GEO DataSets

(Submitter supplied) Using Total RNA sequencing, We report the effects of VapC13 and VapC26 overexpression on the transcriptome of M. tuberculosis. For RNA-seq experiments, early-log phase cultures (OD600nm ~ 0.2-0.3) of M. tuberculosis strains harboring either pTetR or pTetR-vapC13 or pTetR-vapC26 were induced with the addition of 50 ng/ml Atc for 24 h. For total RNA isolation, induced cultures were harvested by centrifugation, washed twice with 1x PBS and lysed by bead beating in Trizol. more...

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29178

9 Samples

Download data: TXT

(Submitter supplied) Listeria monocytogenes causes listeriosis, an infectious and potentially fatal disease of animals and humans. A diverse network of transcriptional regulators, including LysR-type catabolite control protein C (CcpC), is critical for the survival of L. monocytogenes and its ability to transition into the host environment. In this study, we explored the physiological and genetic consequences of deleting ccpC and the effects of such deletion on the ability of L. more...

Organism:

Listeria monocytogenes serotype 4b str. F2365

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34483

9 Samples

Download data: TXT

(Submitter supplied) Methicillin-resistant Staphylococcus aureus (MRSA) is a major threat to human health. Rather than depend on creating new antibiotics (to which bacteria will eventually become resistant), we are employing antibiotic adjuvants that potentiation existing antibiotics. Based on our previous work, loratadine, the FDA-approvide antihistamine, effectively potentiates cell-wall active antibiotics in multiple strains of MRSA. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27158

18 Samples

Download data: XLSX

(Submitter supplied) In nature, bacteria often survive in a stationary state, with low metabolic activity. Phages use the metabolic machinery of the host cell to replicate and, therefore, their efficacy against non-dividing cells is usually limited. Nevertheless, it was previously shown that the Staphylococcus epidermidis phage SEP1 has the remarkable capacity to actively replicate in stationary-phase cells, reducing their numbers. more...

Organism:

Staphylococcus epidermidis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30249

24 Samples

Download data: XLSX

(Submitter supplied) The host protein calprotectin inhibits the growth of a variety of bacterial pathogens through metal sequestration in a process known as 'nutritional immunity'. Staphylococcus aureus growth is inhibited by calprotectin in vitro and calprotectin is localized in vivo to staphylococcal abscesses during infection. However, the staphylococcal adaptations that provide defense against nutritional immunity and the role of metal-responsive regulators are not fully characterized. more...

Organism:

Staphylococcus aureus

Type:

Other

Platform:

GPL19006

10 Samples

Download data: XLSX

(Submitter supplied) The host protein calprotectin inhibits the growth of a variety of bacterial pathogens through metal sequestration in a process known as 'nutritional immunity'. Staphylococcus aureus growth is inhibited by calprotectin in vitro and calprotectin is localized in vivo to staphylococcal abscesses during infection. However, the staphylococcal adaptations that provide defense against nutritional immunity and the role of metal-responsive regulators are not fully characterized. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27158

36 Samples

Download data: XLSX

(Submitter supplied) Cas9 is a transcriptional autoregulator in many strains of S. pyogenes. A natural single guide RNA (tracr-L) directs Cas9 to bind to and repress its promoter. In this study, we aimed to determine whether tracr-L, crRNAs, or other noncanonical guide RNAs direct Cas9 to bind to other regions of the genome and potentially regulate the expression of additional genes.

Organism:

Streptococcus pyogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28678

18 Samples

Download data: SF

(Submitter supplied) Cas9 is a transcriptional autoregulator in many strains of S. pyogenes. A natural single guide RNA (tracr-L) directs Cas9 to bind to and repress its promoter. In this study, we aimed to determine whether tracr-L, crRNAs, or other noncanonical guide RNAs direct Cas9 to bind to other regions of the genome and potentially regulate the expression of additional genes.

Organism:

Streptococcus pyogenes

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19982

12 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Polyamines, crucial molecules involved in cell proliferation and growth, play a pivotal role in cancer development and progression. Within the tumor microenvironment, macrophages, key components of the immune system, exhibit a complex relationship with polyamines. Evidence suggests that polyamines can modulate macrophage polarization, influencing their functional phenotypes. Here, we detected the gene DNA methylation changes in spermine-stimulated human macrophages isolated from PBMCs and TAMs.

Organism:

Leptospira interrogans; Rickettsia typhi; Mycobacterium tuberculosis variant bovis; Mycobacterium tuberculosis; Mycobacterium tuberculosis variant microti; Mycobacterium canetti; Orthohantavirus seoulense; Yersinia pseudotuberculosis; Rickettsia prowazekii; Bartonella quintana; Mycobacterium avium; Homo sapiens; Streptobacillus moniliformis; Bartonella henselae; Francisella tularensis subsp. tularensis; Francisella tularensis subsp. holarctica; Campylobacter jejuni; Francisella tularensis subsp. novicida; Yersinia pestis; Staphylococcus aureus; Mycobacterium avium subsp. paratuberculosis; Cowpox virus; Escherichia coli O157:H7; Francisella tularensis subsp. mediasiatica; Paslahepevirus balayani; Yersinia enterocolitica; Toxoplasma gondii; Salmonella enterica subsp. enterica serovar Typhimurium; Mammarenavirus choriomeningitidis; Orthohantavirus puumalaense

Type:

Methylation profiling by array

Platform:

GPL21445

4 Samples

Download data: IDAT, TXT

(Submitter supplied) Regulation of M. abscessus gene expression in WT or dosR mutant and treated with artemisinin

Organism:

Mycobacteroides abscessus ATCC 19977

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30122

8 Samples

Download data: XLSX

(Submitter supplied) To investigate the in vivo functions of RecJ and RecJ-like, we conducted transcriptome analyses on the wild-type (WT), drrecJ deletion mutant (△J), drrecJ-like deletion mutant (△J-like), and drrecJ-like/recJ double deletion mutant (△J/△J-like) strains. The results of the transcriptome analysis reveal a nuanced interplay between these two proteins in vivo, encompassing both overlapping and antagonistic functions. more...

Organism:

Deinococcus radiodurans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31018

4 Samples

Download data: TXT

(Submitter supplied) The eukaryotic GID/CTLH complex is a highly conserved E3 ubiquitin ligase involved in a broad range of biological processes. However, a role of this complex in host antimicrobial defenses has not been described. We exploited Mycobacterium tuberculosis (Mtb) induced cytotoxicity in macrophages in a FACS based CRISPR genetic screen to identify host determinants of intracellular Mtb growth restriction. more...

Organism:

Mus musculus; Mycobacterium tuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34461

12 Samples

Download data: TXT

(Submitter supplied) The goal of this experiment is to determine the overall relative strength of promoter sequences in Mycoplasma feriruminatoris. For this, 2 replicates were grown in parallel in Hayflick media and the RNA wa extracted at exponential growth phase (20 hours). With this data, new promoter sequences could be designed and further validated by the use of RT-qPCR and reporter assays.

Organism:

Mycoplasma feriruminatoris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33858

2 Samples

Download data: CSV

(Submitter supplied) Extracellular vesicles (EVs) are released by most cell types and are implicated in several biological and pathological processes, including multiple sclerosis (MS). In this study we performed RNA sequencing to analyze the diversity of microorganisms by assignment of reads using different taxa profilers. To diminish the risk of false positive biases derived from sample handling, we performed a similar analysis on EVs derived from known cultured bacterial species, as well as artificially-generated samples. more...

Organism:

Lactobacillus acidophilus; Homo sapiens; Bifidobacterium animalis subsp. lactis; synthetic construct

Type:

Expression profiling by high throughput sequencing

4 related Platforms

15 Samples

Download data: CSV

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

Organism:

Escherichia coli; Clostridium senegalense

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL34292 GPL21222

8 Samples

Download data: BW

(Submitter supplied) TnpB nucleases represent the evolutionary precursors to CRISPR-Cas12 and are widespread in all domains of life. IS605-family TnpB homologs function in bacteria as programmable RNA-guided homing endonucleases driving transposon maintenance through DSB-stimulated homologous recombination. Here we uncover molecular mechanisms of transposition lifecycle of IS607-family elements that, remarkably, also encode group I introns. more...

Organism:

Escherichia coli; Clostridium senegalense

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34292 GPL21222

4 Samples

Download data: BW

(Submitter supplied) Understanding the regulatory roles of small RNAs (sRNAs) in Mycobacterium marinum is crucial for elucidating its pathogenesis. Here, we present transcriptome profiles of M. marinum strains with deletions and completions of sRNA B11. Through RNA sequencing analysis, we identified significant alterations in gene expression patterns between the B11-deleted and completed strains.

Organism:

Mycobacterium marinum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34399

6 Samples

Download data: RTF

(Submitter supplied) Photoautotrophic cyanobacteria assimilate the greenhouse gas carbon dioxide as their sole carbon source for producing useful bioproducts. However, harvesting the cells from their liquid media is a major bottleneck in the process. Thus, an easy-to-harvest method, such as auto-flocculation, is desirable. Here, we found that cyanobacterium Synechocystis sp. PCC 6803 co-flocculated with a natural fungal contamination in the presence of the antibiotic erythromycin (EM) but not without EM. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28944

6 Samples

Download data: TXT

(Submitter supplied) Photoautotrophic cyanobacteria assimilate the greenhouse gas carbon dioxide as their sole carbon source for producing useful bioproducts. However, harvesting the cells from their liquid media is a major bottleneck in the process. Thus, an easy-to-harvest method, such as auto-flocculation, is desirable. Here, we found that cyanobacterium Synechocystis sp. PCC 6803 co-flocculated with a natural fungal contamination in the presence of the antibiotic erythromycin (EM) but not without EM. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28944

6 Samples

Download data: TXT

(Submitter supplied) Transcriptomic analysis of suspended and flocculated (with the fungi) Synechocystis cells suggested that the EM-mediated co-flocculation was a result of down-regulation of the minor pilin genes and up-regulation of several genes including the chaperone gene for pilin regulation, the S-layer protein genes, the exopolysaccharide-polymerization gene, and the genes for signaling proteins involved in cell attachment and abiotic-stress responses. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28944

6 Samples

Download data: TXT