GEO DataSets

(Submitter supplied) Ethylene glycol (EG) is a widely used industrial chemical with manifold applications and is also generated in the degradation of plastics such as PET. Rhodococcus jostii RHA1 (RHA1), a potential biocatalytic chassis, grows on EG. Transcriptomic analyses revealed four clusters of genes potentially involved in EG catabolism: the mad locus, predicted to encode mycofactocin-dependent alcohol degradation, including the catabolism of EG to glycolate; two GCL clusters, predicted to encode glycolate and glyoxylate catabolism; and the mft genes, predicted to specify mycofactocin biosynthesis. more...

Organism:

Rhodococcus jostii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34291

12 Samples

Download data: TSV

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

Organism:

Rhodococcus jostii RHA1; Gordonia sp. KTR9

Type:

Expression profiling by array

Platforms:

GPL26090 GPL26089

12 Samples

Download data: TXT

(Submitter supplied) To further explore potential molecular mechanisms and pathways by which the presence or absence of the pGKT2 plasmid may be affecting the overall fitness cost in a transconjugant Rhodococcus jostii RHA1 strain, transcriptome studies were performed. Transcriptome experiments comparing RHA1 wild-type and RHA1 transconjugant strains grown in rich media confirmed the presence of the pGKT2 plasmid.

Organism:

Rhodococcus jostii RHA1; Gordonia sp. KTR9

Type:

Expression profiling by array

Platform:

GPL26089

6 Samples

Download data: TXT

(Submitter supplied) Transcriptomics of Rhodococcus EP4 on ethylphenol, propylguiacol and succiate

Organism:

Rhodococcus rhodochrous

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24760

9 Samples

Download data: CSV

(Submitter supplied) Transcriptome studies confirm the nitrogen limited physiological state of both the wild-type and mutant cells. In addition, multiple differentially expressed genes involved in the synthesis and consumption of pools of acetyl-CoA, acetoacetyl-CoA and 3-hydroxybutyryl-CoA, key metabolites for PHA and TAG synthesis, were identified. An enrichment analysis of differentially expressed genes in the nitrogen starved wild-type versus the isogenic RHA1_ro02104 mutant strain identified genes in the mutant involved in fatty acid and lipid as well as genes involved in acyl-CoA hydrolysis and triacylglycerol degradation.

Organism:

Rhodococcus jostii RHA1

Type:

Expression profiling by array

Platform:

GPL21549

12 Samples

Download data: TXT

(Submitter supplied) Oleaginous microorganisms have considerable potential for biofuel and commodity chemical production. Under nitrogen-limitation, Rhodococcus jostii RHA1 grown on benzoate, an analog of lignin depolymerization products, accumulated triacylglycerols (TAGs) to 55% of its dry weight during transition to stationary phase, with the predominant fatty acids being C16:0 and C17:0. Transcriptomic analyses of RHA1 grown under conditions of N-limitation and N-excess revealed 1,826 dysregulated genes. more...

Organism:

Rhodococcus jostii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21367

8 Samples

Download data: TXT

(Submitter supplied) p-Hydroxycinnamates, such as p-coumarate and ferulate, are components of plant cell walls and have a number of commercial applications. Previously, we had shown that the soil Actinobacterium Rhodococcus jostii RHA1 (RHA1) grows on ferulate, catabolizing it via vanillate and the β-ketoadipate pathway. We used transcriptomics to identify genes in RHA1 that were specifically up-regulated during growth on ferulate. more...

Organism:

Rhodococcus jostii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18502

2 Samples

Download data: TXT

(Submitter supplied) The marine bacterium Rhodococcus erythropolis PR4 was demonstrated to be able for assimilation/biodegradation of hydrocarbons. Not just the chromosome but two large plasmids provide versatile enzyme sets involved in many metabolic pathways. In order to identify the key elements involved in biodegradation of the model compound, hexadecane, and diesel oil, we performed whole transcriptome analysis on cells grown in the presence of n-hexadecane and diesel oil. more...

Organism:

Rhodococcus erythropolis PR4

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18526

4 Samples

Download data: XLS

(Submitter supplied) Purpose: To delineate mechanisms underlying lipid storage in LDs, we compared the transcriptomes of cells cultivated under three lipid-accumulating conditions. Methods: PD630 mRNA profiles of 3 different conditions (normal condition and LDs acculation conditions) were generated by deep sequencing, using Solid platform. The sequence reads were mapped by using Bowtie followed by Cufflinks. Results: Most genes were either expressed under all three conditions (6,759 genes) or under at least one condition (7,770 genes), but 1,177 genes were not expressed under any of these conditions. more...

Organism:

Rhodococcus opacus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16295

3 Samples

Download data: DIFF, GTF

(Submitter supplied) We have developed a 60-mer oligonucleotide multibacterial microarray for detection and expression profiling of biodegradative genes and bacterial diversity (16S rRNA gene) in different habitats contaminated with varieties of hazardous chemicals. The genes selected were involved in biodegradation and biotransformation of various groups of compounds viz. nitroaromatic compounds (148 genes), chloroaromatic compounds (75 genes), monoaromatic compounds (373 genes), polyaromatic hydrocarbons (174 genes), pesticides/ herbicides (34 genes), alkanes/aliphatics (185 genes) and heavy metals (68 genes), which covered a total number of 133 chemicals. more...

Organism:

Escherichia coli BL21; freshwater sediment metagenome; Escherichia coli K-12; Sphingomonas sp. NM05; soil metagenome; Rhodococcus jostii RHA1; Bordetella sp. IITR-02; synthetic construct; Escherichia coli DH5[alpha]

Type:

Genome variation profiling by array

Platform:

GPL10926

17 Samples

Download data: TXT

(Submitter supplied) Two cultures, one grown on cholic acid and the other on pyruvate.

Organism:

Rhodococcus jostii RHA1

Type:

Expression profiling by array

Platform:

GPL3918

3 Samples

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(Submitter supplied) Transcroptomic analysis of the cells grown on pyruvate in the sterilized soil and those grown on pyruvate to mid-exponenyial phase in a liquid medium

Organism:

Rhodococcus jostii RHA1

Type:

Expression profiling by array

Platform:

GPL7627

4 Samples

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(Submitter supplied) Transcriptomic analysis of the cells grown on biphenyl in the sterilized soil and those grown on biphenyl to mid-exponential phase in a liquid medium

Organism:

Rhodococcus jostii RHA1

Type:

Expression profiling by array

Platform:

GPL7627

4 Samples

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(Submitter supplied) Transcriptomic analysis of the cells grown on biphenyl on a filter placed on a minimal agar medium and those grown on biphenyl to mid-exponential phase in a liquid medium

Organism:

Rhodococcus jostii RHA1

Type:

Expression profiling by array

Platform:

GPL7627

3 Samples

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(Submitter supplied) Transcriptomic analysis of the cells grown on biphenyl to stationary phase and those grown on biphenyl to mid-exponential phase

Organism:

Rhodococcus jostii RHA1

Type:

Expression profiling by array

Platform:

GPL7627

3 Samples

Download data

(Submitter supplied) Transcriptomic analysis of the cells grown on biphenyl to transition phase and those grown on biphenyl to mid-exponential phase

Organism:

Rhodococcus jostii RHA1

Type:

Expression profiling by array

Platform:

GPL7627

3 Samples

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(Submitter supplied) We analyzed the transcriptional response of the actinomycete Rhodococcus aetherivorans I24 to biphenyl and polychlorinated biphenyls (PCBs). This species has not been extensively exposed to PCBs, as it was first isolated from a toluene contaminated aquifer, rather than a site contaminated with polychlorinated hydrocarbons. Using a microarray targeting 3524 genes, we assessed gene expression in minimal medium supplemented with various substrates (e.g. more...

Organism:

Rhodococcus aetherivorans

Type:

Expression profiling by array

Platform:

GPL8836

30 Samples

Download data: PAIR

(Submitter supplied) Here we report the first transcriptomic analysis of a Gram-positive bacterium to desiccation. Filtered RHA1 cells incubated at either low relative humidity (20%), as an air drying treatment, or high relative humidity (100%), as a control, were transcriptionally profiled over a comprehensive time series. Keywords: stress response time course

Organism:

Rhodococcus jostii RHA1

Type:

Expression profiling by array

Platforms:

GPL3918 GPL6703

42 Samples

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(Submitter supplied) three late exponential phase Rhodococcus sp. RHA1 propane-grown cultures compared to pyruvate-grown cultures Keywords: growth substrate

Organism:

Rhodococcus jostii RHA1

Type:

Expression profiling by array

Platform:

GPL3918

3 Samples

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(Submitter supplied) two cultures one grown on cholesterol and other on pyruvate Keywords: growth type

Organism:

Rhodococcus jostii RHA1

Type:

Expression profiling by array

Platform:

GPL3918

3 Samples

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