Project description: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. The 12 h RNA control compares initial gene expression between the wildtype and overproducer strains. Groups of assays that are related as part of a time series. Keywords: time_series_design
Project description: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. The 12 h RNA control compares initial gene expression between the wildtype and overproducer strains.
Project description: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. The 12 h RNA control compares initial gene expression between the wildtype and overproducer strains. Groups of assays that are related as part of a time series. Computed
Project description:The present work aimed at providing noval reference genes (RGs) for streptomycetes by global quantitative analysis of gene expression profile. By using the time-series microarray data obtained in different culture medium (SMM in the present work and modified R5 from publication), the stably expressed genes of S. coelicolor were screened. Further statistical, bioinformatic and biological function analysis picked out 13 candidate RGs. According to qRT-PCR assays, 5 genes with high stability were selected and used for validation in other streptomycetes to assess their prevalence. Additionally, the absolute gene expression level reflcted by RNA-seq was also taken into consideration in the present work to guide the appropriate RGs selection for streptomycetes.
