GEO DataSets

(Submitter supplied) The Enterobacteriaceae are a scientifically and medically important clade of bacteria, containing the gut commensal and model organism Escherichia coli, as well as several major human pathogens including Salmonella enterica and Klebsiella pneumoniae. Essential gene sets have been determined for several members of the Enterobacteriaceae, and the E. coli Keio single-gene deletion library is often regarded as a gold standard for gene essentiality studies. more...

Organism:

Enterobacter cloacae; Escherichia coli; Salmonella enterica subsp. enterica serovar Typhimurium; Klebsiella pneumoniae; Citrobacter rodentium; Salmonella enterica subsp. enterica serovar Enteritidis

Type:

Other

8 related Platforms

13 Samples

Download data: TXT, XLSX

(Submitter supplied) This study characterized the involvement of yihO and yihQ of yih operon associated with O-antigen capsule formation, in phenotypic characteristics, intracellular survival, and virulence in Salmonella Typhimurium (ST). Bacterial fitness screening of the ∆yihO, ∆yihQ, and ∆yihO/Q ST mutants showed impairment in biofilm formation, motility, starvation, and stress survival. In vitro studies using phagocytic and non-phagocytic cells revealed a significant decrease in bacterial invasion and intracellular replication, particularly by the ∆yihO and ∆yihO/Q ST which correlated with the lack of proliferation ability in vivo as observed in the liver and spleen colonization. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30218

4 Samples

Download data: XLSX

(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; 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; Yersinia pseudotuberculosis; Rickettsia prowazekii; Bartonella quintana; Mycobacterium avium; Homo sapiens; Streptobacillus moniliformis; Bartonella henselae; Francisella tularensis subsp. tularensis; Francisella tularensis subsp. holarctica

Type:

Methylation profiling by array

Platform:

GPL21445

4 Samples

Download data: IDAT, TXT

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

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL21220 GPL17070

132 Samples

Download data

(Submitter supplied) RNA decay is a crucial mechanism for regulating gene expression in response to environmental stresses. In bacteria, RNA-binding proteins (RBPs) are known to be involved in post-transcriptional regulation, but their global impact on RNA half-lives has not been extensively studied. To shed light on the role of the major RBPs ProQ and CspC/E in maintaining RNA stability, we performed RNA sequencing of Salmonella enterica over a time course following treatment with the transcription initiation inhibitor rifampicin (RIF-seq) in the presence and absence of these RBPs. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17070

120 Samples

Download data: CSV

(Submitter supplied) RNA decay is a crucial mechanism for regulating gene expression in response to environmental stresses. In bacteria, RNA-binding proteins (RBPs) are known to be involved in post-transcriptional regulation, but their global impact on RNA half-lives has not been extensively studied. To shed light on the role of the major RBPs ProQ and CspC/E in maintaining RNA stability, we performed RNA sequencing of Salmonella enterica over a time course following treatment with the transcription initiation inhibitor rifampicin (RIF-seq) in the presence and absence of these RBPs. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Other

Platform:

GPL21220

12 Samples

Download data: CSV, GFF

(Submitter supplied) An ex vivo system was developed to monitor Salmonella growth, virulence (SPI1 expression) and gene expression (measured by microarray) in response to the permissive and exclusive communities. Yellow fluorescent protein (yfp) and cyan fluorescent protein (cfp) variants were fused to the rrn growth-dependent promoter and the hilA operon (SPI-1 cell invasion locus), respectively, in Salmonella. Fluorescence associated with the YFP and CFP reporters was used to monitor Salmonella growth and SPI1 virulence gene expression in co-culture with cecal communities ex vivo. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium; Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Type:

Expression profiling by array

Platform:

GPL14855

11 Samples

Download data: XYS

(Submitter supplied) Antisense oligomer (ASO)-based antibiotics that target mRNAs of essential bacterial genes bear great potential in the fight against antimicrobial resistance and for precision microbiome editing. The development of such antisense antibiotics has primarily focused on using phosphoramidite morpholino (PMO) and peptide nucleic acid (PNA) backbones, largely ignoring the growing number of chemical modalities that have spurred the success of ASO-based therapy in general. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21220

20 Samples

Download data: TSV

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

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30637

396 Samples

Download data

(Submitter supplied) In this work, we have improved our previously published bacterial single-cell RNA-sequencing protocol (MATQ-seq), providing enhancements that achieve a higher cell throughput while also including integration of automation. We selected a more efficient reverse transcriptase which led to a lower drop-out rate and higher workflow robustness, and we also successfully implemented a Cas9-based ribosomal RNA depletion protocol into the MATQ-seq workflow. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30637

384 Samples

Download data: TSV

(Submitter supplied) In this work, we have improved our previously published bacterial single-cell RNA-sequencing protocol (MATQ-seq), providing enhancements that achieve a higher cell throughput while also including integration of automation. We selected a more efficient reverse transcriptase which led to a lower drop-out rate and higher workflow robustness, and we also successfully implemented a Cas9-based ribosomal RNA depletion protocol into the MATQ-seq workflow. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30637

12 Samples

Download data: TSV

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

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24107 GPL19057 GPL27640

72 Samples

Download data: TXT

(Submitter supplied) Intracellular pathogens, such as Salmonella enterica serovar Typhimurium (S.Tm), are able to sense and respond to a changing host cell environment. Macrophages exposed to microbial products undergo metabolic changes that are increasingly understood to drive a productive inflammatory response. However, the role of macrophage metabolic reprogramming in bacterial adaptation to the intracellular environment has not been explored. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27640

6 Samples

Download data: TXT

(Submitter supplied) Intracellular pathogens, such as Salmonella enterica serovar Typhimurium (S.Tm), are able to sense and respond to a changing host cell environment. Macrophages exposed to microbial products undergo metabolic changes that are increasingly understood to drive a productive inflammatory response. However, the role of macrophage metabolic reprogramming in bacterial adaptation to the intracellular environment has not been explored. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27640

12 Samples

Download data: TXT

(Submitter supplied) Intracellular pathogens, such as Salmonella enterica serovar Typhimurium (S.Tm), are able to sense and respond to a changing host cell environment. Macrophages exposed to microbial products undergo metabolic changes that are increasingly understood to drive a productive inflammatory response. However, the role of macrophage metabolic reprogramming in bacterial adaptation to the intracellular environment has not been explored. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24107 GPL19057

54 Samples

Download data: TXT

(Submitter supplied) To investigate the effects of MccY on Salmonella Typhimurium, Ton system genes mutants were constructed and RNA-seq analysis were performed.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30218

12 Samples

Download data: XLSX

(Submitter supplied) Upon entering host cells, Salmonella quickly turn off flagella biogenesis to avoid recognition by the host immune system. However, it is not clear which host signal(s) Salmonella senses to initiate flagellum control.During the infection of a host,acid pH acts as an important environmental factor to triggers some genes expression. To investigate the effect of environmental acid signaling on the regulation of Salmonella flagella synthesis, we cultivated Salmonella typhimurium ATCC 14028s to an OD600 of 0.4, and then continued to culture for 2 h at pH 7.0 or pH 5.0. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30218

6 Samples

Download data: TXT

(Submitter supplied) Physical forces associated with spaceflight and spaceflight analogue culture regulate a wide range of physiological responses by both bacterial and mammalian cells that can impact infection. However, our mechanistic understanding of how these environments regulate host-pathogen interactions in humans is poorly understood. Using a spaceflight analogue low fluid shear culture system, we investigated the effect of Low Shear Modeled Microgravity (LSMMG) culture on the colonization of Salmonella Typhimurium in a 3-D biomimetic model of human colonic epithelium containing macrophages. more...

Organism:

Homo sapiens; Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28222 GPL28223 GPL21697

72 Samples

Download data: TXT

(Submitter supplied) RNA sequencing (RNA-seq) is the gold standard for the discovery of small non-coding RNAs. Following a long-standing approach, reads shorter than 16 nucleotides (nt) are removed from the small RNA sequencing libraries or datasets. The serendipitous discovery of a 12 nt-long RNA species capable of modulating the microRNA from which they derive prompted us to challenge this dogma, and by expanding the window of RNA sizes down to 8 nt, to confirm the existence of functional very small RNAs (vsRNAs <16nt). more...

Organism:

Legionella pneumophila; synthetic construct; Salmonella enterica subsp. enterica serovar Typhimurium; Pseudomonas aeruginosa PA7; Pseudomonas aeruginosa PAO1; Escherichia coli str. K-12 substr. MG1655; Staphylococcus aureus

Type:

Non-coding RNA profiling by high throughput sequencing

7 related Platforms

12 Samples

Download data: FA, PDF

(Submitter supplied) Plasmid maintenance costs to bacterial hosts is closely linked to the mechanisms that underlie plasmid fitness and how these costs are resolved. Herein, we performed multiple (63) serial passage to explore the compensatory mechanisms of co-evolution of multidrug-resistant IncHI2 plasmid pJXP9 and S. Typhimurium strain ATCC 14028 with or without antibiotic selection. pJXP9 could be maintained at for hundreds of generations even without drug exposure. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17070

8 Samples

Download data: TXT