GEO DataSets

(Submitter supplied) We report the high-throughput profiling of saccharopolyspora erythraea life cycle in bioreactors. RNA was harvested at seven time-points from bioreactors, three points immediately before, one during and three following the metabolic switch (as evidenced by biomass cell dry weight). We prepared unstranded RNA libraries and sequenced 363 million reads for a total of 32.7Gb and a mean ~4,000 fold coverage of the genome. more...

Organism:

Saccharopolyspora erythraea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15864

7 Samples

Download data: TXT

(Submitter supplied) We report the effect of addition of N-acetylglucosamine in Saccharopolyspora erythraea reactor cultures on the transcription of genes related to dasR regulon

Organism:

Saccharopolyspora erythraea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15864

3 Samples

Download data: FPKM_TRACKING

(Submitter supplied) Saccharopolyspora erythraea is used for industrial-scale production of erythromycin. To explore the physiological role of co-factors in regulation of primary and secondary metabolism of S. erythraea, we initially overexpressed the endogenous F1-ATPase in an erythromycin high-producing strain, E3. The engineered strain is named EA. The F1-ATPase expression resulted in a lower [ATP]/[ADP] ratio, which was accompanied by a dramatic increased production of a reddish pigment and a decreased erythromycin production. more...

Organism:

Saccharopolyspora erythraea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26951

8 Samples

Download data: TSV

(Submitter supplied) Information about molecular mechanisms underlying improvement of antibiotic-producing microorganisms with traditional mutation and screening approach is largely missing. This information is essential to develop rational approaches to strain improvement. In this study by using comparative genomic analysis we have identified all genetic changes that have occurred during development of an erythromycin overproducer, which was obtained by the traditional mutate-and-screen method. more...

Organism:

Saccharopolyspora erythraea

Type:

Expression profiling by array

Platform:

GPL6051

22 Samples

Download data: CEL, CHP

(Submitter supplied) Erythromycin is a medically important antibiotic, biosynthesized by the actinomycete Saccharopolyspora erythraea. We used transcriptomic approach to compare whole genome expression in erythromycin high-producing strain, compared to the wild type S. erythraea strain in four stages of fermentation.

Organism:

Saccharopolyspora erythraea

Type:

Expression profiling by array

Platform:

GPL19656

22 Samples

Download data: TXT

(Submitter supplied) Abstract: Transcript levels in production cultures of wildtype and classically improved strains of the actinomycete bacteria Saccharopolyspora erythraea and Streptomyces fradiae were monitored using microarrays of the sequenced actinomycete S. coelicolor. Sac. erythraea and S. fradiae synthesize the polyketide antibiotics erythromycin and tylosin, respectively, and the classically improved strains contain unknown overproduction mutations. more...

Organism:

Streptomyces coelicolor

Type:

Expression profiling by array; Genome variation profiling by array

Platforms:

GPL2620 GPL2619

43 Samples

Download data

(Submitter supplied) The promoter upstream from eryAI (eryAp) was cloned in front of EGFP in pIJ8660. This vector was integrated into the chromosome of K24-1, a clean host version of K41-135 (the overproducer strain obtained from Kosan Biosciences). This strain was then grown in shake flask culture in R5 medium. RNA was harvested up through three days. The 12 h RNA sample was used as the reference sample for all RNA hybridizations. more...

Organism:

Streptomyces coelicolor

Type:

Expression profiling by array; Genome variation profiling by array

Platform:

GPL2620

7 Samples

Download data

(Submitter supplied) Saccharopolyspora erythraea NRRL2338 (wildtype) and K41-135 (overproducer strain from Kosan Biosciences, KOVP) were grown in shake flask cultures in rich medium R5. RNA samples were harvested for each strain over 5 days. 12 h samples taken for each strain were used as their respective reference ("time zero") samples. The genomic DNA control compares NRRL2338 gDNA to NRRL2338 12 h RNA to show relative gene expression at the start of the timecourse. more...

Organism:

Streptomyces coelicolor

Type:

Expression profiling by array; Genome variation profiling by array

Platform:

GPL2619

18 Samples

Download data

(Submitter supplied) RNA timecourse data for Streptomyces fradiae wildtype (ATCC19609) and overproducing strain KOS155-3C(RUS). Strains were grown at 30 C in shake flask cultures in R5 medium with no glucose. RNA samples were harvested over 5 days as tylosin was produced. 12 h RNA samples of each strain were used as the reference sample(green) within their respective timecourses. The WT gDNA vs. 12 h RNA control displays relative gene expression at the beginning of the timecourse. more...

Organism:

Streptomyces coelicolor

Type:

Expression profiling by array; Genome variation profiling by array

Platform:

GPL2620

18 Samples

Download data

(Submitter supplied) Bacteria have to continuously adjust to nutrient fluctuations from favorable to less favorable conditions and carbon starvation. The glucose-acetate transition followed by carbon starvation is representative of such carbon fluctuations observed by E. coli in many environments. Regulation of gene expression through fine-tuning of mRNA pools constitutes one of the regulation levels required for such a metabolic adaptation. more...

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL25406

9 Samples

Download data: PAIR

(Submitter supplied) Bacteria have to continuously adjust to nutrient fluctuations from favorable to less favorable conditions and carbon starvation. The glucose-acetate transition followed by carbon starvation is representative of such carbon fluctuations observed by E. coli in many environments. Regulation of gene expression through fine-tuning of mRNA pools constitutes one of the regulation levels required for such a metabolic adaptation. more...

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL25406

35 Samples

Download data: PAIR

(Submitter supplied) A DNA microarray was designed and constructed using the genome sequence of Saccharopolyspora erythraea strain NRRL 2338. Following growth in liquid medium, we analysed the expression of 6494 ORFs along the time course. The results indicated that the 404 genes, whose expression significatively correlated with the time course, identify three distinct growth phases: a rapid growth until 32 h (phase A); a growth slowdown until 52 h (phase B); another rapid growth phase from 56 h to 72 h (phase C) before entering the stationary phase. more...

Organism:

Saccharopolyspora erythraea

Type:

Expression profiling by array

Platform:

GPL6051

20 Samples

Download data: CEL