GEO DataSets

(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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(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

Type:

Expression profiling by array

Platform:

GPL3918

9 Samples

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(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) Mycobacterium tuberculosis (Mtb) assimilates cholesterol during chronic infection, and its in vitro growth in presence of cholesterol requires Mycofactocin (MFT) biosynthesis genes, although the basis of this requirement is unclear. MFT belongs to the class of ribosomally synthesized and post-translationally modified peptides conserved in many Actinobacteria, and its biological function and structure requires further confirmation. more...

Organism:

Mycolicibacterium smegmatis; Mycobacterium tuberculosis variant bovis; Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by array

Platforms:

GPL25686 GPL25708

30 Samples

Download data: TXT

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

Organism:

Rhodococcus jostii RHA1

Type:

Expression profiling by array

Dataset:

GDS2683

Platform:

GPL3918

6 Samples

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

Organism:

Rhodococcus jostii RHA1

Type:

Expression profiling by array

Platform:

GPL3918

3 Samples

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

Organism:

Rhodococcus jostii RHA1

Type:

Expression profiling by array

Platform:

GPL3918

3 Samples

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Analysis of Rhodococcus sp. strain RHA1 cells exposed to the pollutant phthalate (PTH) or terephthalate (TPA). Phthalate esters are used as plastic additives. RHA1 is able to degrade a wide range of aromatic compounds including PTH. Results provide insight into the ability of RHA1 to degrade TPA.

Organism:

Rhodococcus jostii RHA1

Type:

Expression profiling by array, log2 ratio, 2 agent sets

Platform:

GPL3918

Series:

GSE6685

6 Samples

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(Submitter supplied) We analyzed the genes expressed, or the transcriptome, of bacilli Mycobacterium bovis BCG Pasteur (wtBCG) and a mutant strain obtained by transposition of the gene BCG_ BCG_2177c (mtBCG), cultured in the presence of a lipid mixture (fatty acids/cholesterol) as main carbon source. Using RNAseq we identified a group of genes that provides novel insight regarding the metabolic pathways and transcriptional regulation, and pathogenic features that were influenced by BCG_2177c gene, a TetR-like repressor, during the lipid metabolism in slow-growing mycobacteria that could be extrapolated to other members of the MTBC.

Organism:

Mycobacterium tuberculosis variant bovis BCG

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29423

8 Samples

Download data: TXT

(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:

GPL6703 GPL3918

42 Samples

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(Submitter supplied) The upsurge of multidrug-resistant infections has rendered tuberculosis the principal cause of death among infectious diseases. A clonal outbreak multidrug-resistant triggering strain of Mycobacterium tuberculosis was identified in Kanchanaburi Province, designated “MKR superspreader”, which was found to subsequently spread to other regions, as revealed by prior epidemiological reports in Thailand. Herein, we showed that the MKR displayed a higher growth rate upon infection into host macrophages in comparison with the H37Rv reference strain. To further elucidate the MKR’s biology, we utilised RNA-Seq and differential gene expression analyses to identify host factors involved in the intracellular viability of the MKR. A set of host genes function in the cellular response to lipid pathway was found to be uniquely up-regulated in host macrophages infected with the MKR, but not those infected with H37Rv. Within this set of genes, the IL-36 cytokines which regulate host cell cholesterol metabolism and resistance against mycobacteria attracted our interest, as our previous study revealed that the MKR elevated genes associated with cholesterol breakdown during its growth inside host macrophages. Indeed, when comparing macrophages infected with the MKR to H37Rv-infected cells, our RNA-Seq data showed that the expression ratio of IL-36RN, the negative regulator of the IL-36 pathway, to that of IL-36G was greater in macrophages infected with the MKR. Furthermore, the intracellular survival of MKR was diminished with decreased IL-36RN expression. Overall, our results indicate that IL-36RN is critical for MKR intracellular survival and could serve as a new target against this emerging multidrug-resistant M. tuberculosis strain.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

12 Samples

Download data: TXT