Metz et al. 2021 (PRJNA578863)
General Details
| Title | High-Throughput Translational Profiling with riboPLATE-seq |
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| Organism | |
| Number of Samples | 12 |
| Release Date | 2019/10/22 00:00 |
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| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP226588 |
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| ENA | SRP226588 |
| GEO | |
| BioProject | PRJNA578863 |
Publication
| Title | |
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| Authors | Metz JB,Hornstein NJ,Sharma SD,Worley J,Gonzalez C,Sims PA |
| Journal | Scientific reports |
| Publication Date | 2022 Apr 5 |
| Abstract | Protein synthesis is dysregulated in many diseases, but we lack a systems-level picture of how signaling molecules and RNA binding proteins interact with the translational machinery, largely due to technological limitations. Here we present riboPLATE-seq, a scalable method for generating paired libraries of ribosome-associated and total mRNA. As an extension of the PLATE-seq protocol, riboPLATE-seq utilizes barcoded primers for pooled library preparation, but additionally leverages anti-rRNA ribosome immunoprecipitation on whole polysomes to measure ribosome association (RA). We compare RA to its analogue in ribosome profiling and RNA sequencing, translation efficiency, and demonstrate both the performance of riboPLATE-seq and its utility in detecting translational alterations induced by specific inhibitors of protein kinases. © 2022. The Author(s). |
| PMC | PMC8983706 |
| PMID | 35383235 |
| 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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| SRR17007090 | PRJNA578863 | Homo sapiens | TS543 glioblastoma | OTHER: (riboPLATE-seq) |  |
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| SRR17007092 | PRJNA578863 | Homo sapiens | Wi38 fibroblasts | OTHER: (riboPLATE-seq) | |
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| SRR17007093 | PRJNA578863 | Homo sapiens | TS543 glioblastoma | Ribo-Seq | |
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| SRR17007094 | PRJNA578863 | Homo sapiens | TS543 glioblastoma | Ribo-Seq | |
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| SRR17007095 | PRJNA578863 | Homo sapiens | TS543 glioblastoma | Ribo-Seq | |
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| SRR17007096 | PRJNA578863 | Homo sapiens | TS543 glioblastoma | Ribo-Seq | |
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| SRR17007097 | PRJNA578863 | Homo sapiens | TS543 glioblastoma | Ribo-Seq | |
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| SRR17007098 | PRJNA578863 | Homo sapiens | TS543 glioblastoma | Ribo-Seq | |
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| SRR17007099 | PRJNA578863 | Homo sapiens | TS543 glioblastoma | Ribo-Seq | |
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| SRR17007100 | PRJNA578863 | Homo sapiens | TS543 glioblastoma | Ribo-Seq | |
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| SRR17007101 | PRJNA578863 | Homo sapiens | TS543 glioblastoma | Ribo-Seq | |
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| SRR17007102 | PRJNA578863 | Homo sapiens | TS543 glioblastoma | 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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