Streptomyces
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA746445 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15130305.fastq.gz | Fastqsanger.gz | |||
| SRR15130306.fastq.gz | Fastqsanger.gz | |||
| SRR15130307.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
Similar Datasets
Project description:Genomes of streptomycetes isolated from beehives
| PRJNA746445 | ENA
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.
2013-12-31 | GSE53562 | GEO
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.
2013-12-31 | GSE53563 | GEO
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. Transcriptional profiling of S. coelicolor M145 at different growth phases (exponential, transitional and stationary phase)
2013-12-31 | E-GEOD-53562 | biostudies-arrayexpress
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. Transcriptional profiling variation of S. coelicolor M145, M-NM-^TscbR2 mutation with jadomycin addition at 30 h.
2013-12-31 | E-GEOD-53563 | biostudies-arrayexpress
Project description:The Streptomyces lividans lsp gene encodes a type II signal peptidase (Lsp) that cleaves the type II leader peptides of lipoproteins. Transcriptional profiling of the bacterium depleted of the lsp gene mainly resulted in deactivation of the sigma U regulon, as well as in downregulation of genes involved in the biogenesis and function of ribosomes and genes encoding some major secretory proteins as determined by hybridisation of commercially available S. lividans genome-wide microarrays. Almost 50% of the dowregulated genes have been described as forming part of the stringent response in streptomycetes. The gene encoding the S. lividans extracellular foldase, the lipoprotein FkpA, is equally downregulated. Therefore, the deletion of lsp from the S. livdans genome temporarily triggers a cellular stress where the stringent response is, at least, partially induced.
2014-05-22 | GSE30728 | GEO
Project description:The gene dagA encoding agarase in Streptomyces coelicolor was cloned in the multicopy plasmid pIJ486 generating plasmid pAGAs5. Plasmid pAGAs5 and pIJ486 were propagated in S. lividans TK21 to obtain S. lividans TK21(pAGAs5) and its isogenic strain S. lividans TK21(pIJ486). Transcriptional profiling of the bacterium that overproduces agarase mainly resulted in the downregulation of the genes involved in the biogenesis and function of ribosomes, together with the downregulation of the genes involved in nitrogen, aminoacids, purine/pyrimidine and central carbon metabolism as well as ABC transporters, redox processes and fatty acids biosynthesis. The number of genes upregulated in the agarase overproducer strain is lower than in the downregulated ones. Almost 50% of the dowregulated genes have been described as forming part of the stringent response in streptomycetes. Therefore, the overproduction of agarase may lead to a condition of nutrient depletion that triggers the stringent response.
2015-07-23 | GSE61447 | GEO
Project description:6S RNA is a small RNA with specific secondary structure that associates with the complex of RNA polymerase (RNAP) and the primary sigma factor in majority of bacteria. In mycobacteria, Ms1 interacts with the RNAP core without the sigma factor and probably replaces 6S RNA. It is unclear if S. coelicolor has any 6S RNA or Ms1 RNA. To identify putative Ms1/6S RNA or any other similar RNAs in Streptomycetes, we sequenced RNAs that co-immunoprecipitated with RNAP or the primary sigma factor HrdB. We also sequenced total RNA isolated from the lysate (input sample). We expect that putative Ms1/6S-like RNAs are enriched in RNA polymerase or sigma A samples compared to the inputs. The experiment was performed 42 hrs and 66 hrs after germination.
2024-02-09 | E-MTAB-11694 | biostudies-arrayexpress
Project description:The Streptomyces lividans lsp gene encodes a type II signal peptidase (Lsp) that cleaves the type II leader peptides of lipoproteins. Transcriptional profiling of the bacterium depleted of the lsp gene mainly resulted in deactivation of the sigma U regulon, as well as in downregulation of genes involved in the biogenesis and function of ribosomes and genes encoding some major secretory proteins as determined by hybridisation of commercially available S. lividans genome-wide microarrays. Almost 50% of the dowregulated genes have been described as forming part of the stringent response in streptomycetes. The gene encoding the S. lividans extracellular foldase, the lipoprotein FkpA, is equally downregulated. Therefore, the deletion of lsp from the S. livdans genome temporarily triggers a cellular stress where the stringent response is, at least, partially induced. All microarray analyses were performed with RNA samples obtained from three independent cultures grown under identical conditions. The cDNA obtained from each RNA preparation of the Lsp-deficient strain was hybridised with the cDNA obtained from the equivalent RNA preparation of the wild type strain (S. lividans TK21).
2014-05-22 | E-GEOD-30728 | biostudies-arrayexpress