musculus | Ribo-Seq | |
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| SRR7883720 | PRJNA477831 | Mus musculus | Ribo-Seq | |
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| SRR7883721 | PRJNA477831 | Mus musculus | Ribo-Seq | |
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| SRR7883722 | PRJNA477831 | Mus musculus | Ribo-Seq | |
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| SRR7883723 | PRJNA477831 | Mus musculus | Ribo-Seq | |
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| SRR7883724 | PRJNA477831 | Mus musculus | Ribo-Seq | |
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| SRR7883725 | PRJNA477831 | Mus musculus | Ribo-Seq | |
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| SRR7883726 | PRJNA477831 | Mus musculus | Ribo-Seq | |
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| SRR7883727 | PRJNA477831 | Mus musculus | Ribo-Seq | |
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| SRR7883728 | PRJNA477831 | Mus musculus | Ribo-Seq | |
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| SRR7883729 | PRJNA477831 | Mus musculus | Ribo-Seq | |
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| SRR7883730 | PRJNA477831 | Mus musculus | Ribo-Seq | |
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| SRR7883731 | PRJNA477831 | Mus musculus | Ribo-Seq | |
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| SRR7883746 | PRJNA477831 | Mus musculus | Ribo-Seq | |
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| SRR7883747 | PRJNA477831 | Mus musculus | Ribo-Seq | |
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| SRR7883748 | PRJNA477831 | Homo sapiens | iPSC | Ribo-Seq | Cycloheximide | |
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| SRR7883749 | PRJNA477831 | Homo sapiens | iPSC | Ribo-Seq | Cycloheximide | |
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| SRR7883750 | PRJNA477831 | Homo sapiens | iPSC | Ribo-Seq | Cycloheximide | |
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| SRR7883751 | PRJNA477831 | Homo sapiens | iPSC | Ribo-Seq | Cycloheximide | |
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| SRR7883752 | PRJNA477831 | Homo sapiens | iPSC | Ribo-Seq | Cycloheximide | |
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| SRR7883753 | PRJNA477831 | Homo sapiens | iPSC | Ribo-Seq | Cycloheximide | |
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| SRR7883754 | PRJNA477831 | Homo sapiens | iPSC | Ribo-Seq | Cycloheximide | |
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| SRR7883755 | PRJNA477831 | Homo sapiens | iPSC | Ribo-Seq | Cycloheximide | |
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| SRR7883756 | PRJNA477831 | Homo sapiens | iPSC | Ribo-Seq | Cycloheximide | |
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| SRR7883757 | PRJNA477831 | Homo sapiens | iPSC | Ribo-Seq | Cycloheximide | |
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| SRR7883758 | PRJNA477831 | Homo sapiens | iPSC | Ribo-Seq | Cycloheximide | |
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| SRR7883759 | PRJNA477831 | Homo sapiens | iPSC | Ribo-Seq | Cycloheximide | |
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| SRR7883760 | PRJNA477831 | Homo sapiens | iPSC | Ribo-Seq | Cycloheximide | |
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| SRR7883761 | PRJNA477831 | Homo sapiens | iPSC | Ribo-Seq | Cycloheximide | |
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| SRR7883762 | PRJNA477831 | Homo sapiens | iPSC | Ribo-Seq | Cycloheximide | |
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| SRR7883763 | PRJNA477831 | Homo sapiens | iPSC | Ribo-Seq | Cycloheximide | |
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| SRR7883764 | PRJNA477831 | Homo sapiens | iPSC | Ribo-Seq | Cycloheximide | |
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| SRR7883765 | PRJNA477831 | Homo sapiens | iPSC | Ribo-Seq | Cycloheximide | |
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| SRR7883766 | PRJNA477831 | Homo sapiens | iPSC | Ribo-Seq | Cycloheximide | |
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| SRR7883767 | PRJNA477831 | Homo sapiens | iPSC | 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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