Pavlov et al. 2021 (PRJNA607566)
General Details
| Title | Estimation of peptide elongation times from ribosome profiling spectra |
|---|---|
| Organism | |
| Number of Samples | 3 |
| Release Date | 2020/02/19 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
|---|---|
Repository Details
| SRA | SRP250036 |
|---|---|
| ENA | SRP250036 |
| GEO | GSE145571 |
| BioProject | PRJNA607566 |
Publication
| Title | |
|---|---|
| Authors | Pavlov MY, Ullman G, Ignatova Z, Ehrenberg M |
| Journal | Nucleic acids research |
| Publication Date | 2021 May 21 |
| Abstract | Ribosome profiling spectra bear rich information on translation control and dynamics. Yet, due to technical biases in library generation, extracting quantitative measures of discrete translation events has remained elusive. Using maximum likelihood statistics and data set from Escherichia coli we develop a robust method for neutralizing technical biases (e.g. base specific RNase preferences in ribosome-protected mRNA fragments (RPF) generation), which allows for correct estimation of translation times at single codon resolution. Furthermore, we validated the method with available datasets from E. coli treated with antibiotic to inhibit isoleucyl-tRNA synthetase, and two datasets from Saccharomyces cerevisiae treated with two RNases with distinct cleavage signatures. We demonstrate that our approach accounts for RNase cleavage preferences and provides bias-corrected translation times estimates. Our approach provides a solution to the long-standing problem of extracting reliable information about peptide elongation times from highly noisy and technically biased ribosome profiling spectra. © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. |
| PMC | PMC8136808 |
| PMID | 33885812 |
| DOI |
| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SRR11114802 | PRJNA607566 | Escherichia coli | 0.0 | Ribo-Seq | 0.0 |  |
 |
 |
 |
|
|
||
| SRR11114803 | PRJNA607566 | Escherichia coli | 0.0 | Ribo-Seq | 0.0 | |
|
|
|
|
|
||
| SRR11114804 | PRJNA607566 | Escherichia coli | 0.0 | Ribo-Seq | 0.0 | |
|
|
|
|
|
||
| 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