Kim et al. 2020 (PRJNA575265)
General Details
| Title | Ribosome profiling of Streptomyces griseus NBRC13350 and Streptomyces venezuelae ATCC15439 |
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| Organism | |
| Number of Samples | 16 |
| Release Date | 2019/10/01 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP223903 |
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| ENA | SRP223903 |
| GEO | |
| BioProject | PRJNA575265 |
Publication
| Title | |
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| Authors | Kim W,Hwang S,Lee N,Lee Y,Cho S,Palsson B,Cho BK |
| Journal | Scientific data |
| Publication Date | 2020 May 8 |
| Abstract | Streptomyces are efficient producers of various bioactive compounds, which are mostly synthesized by their secondary metabolite biosynthetic gene clusters (smBGCs). The smBGCs are tightly controlled by complex regulatory systems at transcriptional and translational levels to effectively utilize precursors that are supplied by primary metabolism. Thus, dynamic changes in gene expression in response to cellular status at both the transcriptional and translational levels should be elucidated to directly reflect protein levels, rapid downstream responses, and cellular energy costs. In this study, RNA-Seq and ribosome profiling were performed for five industrially important Streptomyces species at different growth phases, for the deep sequencing of total mRNA, and only those mRNA fragments that are protected by translating ribosomes, respectively. Herein, 12.0 to 763.8 million raw reads were sufficiently obtained with high quality of more than 80% for the Phred score Q30 and high reproducibility. These data provide a comprehensive understanding of the transcriptional and translational landscape across the Streptomyces species and contribute to facilitating the rational engineering of secondary metabolite production. |
| PMC | PMC7210306 |
| PMID | 32385251 |
| 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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| SRR10212832 | PRJNA575265 | Streptomyces griseus | Ribo-Seq |  |
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| SRR10212833 | PRJNA575265 | Streptomyces griseus | Ribo-Seq | |
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| SRR10212834 | PRJNA575265 | Streptomyces griseus | Ribo-Seq | |
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| SRR10212835 | PRJNA575265 | Streptomyces griseus | Ribo-Seq | |
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| SRR10212836 | PRJNA575265 | Streptomyces griseus | Ribo-Seq | |
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| SRR10212837 | PRJNA575265 | Streptomyces griseus | Ribo-Seq | |
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| SRR10212838 | PRJNA575265 | Streptomyces griseus | Ribo-Seq | |
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| SRR10212839 | PRJNA575265 | Streptomyces venezuelae | Ribo-Seq | |
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| SRR10212840 | PRJNA575265 | Streptomyces venezuelae | Ribo-Seq | |
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| SRR10212841 | PRJNA575265 | Streptomyces venezuelae | Ribo-Seq | |
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| SRR10212842 | PRJNA575265 | Streptomyces venezuelae | Ribo-Seq | |
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| SRR10212843 | PRJNA575265 | Streptomyces venezuelae | Ribo-Seq | |
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| SRR10212844 | PRJNA575265 | Streptomyces venezuelae | Ribo-Seq | |
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| SRR10212845 | PRJNA575265 | Streptomyces venezuelae | Ribo-Seq | |
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| SRR10212846 | PRJNA575265 | Streptomyces venezuelae | Ribo-Seq | |
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| SRR10212831 | PRJNA575265 | Streptomyces griseus | 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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