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
Organism
Number of Samples 8
Release Date 2017/04/11 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP103795
ENA SRP103795
GEO GSE97637
BioProject PRJNA382534

Publication

Title
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)
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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