GEO DataSets

(Submitter supplied) Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based, transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hindered by the massive density of bacterial mRNA. To overcome this challenge, we combine 1000-fold volumetric expansion with multiplexed error robust fluorescence in situ hybridization (MERFISH) to create bacterial-MERFISH, a method enabling high-throughput, spatially resolved profiling of thousands of operons within individual bacteria. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21117 GPL26592

3 Samples

Download data: FASTA, SF

(Submitter supplied) Vibrio vulnificus (V. vulnificus) is an opportunistic human pathogen known for causing various illnesses such as gastroenteritis, skin and muscle necrosis, septic shock, and sepsis. This halophilic estuarine bacterium's growth and infection process involves adaptation to both the natural briny environments and the host. OmpR, a response regulator in the EnvZ/OmpR two-component regulatory system (TCS), is crucial for environmental adaptation and pathogenicity. more...

Organism:

Vibrio vulnificus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL35086

6 Samples

Download data: TXT

(Submitter supplied) Polymyxin B is considered as a last-resort antibiotic for multidrug-resistant or extensively drug-resistant gram-negative bacterial infections. Addressing Salmonella resistance to polymyxin B is crucial for global public health. In this study, transcriptomic detection and analysis were used to clarify the mechanisms by which CpxA-deleted S.typhimurium is involved in resistance to polymyxin B stress, which may be related to processes such as increased assembly of bacterial flagella.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL35078

6 Samples

Download data: XLS

(Submitter supplied) In our previous work, we found that the root exudates of sgn3 myb36 promoted the colonization of CHA0 on roots. Through LC-MS, we identified a large amount of glutamine (Gln) in the root exudates of sgn3 myb36. Therefore, we aim to use RNA-seq to uncover whether the root exudates of sgn3 myb36 and Gln have the same regulatory effects on CHA0. By conducting differential analysis with the CK (CHA0 treated with wild-type root exudates), we hope to identify the specific regulatory mechanisms of sgn3 myb36 and Gln on CHA0.

Organism:

Pseudomonas protegens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL35063

9 Samples

Download data: CSV

(Submitter supplied) To study the biological function of the novel 3′ UTR-derived sRNA, ManS, originating from a S. enterica-specific genomic island, STM1127-STM1131, we conducted RNA-pulse expression combined with RNA sequencing to screen for mRNAs repressed by ManS. Additionally, we compared the transcriptomic changes between wild-type and ManS-deleted strains during N-acetylmannosamine (ManNAc) metabolism.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31144

10 Samples

Download data: TXT

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

Organism:

Escherichia coli; Streptococcus agalactiae

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL28679 GPL25368 GPL29157

26 Samples

Download data

(Submitter supplied) Bacterial CRISPR-Cas9 immune systems protect against foreign DNA. However, immune efficiency is constrained by Cas9 off-target effects and toxicity. Here, we demonstrate that CRISPR-Cas9 immunity is regulated by CovR, the major regulator of virulence in Group B Streptococcus, a pathobiont responsible for neonatal invasive infections. We show that CovR binds to and represses a distal promoter of the cas operon, embedding immunity in the virulence regulatory network. more...

Organism:

Escherichia coli; Streptococcus agalactiae

Type:

Other

Platforms:

GPL28679 GPL25368

8 Samples

Download data: XLSX

(Submitter supplied) RNA-seq analysis of Pseudomonas sp OST1909 exposed to various preparations of naphthenic acids samples led to the identiifcation of many NA-induced genes.

Organism:

Pseudomonas sp. OST1909

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34317

8 Samples

Download data: TSV

(Submitter supplied) Pathogenic bacteria sense and respond to environmental fluctuations, a capability essential for establishing successful infections. The YmoA/Hha protein family are conserved transcription regulators in Enterobacteriaceae, playing a critical role in these responses. Specifically, YmoA in Yersinia adjusts the expression of virulence-associated traits upon temperature shift. Still, the molecular mechanisms transducing environmental signals through YmoA remain elusive. more...

Organism:

Yersinia pseudotuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL35020

9 Samples

Download data: TXT

(Submitter supplied) The heterogeneity of bacterial cells in biofilms is an important property. We performed single-cell sequencing to profile heterogeneous cell populations within Vibrio alginolyticus biofilm. Our analysis has revealed the key functional compartments for the composition and development of biofilms

Organism:

Vibrio alginolyticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32345

1 Sample

Download data: MTX, TSV

(Submitter supplied) Whether the emergence of a nascent protein from the ribosome and the formation of structural elements are synchronized has been a longstanding question. Paradoxically, kinetically efficient translation can induce mis-folding and aggregation despite the presence of molecular chaperones, which in Escherichia coli are induced by unfolded protein via σ32. The molecular mechanisms mediating translation efficiency and protein folding efficiency remain poorly understood. more...

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL18956 GPL18133

30 Samples

Download data: TSV

(Submitter supplied) Using transcriptomics, we studied the transcriptional response of Vibrio cholerae to 10 min of exogenously supplied peptidoglycan at 300 µg/mL.

Organism:

Vibrio cholerae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30059

6 Samples

Download data: XLSX

(Submitter supplied) Salmonella enterica serovar Typhimurium (S. Typhimurium) infection triggers an inflammatory response that changes the concentration of luminal metabolites in the gut, resulting in a distinct environment from a healthy one. We recently demonstrated that S. Typhimurium possesses the ability to form biofilms within the host environment and responds to nitrate as a signaling molecule, enabling it to modulate the transition between sessile and planktonic states. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33626

6 Samples

Download data: XLSX

(Submitter supplied) The effectiveness of antibacterial agents is strongly influenced by its antibacterial mechanism, which, in turn, is dependent on the agent’s topological structure. In addition to oxidative stress (especially caused by reactive oxygen species), known to be a key mechanism for 2D phosphorene structures, physical penetration of bacterial cell membranes is predicted for violet phosphorene nanosheets. In this study, we demonstrate that violet phosphorus (VP) and its exfoliated product, violet phosphorene nanosheets (VPNS), have superior antibacterial capability against pathogens.A series of antibacterial tests and theoretical calculations show that VPNS can inactivate >99.9% of two common pathogens (Escherichia coli and Staphylococcus aureus) and >99% of two “superbugs” (i.e., antibiotic-resistant bacteria, Escherichia coli pUC19 and methicillin-resistant Staphylococcus aureus) via oxidative stress combined with cell membrane penetration by VPNS Moreover, VPNS have higher antibacterial activity than black phosphorene nanosheets in vitro and in vivo. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

6 Samples

Download data: TXT

(Submitter supplied) Vibrio cholerae harbours a primary chromosome derived from the monochromosomal ancestor of the Vibrionales (ChrI) and a secondary chromosome derived from a megaplasmid (ChrII). Both carry a single origin of replication with replication terminating in a diametrically opposite zone, TerI and TerII, respectively. The choreography of TerI and TerII segregation determines when and where cell division occurs. more...

Organism:

Vibrio cholerae

Type:

Other

Platforms:

GPL34020 GPL25005

23 Samples

Download data: FA, TXT

(Submitter supplied) Vibrio cholerae harbours a primary chromosome derived from the monochromosomal ancestor of the Vibrionales (ChrI) and a secondary chromosome derived from a megaplasmid (ChrII). Both carry a single origin of replication with replication terminating in a diametrically opposite zone, TerI and TerII, respectively. The choreography of TerI and TerII segregation determines when and where cell division occurs. more...

Organism:

Vibrio cholerae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL31913

14 Samples

Download data: FA, TXT

(Submitter supplied) Vibrio cholerae harbours a primary chromosome derived from the monochromosomal ancestor of the Vibrionales (ChrI) and a secondary chromosome derived from a megaplasmid (ChrII). Both carry a single origin of replication with replication terminating in a diametrically opposite zone, TerI and TerII, respectively. The choreography of TerI and TerII segregation determines when and where cell division occurs. more...

Organism:

Vibrio cholerae

Type:

Other

Platform:

GPL19265

2 Samples

Download data: FA, MATRIX

(Submitter supplied) We present genome-wide RpoD-family sigma factors (RpoD, RpoS, and RpoH) binding profiles and transcriptome profiles in Salmonella Typhimurium 14028s under both control (37°C) and sublethal heat shock conditions (42°C). These genome-scale experimental data show how three RpoD-family sigma factors simultaneously coordinate many types of cellular processes to orchestrate the overall response of S. Typhimurium to heat stress.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL28222

12 Samples

Download data: XLSX

(Submitter supplied) We present genome-wide RpoD-family sigma factors (RpoD, RpoS, and RpoH) binding profiles and transcriptome profiles in Salmonella Typhimurium 14028s under both control (37°C) and sublethal heat shock conditions (42°C). These genome-scale experimental data show how three RpoD-family sigma factors simultaneously coordinate many types of cellular processes to orchestrate the overall response of S. Typhimurium to heat stress.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28222

8 Samples

Download data: TSV

(Submitter supplied) Metagenome sequencing enables discovery and genetic characterization of complex microbial communities from diverse ecosystems. However, determining the activity of isolates within a community using transcriptomics presents several challenges including the wide dynamic range of organismal and gene expression abundances, the presence of host RNA, and low microbial biomass at many body sites. To address these limitations, we developed “Targeted Expression Analysis Sequencing” or TEAL-seq. more...

Organism:

Staphylococcus epidermidis; Homo sapiens; Escherichia coli; Staphylococcus aureus; Mus musculus

Type:

Expression profiling by high throughput sequencing

6 related Platforms

129 Samples

Download data: XLSX