Schrader et al. 2015 (PRJNA237963)
General Details
| Title | The coding and noncoding architecture of the Caulobacter crescentus genome |
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| Organism | |
| Number of Samples | 2 |
| Release Date | 2014/02/11 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP037582 |
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| ENA | SRP037582 |
| GEO | GSE54883 |
| BioProject | PRJNA237963 |
Publication
| Title | |
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| Authors | Schrader JM, Zhou B, Li GW, Lasker K, Childers WS, Williams B, Long T, Crosson S, McAdams HH, Weissman JS, Shapiro L |
| Journal | PLoS genetics |
| Publication Date | 2014 Jul |
| Abstract | Caulobacter crescentus undergoes an asymmetric cell division controlled by a genetic circuit that cycles in space and time. We provide a universal strategy for defining the coding potential of bacterial genomes by applying ribosome profiling, RNA-seq, global 5'-RACE, and liquid chromatography coupled with tandem mass spectrometry (LC-MS) data to the 4-megabase C. crescentus genome. We mapped transcript units at single base-pair resolution using RNA-seq together with global 5'-RACE. Additionally, using ribosome profiling and LC-MS, we mapped translation start sites and coding regions with near complete coverage. We found most start codons lacked corresponding Shine-Dalgarno sites although ribosomes were observed to pause at internal Shine-Dalgarno sites within the coding DNA sequence (CDS). These data suggest a more prevalent use of the Shine-Dalgarno sequence for ribosome pausing rather than translation initiation in C. crescentus. Overall 19% of the transcribed and translated genomic elements were newly identified or significantly improved by this approach, providing a valuable genomic resource to elucidate the complete C. crescentus genetic circuitry that controls asymmetric cell division. |
| PMC | PMC4117421 |
| PMID | 25078267 |
| 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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| SRR1167750 | PRJNA237963 | Caulobacter vibrioides | 0.0 | Ribo-Seq | 0.0 |  |
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| SRR1167751 | PRJNA237963 | Caulobacter vibrioides | 0.0 | Ribo-Seq | 0.0 | |
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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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