GEO DataSets

(Submitter supplied) Nine Curtobacterium strains (three from three clades) were subjected to a lab desiccation experiment with no access to moisture or nutrients to compare between clades. RNA was extracted at days 0, 1, and 32 and sequenced

Organism:

Curtobacterium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33356

81 Samples

Download data: CSV, SF

(Submitter supplied) Mycobacterium avium subsp. paratuberculosis (MAP) carries MAP3773c, a putative metal regulator, on its genome which is absent in other mycobacteria. Homologues of this gene in enterobacteria have roles in global iron regulation and homeostasis. The role of MAP3773c in regulating intracellular iron in MAP is poorly understood. Functional analysis of DEGs in ΔMAP3773c revealed that pantothenate (Pan) biosynthesis, polysaccharide biosynthesis, sugar metabolism and N-acetyltransferase enhanced intracellular survival genes were downregulated at 30 minutes post-iron starvation whereas ATP-binding cassette (ABC) type metal transporters, putative siderophore biosynthesis, arginine and proline metabolism, PPE, PE family and mammalian cell entry (MCE) genes were upregulated at that same time point. more...

Organism:

Mycobacterium avium subsp. paratuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33823

20 Samples

Download data: TXT

(Submitter supplied) Seven carbon autotrophic fixation pathways were described so far. However, it is not common to find the co-existence of more than one cycle in a single cell. Here, we describe a thermophilic bacterium Carbonactinospora thermoautotrophica StC with a unique and versatile carbon metabolism. StC was isolated from a consortium found in a burning organic pile that exhibits an optimal growth temperature between 55° and 65° C. more...

Organism:

Carbonactinospora thermoautotrophica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34357

14 Samples

Download data: FA, TXT

(Submitter supplied) The bacterial world offers diverse strains for understanding medical and environmental processes and for engineering synthetic-biology chasses. However, genetically manipulating these strains has faced a long-standing bottleneck: how to efficiently transform DNA. Here we report IMPRINT, a generalized, rapid and scalable approach to overcome DNA restriction, a prominent barrier to transformation. IMPRINT utilizes cell-free systems to express DNA methyltransferases from the bacterial host’s restriction-modification systems. more...

Organism:

Escherichia coli; Bifidobacterium breve

Type:

Other

Platforms:

GPL25368 GPL33564

7 Samples

Download data: TSV

(Submitter supplied) Root exudates contain specialised metabolites that affect the plant’s root microbiome. How host-specific microbes cope with these bioactive compounds, and how this ability shapes root microbiomes, remains largely unknown. We investigated how maize root bacteria metabolise benzoxazinoids, the main specialised metabolites of maize. Diverse and abundant bacteria metabolised the major compound in the maize rhizosphere MBOA and formed AMPO. more...

Organism:

Microbacterium sp. LMB2-1.2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34376

10 Samples

Download data: TXT

(Submitter supplied) C-di-AMP is primarily associated with the regulation of carbon utilization as well as other central traits, central metabolism, and bacterial stringent response to environmental changes. Elevated c-di-AMP levels result in aberrant physiology for most c-di-AMP synthesizing organisms, drawing particular attention to the importance of the c-di-AMP homeostasis and the molecular mechanisms pertaining to nucleotide metabolism and signal transduction. more...

Organism:

Saccharopolyspora erythraea

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL33125

4 Samples

Download data: TDF

(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) To further development of our gene expression approach in different groups of leprosy, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish leprosy reactions and relapse cases from healthy controls. Human biopsy and skin slit were collected from reaction cases, PB cases, MB cases, relapse cases and healthy contacts. more...

Organism:

Mycobacterium leprae

Type:

Expression profiling by array

Platform:

GPL33105

45 Samples

Download data: TXT

(Submitter supplied) Streptomyces has the largest repertoire of natural product biosynthetic gene clusters (BGCs), yet developing a universal engineering strategy for each Streptomyces species is challenging. Given that some Streptomyces species have larger BGC repertoires than others, we hypothesized that a set of genes co-evolved with BGCs to support biosynthetic proficiency must exist in those strains, and that their identification may provide universal strategies to improve the productivity of other strains. more...

Organism:

Streptomyces griseus; Streptomyces rapamycinicus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27559 GPL34215

12 Samples

Download data: CSV

(Submitter supplied) Mycofactocin is a redox cofactor essential for the alcohol metabolism of Mycobacteria. While the biosynthesis of mycofactocin is well established, the mftG gene, which encodes an oxidoreductase of the glucose-methanol-choline superfamily remained functionally uncharacterized. Here, we show that MftG enzymes strictly require mft biosynthetic genes, and are found in 75% of organisms harboring these genes. more...

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28006

12 Samples

Download data: XLSX

(Submitter supplied) Ribosome profiling analysis of wild type prototrophic Streptomyces coelicolor A3(2) MT1110 strain to examine global translational vs transcriptional profile change when exposed to cold shock from 30°C to 10°C in minimal liquid medium.

Organism:

Streptomyces coelicolor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28977

30 Samples

Download data: CSV, TSV

(Submitter supplied) Polysome profiling analysis of wild type prototrophic Streptomyces coelicolor A3(2) MT1110 strain to examine global translational vs transcriptional profile change when exposed to cold shock from 30°C to 10°C in minimal liquid medium.

Organism:

Streptomyces coelicolor A3(2)

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26763

27 Samples

Download data: CSV, TSV

(Submitter supplied) RNA-seq analysis of wild type prototrophic Streptomyces coelicolor A3(2) MT1110 strain to examine global transcriptional profile change when exposed to cold shock from 30°C to 10°C in rich liquid medium, minimal solid medium and in minimal liquid medium

Organism:

Streptomyces coelicolor A3(2)

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26763

36 Samples

Download data: CSV, TSV

(Submitter supplied) RNA-seq analysis of wild type Streptomyces coelicolor A3(2) MT1110 to examine global transcriptional profile change when exposed to cold shock from 30°C to 10°C in rich liquid medium and from 30°C to 4°C on minimal solid medium.

Organism:

Streptomyces coelicolor A3(2)

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26763

24 Samples

Download data: TSV

(Submitter supplied) Mycobacterium avium complex (MAC), including Mycobacterium avium and Mycobacterium intracellulare (MI), accounts for a significant portion of nontuberculous mycobacterial lung disease affecting immunocompromised and lung structural disease patients. Adapting pathogens to a host-induced hostile environment is critical to establishing infection and persistence within the host. However, the cellular and molecular mechanisms of stress response for MAC still need to be elucidated. more...

Organism:

Mycobacterium intracellulare

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33797

9 Samples

Download data: TXT

(Submitter supplied) Superbugs such as drug-resistant Mycobacterium tuberculosis (DR-M.tb) poses a serious global health threat. Upon infection, M.tb reaches the alveolar space and comes in close contact with soluble components of the human alveolar lining fluid (ALF) for an uncertain period of time prior to and following its encounter with alveolar compartment cells. Homeostatic ALF hydrolases, which main function is maintaining lung health, modify the M.tb cell envelope, driving M.tb-host cell interactions. more...

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22688

32 Samples

Download data: TXT

(Submitter supplied) The production of daptomycin (DAP) is precisely regulated by a complex regulatory network in Streptomyces roseosporus (S. roseosporus). Although the most biosynthetic pathway of DAP has been elucidated, the regulatory mechanism of its biosynthesis at transcriptional level is not fully understood. In the present study, a transcriptional regulator DhyR has been identified based on our previous quantification proteomics identification in S. more...

Organism:

Streptomyces filamentosus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34032

2 Samples

Download data: TXT

(Submitter supplied) To find potential regulatory targets of the anti-virulence compound S3 in Mycobacterium tubercuolsis.

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27507

4 Samples

Download data: TXT

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

Organism:

Corynebacterium glutamicum

Type:

Expression profiling by array

Platform:

GPL32785

12 Samples

Download data: TXT

(Submitter supplied) mRNA was sampled during exponential growth (OD660 = 4) strains: LPA-0 (L-lysine hyperproducing strain C. glutamicum LYS-12 (Becker et al. 2011) + pClik5a_MCS), C. glutamicum LPA-5 (C. glutamicum LPA-0 + pClik5a_peftu_lat_proC)

Organism:

Corynebacterium glutamicum

Type:

Expression profiling by array

Platform:

GPL32785

6 Samples

Download data: TXT, XLSX