GEO DataSets

(Submitter supplied) tRNA modifications help maintain tRNA structure and facilitate stress responses. Found in all three kingdoms of life, m1A tRNA modification occurs in the T loop of many tRNAs and stabilizes tertiary tRNA structure and impacts translation. M1A in T loop is known to be reversible by three mammalian demethylase enzymes, which bypasses the need of turning over the tRNA molecule to adjust their m1A levels in cells. more...

Organism:

Streptomyces venezuelae

Type:

Other

Platform:

GPL32677

52 Samples

Download data: TSV

(Submitter supplied) We isolated and sequenced mRNA from Streptomyces venezuelae grown on two different solid media that promote different growth behaviour in this bacterial species. The data was analyzed using DeSeq2 to identify genes that undergo changes in expression over time as well as differences in gene expression patterns between the two media conditions.

Organism:

Streptomyces venezuelae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25163

10 Samples

Download data: CSV

(Submitter supplied) To gain insights into the processes underlying adaptation to phage infection, we performed RNA-seq analysis of infected mycelium from the plaque interface of S. venezuelae wild type harvested 24 h and 72 h after infection with Alderaan.

Organism:

Streptomyces venezuelae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32677

8 Samples

Download data: TXT

(Submitter supplied) We isolated and sequenced mRNA from Streptomyces venezuelae grown on solid medium that promotes exploratory behaviour in this bacterial species. The data was analyzed using DeSeq2 to identify genes that undergo changes in expression over time.

Organism:

Streptomyces venezuelae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25162

6 Samples

Download data: CSV

(Submitter supplied) We isolated and sequenced mRNA from Streptomyces venezuelae grown on two different solid media that promote exploratory behaviour in this bacterial species. The data was analyzed using DeSeq2 to identify genes that undergo changes in expression over time as well as differences in gene expression patterns between the two media conditions.

Organism:

Streptomyces venezuelae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25163 GPL25162

12 Samples

Download data: CSV

(Submitter supplied) Bacterial populations face the constant threat of viral predation exerted by bacteriophages (or phages). In response, bacteria have evolved a wide range of defense mechanisms against phage challenges. Here, we show that aminoglycosides, a well-known class of antibiotics produced by Streptomyces, are potent inhibitors of phage infection. We observed a broad phage inhibition by aminoglycosides. We demonstrate that aminoglycosides do not prevent the injection of phage DNA into bacterial cells but instead block an early step of the viral life cycle. more...

Organism:

Streptomyces venezuelae ATCC 10712

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29993

8 Samples

Download data: TXT

(Submitter supplied) We performed ribosome profiling which is the deep-sequencing of mRNA fragments protected by translating ribosome for two Streptomyces species through different growth phases to provide the translatome data

Organism:

Streptomyces venezuelae; Streptomyces griseus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL27559 GPL27560

16 Samples

Download data: TXT

(Submitter supplied) The goal of this work was to determine where Lsr2 binds within the S. venezuelae chromosome, and to differentiate between direct versus indirect effects by comparing our ChIP-seq results with RNA-seq results

Organism:

Streptomyces venezuelae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25163

4 Samples

Download data: CSV

(Submitter supplied) Comparing gene expression of wild type and lsr2 mutants, to determine the effect of Lsr2 on Streptomyces development and metabolism

Organism:

Streptomyces venezuelae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25162

12 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Streptomyces venezuelae

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL25163 GPL25162

16 Samples

Download data

(Submitter supplied) We report here the sequence results of S. venezualae WT and the mutant mtrB::apr strains at 14h and 20h and the differential expression profile of WT vs. Mutant.

Organism:

Streptomyces venezuelae ATCC 10712

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21811

8 Samples

Download data: FASTA, TXT, XLSX

(Submitter supplied) We report the results of ChIP-Seq experiment investigating the MtrA TCS response regulator. The experiment utilised an in trans copy of mtrA with an N-terminal 3xFlag tag encoded on the plasmid pMS82 (containing a phiBT1 integration site). The experiment utilised beads associated with anti-flag antibodies, specific for the Flag tagged protein. We report important targets involved in cell division and salt stress with key findings supporting the hypothesis that MtrA is essential. more...

Organism:

Streptomyces venezuelae ATCC 10712

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL22148 GPL21809

7 Samples

Download data: WIG

(Submitter supplied) We discovered the bacteria Streptomyces venezuelae can display a new form of growth termed exploration, and we used NGS to compare transcriptome profiles of cells demonstrating exploration versus static cells (not demonstrating exploration)

Organism:

Streptomyces venezuelae ATCC 10712

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22391

4 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Streptomyces venezuelae ATCC 10712; Streptomyces venezuelae

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other

Platforms:

GPL21809 GPL17014 GPL21811

9 Samples

Download data: TXT, WIG

(Submitter supplied) We report here the sequence results of S. venezualae WT and the mutant sven6563::apr (rsrR::apr) strains at 16h and the differential expression profile of WT vs. Mutant. Additionally we report the resulting TSSAR analysis of the transcriptional start site information for the genes expressed at this time point.

Organism:

Streptomyces venezuelae ATCC 10712

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21811

4 Samples

Download data: TXT, WIG, XLSX

(Submitter supplied) We report the results of ChIP-Seq experiment investigating the Rrf2 family transciptional regulator RsrR (putatively name Redox sensitive response regulator). The experiment utilized an in trans copy of rsrR with an N-terminal 3xFlag tag encoded on the plasmid pMS82 (containing a phiBT1 integration site). The experiment utilized beads associated with anti-flag antibodies, specific for the Flag tagged protein and a WT host strain. more...

Organism:

Streptomyces venezuelae ATCC 10712

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21809

4 Samples

Download data: TXT, WIG

(Submitter supplied) We report the results of ChIP-Seq experiment investigating the Rrf2 family transciptional regulator RsrR (putativeily name Redox sensitive response regulator). The experiment utilised an in trans copy of rsrR with an N-terminal 3xFlag tag encoded on the plasmid pMS82 (containing a phiBT1 integration site). The experiment utilised beads associated with anti-flag antibodies, specific for the Flag tagged protein and a WT host strain. more...

Organism:

Streptomyces venezuelae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17014

1 Sample

Download data: TXT, WIG

(Submitter supplied) We report the mRNA and small RNA transcriptomes of Streptomyces coelicolor, Streptomyces avermitilis, and Streptomyces venezuelae. We identified dozens of new conserved sRNAs and antisense RNAs, including a prominent group of antisense RNAs termed ‘cutoRNAs’ that result from overlap of the 3′ ends of convergently transcribed mRNAs. In addition, we observed abundant unique ncRNAs, including many within secondary metabolic gene clusters.

Organism:

Streptomyces venezuelae; Streptomyces coelicolor; Streptomyces avermitilis

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL17014 GPL17012 GPL17013

6 Samples

Download data: TXT

(Submitter supplied) Two component sensor-response regulator systems (TCSs) are very common in the genomes of the Streptomyces species that have been fully sequenced to date. It has been suggested that this large number is an evolutionary response to the variable environment that Streptomyces encounter in soil. Notwithstanding this, TCSs are also more common in the sequenced genomes of other Actinomycetales when these are compared to the genomes of most other eubacteria. more...

Organism:

Streptomyces bikiniensis; Streptomyces clavuligerus; Streptomyces rochei; Streptomyces virginiae; Streptomyces exfoliatus; Streptomyces tanashiensis; Streptomyces antibioticus; Streptomyces fradiae; Streptomyces griseus; Streptomyces microflavus; Streptomyces maritimus; Kitasatospora aureofaciens; Streptosporangium roseum; Streptantibioticus cattleyicolor; Streptomyces venezuelae; Streptomyces coelicolor A3(2)

Type:

Genome variation profiling by array

Platform:

GPL7637

15 Samples

Download data: XLS