Schott et al. 2021 (PRJNA649003)
General Details
| Title | Ribo-Seq timecourse in RAW264.7 cells upon LPS treatment |
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| Organism | |
| Number of Samples | 8 |
| Release Date | 2020/07/27 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP273780 |
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| ENA | SRP273780 |
| GEO | GSE155233 |
| BioProject | PRJNA649003 |
Publication
| Title | |
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| Authors | Schott J,Reitter S,Lindner D,Grosser J,Bruer M,Shenoy A,Geiger T,Mathes A,Dobreva G,Stoecklin G |
| Journal | Nature methods |
| Publication Date | 2021 Sep |
| Abstract | In general, mRNAs are assumed to be loaded with ribosomes instantly upon entry into the cytoplasm. To measure ribosome density (RD) on nascent mRNA, we developed nascent Ribo-Seq by combining Ribo-Seq with progressive 4-thiouridine labeling. In mouse macrophages, we determined experimentally the lag between the appearance of nascent mRNA and its association with ribosomes, which was calculated to be 20-22 min for bulk mRNA. In mouse embryonic stem cells, nRibo-Seq revealed an even stronger lag of 35-38 min in ribosome loading. After stimulation of macrophages with lipopolysaccharide, the lag between cytoplasmic and translated mRNA leads to uncoupling between input and ribosome-protected fragments, which gives rise to distorted RD measurements under conditions where mRNA amounts are far from steady-state expression. As a result, we demonstrate that transcriptional changes affect RD in a passive way. © 2021. The Author(s), under exclusive licence to Springer Nature America, Inc. |
| PMC | |
| PMID | 34480152 |
| 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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| SRR12333532 | PRJNA649003 | Mus musculus | RAW264.7 | Ribo-Seq |  |
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| SRR12333533 | PRJNA649003 | Mus musculus | RAW264.7 | Ribo-Seq | |
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| SRR12333534 | PRJNA649003 | Mus musculus | RAW264.7 | Ribo-Seq | |
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| SRR12333535 | PRJNA649003 | Mus musculus | RAW264.7 | Ribo-Seq | |
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| SRR12333536 | PRJNA649003 | Mus musculus | RAW264.7 | Ribo-Seq | |
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| SRR12333537 | PRJNA649003 | Mus musculus | RAW264.7 | Ribo-Seq | |
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| SRR12333538 | PRJNA649003 | Mus musculus | RAW264.7 | Ribo-Seq | |
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| SRR12333531 | PRJNA649003 | Mus musculus | RAW264.7 | Ribo-Seq | untreated | |
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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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