GEO DataSets

(Submitter supplied) We identified genome-wide binding regions of NdgR in Streptomyces coelicolor using chromatin immunoprecipitation sequencing (ChIP-seq). We constructed 6×myc-tagged NdgR strain using homologous recombination with myc-tagging vector. Analysis of the sequencing data aligned to Streptomyces coelicolor genome database (NC_003888).

Organism:

Streptomyces coelicolor

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18886

1 Sample

Download data: GFF

(Submitter supplied) We determined the genomic locations of the SigR binding sites by chromatin immuno-precipitation of cross-linked DNA and hybridization on a tilling oligonucleotide array after 20 minutes of diamide treatment on cell cultures.

Organism:

Streptomyces coelicolor A3(2)

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL14825

1 Sample

Download data: PAIR

(Submitter supplied) We report 6 genes that were found to be regulated by SoxR in stationary phase when the bacteria produce the antibiotic actinorhodin. Five of these genes are previously confirmed SoxR targets; the sixth is a novel SoxR-target.

Organism:

Streptomyces coelicolor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17012

6 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Transcriptional regulation is a critical process to ensure expression of genes necessary for growth and survival in diverse environments. Transcription is mediated by multiple transcriptional factors including activators, repressors and sigma factors. Accurate computational prediction of the regulon of target genes for transcription factors is difficult and experimental identification is a laborious process and not scalable. more...

Organism:

Streptomyces coelicolor A3(2)

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30648

68 Samples

Download data: CSV

(Submitter supplied) Transcriptional regulation is a critical process to ensure expression of genes necessary for growth and survival in diverse environments. Transcription is mediated by multiple transcriptional factors including activators, repressors and sigma factors. Accurate computational prediction of the regulon of target genes for transcription factors is difficult and experimental identification is a laborious process and not scalable. more...

Organism:

Streptomyces coelicolor A3(2)

Type:

Other

Platform:

GPL30647

51 Samples

Download data: CSV

(Submitter supplied) Like other bacterial species, Mycobacterium tuberculosis has multiple sigma (s) factors encoded in its genome. In previously published work, we and others have shown that mutations in some of these transcriptional activators render M. tuberculosis sensitive to various environmental stresses and, in some cases, cause attenuated virulence phenotypes. In this paper, we characterize a M. tuberculosis mutant lacking the ECF s factor sigma-H. more...

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by array

Platform:

GPL2787

15 Samples

Download data: TXT

(Submitter supplied) Comparing transciptional profile of a M. smegmatis mc2155 ΔsigF strain and wild type (control) in in vitro culture at two time points (exponential phase and stationary phase) for identification of SigF-dependent genes.

Organism:

Mycolicibacterium smegmatis

Type:

Expression profiling by array

Platform:

GPL5862

8 Samples

Download data: TXT

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

Organism:

Streptomyces coelicolor

Type:

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

Platform:

GPL27129

10 Samples

Download data

(Submitter supplied) We determined Streptomyces coelicolor genes that are directly regulated by WblC (or WhiB7), an actinobacterial transcription factor that activates expression of intrinsic resistance in response to translation-inhibitory antibiotic stress. Identification of differentially expressed genes in wblC mutant by RNA-seq and WblC binding sites in wild type by ChIP-seq identified more than 300 genes as WblC regulon. more...

Organism:

Streptomyces coelicolor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27129

8 Samples

Download data: TXT

(Submitter supplied) We determined Streptomyces coelicolor genes that are directly regulated by WblC (or WhiB7), an actinobacterial transcription factor that activates expression of intrinsic resistance in response to translation-inhibitory antibiotic stress. Identification of differentially expressed genes in wblC mutant by RNA-seq and WblC binding sites in wild type by ChIP-seq identified more than 300 genes as WblC regulon. more...

Organism:

Streptomyces coelicolor

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27129

2 Samples

Download data: TXT

(Submitter supplied) BldD is a transcriptional regulator essential for morphological development and antibiotic production in Streptomyces coelicolor. Here we identify the BldD regulon by means of chromatin immunoprecipitation. The BldD regulon encompasses ~167 transcriptional units, of which more than 20 are known to play important roles in development and/or secondary metabolism. Strikingly, 42 BldD target genes (~25% of the regulon) encode regulatory proteins, stressing the central, pleiotropic role of BldD. more...

Organism:

Streptomyces coelicolor

Type:

Genome binding/occupancy profiling by array

Platform:

GPL10757

4 Samples

Download data: TXT

(Submitter supplied) Chitin is the second most abundant biopolymer present in soils and is utilized by antibiotic-producing Streptomyces species. Its monomer, N-acetylglucosamine (NAG), regulates the developmental program of the model organism Streptomyces coelicolor. NAG blocks differentiation when growing on rich medium whilst it promotes development on poor culture media. We report here the negative effect of NAG on tacrolimus (FK506) production in Streptomyces tsukubaensis NRRL 18488 growing on a defined rich medium. more...

Organism:

Streptomyces tsukubensis NRRL18488

Type:

Expression profiling by array

Platform:

GPL23554

16 Samples

Download data: TXT

(Submitter supplied) By ChIP-seq of ScbR and ScbR2 binding sites across M145 chromosome, 143 and 492 peaks of ScbR and ScbR2 were identified, respectively. And they shared numurous same sites.

Organism:

Streptomyces coelicolor

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17012

3 Samples

Download data: TXT

(Submitter supplied) To help understand the functions of GBL receptor ScbR and antibiotic receptor ScbR2, the global transcriptional profiles of scbRDM and scbR2DM compared to WT were studied.

Organism:

Streptomyces coelicolor

Type:

Expression profiling by array

Platform:

GPL19598

12 Samples

Download data: TXT

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

Organism:

Corynebacterium glutamicum R

Type:

Expression profiling by array; Genome binding/occupancy profiling by array

Platform:

GPL17881

20 Samples

Download data: TXT

(Submitter supplied) The extracytoplasmic function sigma factor SigH is responsible for heat and oxidative stress response in a biotechnologically -important bacterium Corynebacterium glutamicum. Due to the hierarchical nature of the regulatory network, it has not been possible to fully determine the SigH regulon by previous transcriptome analyses. Here, we determined the direct genome-wide targets of SigH were determined by ChIP-chip analysis using a deletion mutant of rshA, encoding an anti-sigma factor of SigH. more...

Organism:

Corynebacterium glutamicum R

Type:

Genome binding/occupancy profiling by array

Platform:

GPL17881

10 Samples

Download data: TXT

(Submitter supplied) The extracytoplasmic function sigma factor SigH is responsible for heat and oxidative stress response in a biotechnologically -important bacterium Corynebacterium glutamicum. Due to the hierarchical nature of the regulatory network, it has not been possible to fully determine the SigH regulon by previous transcriptome analyses. Here, we determined the direct genome-wide targets of SigH were determined by ChIP-chip analysis using a deletion mutant of rshA, encoding an anti-sigma factor of SigH. more...

Organism:

Corynebacterium glutamicum R

Type:

Expression profiling by array

Platform:

GPL17881

10 Samples

Download data: TXT

(Submitter supplied) DNA Microarray based comparison of M. tuberculosis and its isogenic delta-sigmaH mutant for an extended period of time, using a diamide-stress and removal strategy (post-diamide stress or PDS) Raw data has been requested of, but not provided by, the submitter.

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by array

Platform:

GPL8382

12 Samples

Download data

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

Organism:

Streptomyces coelicolor

Type:

Expression profiling by array

Platform:

GPL4908

43 Samples

Download data: GPR, TXT

(Submitter supplied) Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) M752 mutant strain, which has an in frame deletion of scbR (SCO6265) and compare it to the wild-type M145 strain. more...

Organism:

Streptomyces coelicolor

Type:

Expression profiling by array

Platform:

GPL4908

9 Samples

Download data: GPR, TXT