Kim et al. 2019 (PRJNA382534)
General Details
Title | Ribosome pausing at the AT-rich codons regulates the protein expression of secondary metabolite gene clusters in the Streptomyces tsukubaensis NRRL 18488 |
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Organism | |
Number of Samples | 8 |
Release Date | 2017/04/11 00:00 |
Sequencing Types | |
Protocol Details |
Study Links
GWIPS-viz | Trips-Viz |
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Repository Details
SRA | SRP103795 |
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ENA | SRP103795 |
GEO | GSE97637 |
BioProject | PRJNA382534 |
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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SRR5443325 | PRJNA382534 | Streptomyces tsukubensis | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR5443326 | PRJNA382534 | Streptomyces tsukubensis | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR5443327 | PRJNA382534 | Streptomyces tsukubensis | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR5443328 | PRJNA382534 | Streptomyces tsukubensis | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR5443329 | PRJNA382534 | Streptomyces tsukubensis | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR5443330 | PRJNA382534 | Streptomyces tsukubensis | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR5443331 | PRJNA382534 | Streptomyces tsukubensis | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR5443332 | PRJNA382534 | Streptomyces tsukubensis | 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) |
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