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GEO DataSets

Functional Genomics Studies

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Items: 1 to 20 of 150994

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Select item 2002996701.

Impact of Electric Potential on the Transcriptome of Paracoccus denitrificans in denitrification Conditions

(Submitter supplied) This study aimed to evaluate the transcriptomic response of Paracoccus denitrificans PD1222 exposed to an applied electric potential of +200 mV under aerobic denitrification conditions. RNA-seq analysis was conducted on five biological samples: three independent replicates under 200 mV and two control samples at 0 mV. Differential gene expression changes revealed genes associated with amino acid metabolism, carbohydrate metabolism, membrane transport, and energy metabolism.

Organism:: Paracoccus denitrificans PD1222

Type:: Expression profiling by high throughput sequencing

Platform:: GPL35941
5 Samples

Download data: TXT

Series

Accession:: GSE299670

ID:: 200299670

Select item 2002812612.

Tungsten is Utilized for Lactate Consumption and SCFA Production by a Dominant Human Gut Microbe Eubacterium limosum

(Submitter supplied) Eubacterium limosum is a dominant member of the human gut microbiome and produces short-chain fatty acids (SCFAs). These promote immune system function and inhibit inflammation, making this microbe important for human health. Lactate is a primary source of gut SCFAs but its utilization by E. limosum has not been explored. We show that E. limosum growing on lactate takes up added tungstate rather than molybdate and produces the SCFAs acetate and butyrate, but not propionate. more...

Organism:: Eubacterium limosum

Type:: Expression profiling by high throughput sequencing

Platform:: GPL35080
12 Samples

Download data: TXT

Series

Accession:: GSE281261

ID:: 200281261

Select item 2003012523.

A widely-occurring family of pore-forming effectors broadens the impact of the Serratia Type VI secretion system

(Submitter supplied) The ability to compete with diverse competitors is essential for bacteria to succeed in microbial communities. A widespread strategy for inter-bacterial competition is the delivery of antibacterial toxins, or effector proteins, directly into rival cells using the Type VI secretion system (T6SS). Whilst a large number of broad-spectrum enzymatic T6SS effectors have been described, relatively few which form pores in target cell membranes have been reported. more...

Organism:: Pseudomonas simiae

Type:: Other

Platform:: GPL35988
9 Samples

Download data: XLSX

Series

Accession:: GSE301252

ID:: 200301252

Select item 2002944684.

Influenza A virus modulation of Streptococcus pneumoniae infection using ex vivo transcriptomics in a human primary lung epithelial cell

(Submitter supplied) Nanostring validation of deep sequencing of cDNA from Streptococcus pneumoniae EF3030 bacteria and normalized human broncial epithelial cells (nHBEC), together, and after coincubation with Influenza A virus pH1N1. (Accession:GSE225108)

Organism:: Influenza A virus; Streptococcus pneumoniae; Homo sapiens

Type:: Expression profiling by array

Platform:: GPL35757
12 Samples

Download data: RCC

Series

Accession:: GSE294468

ID:: 200294468

Analyze with GEO2R

Select item 2002696535.

Identification of strong constitutive promoters in Burkholderia to activate natural product production in Gram-negative bacteria

(Submitter supplied) Gram-negative bacteria are an emerging source of natural products with pharmaceutical potential. However, the limited availability of essential genetic tools for drug discovery and sustainable production remains a challenge. Burkholderia serves as a promising source for such tools, as it produces diverse natural products and can be experimentally manipulated in the laboratory. Hence, this study aimed to identify strong and constitutive promoters from Burkholderia stagnalis TBRC 18363 for unlocking the potential of cryptic biosynthetic genes and enhance natural product production. more...

Organism:: Burkholderia stagnalis

Type:: Expression profiling by high throughput sequencing

Platform:: GPL34582
18 Samples

Download data: CSV, CT

Series

Accession:: GSE269653

ID:: 200269653

Select item 2002862936.

A small cationic probe highly selective for RNA tertiary structure

(Submitter supplied) RNA is unique among the large biomolecules due to the intersection of its distinctive electrostatic properties, created by the permanent charge at each phosphate group, coupled with its ability to form diverse three-dimensional tertiary structures. We demonstrate that at rare, but distinctive, sites tertiary folding creates electronegative pockets that preferentially react with a small positively-charged chemical probe, trimethyloxonium (TMO), which alkylates RNA. more...

Organism:: Oceanobacillus iheyensis; Orthoflavivirus denguei; Geobacillus stearothermophilus; Escherichia coli

Type:: Other

4 related Platforms
41 Samples

Download data: TXT

Series

Accession:: GSE286293

ID:: 200286293

Select item 2002457547.

CRISPR RNA and tracrRNA serve as a regulatory switch for apoCas9-mediated viral memorization in Neisseria

(Submitter supplied) Prokaryotes adapt to viral challenges by acquiring CRISPR memories from invaders through a process called adaptation. Previous study showed that this process requires Cas9 complexed with its RNA partners in type II-A system. How Cas9 functions in adaptation in other type II systems is poorly understood. Here using type II-C system of N. meningitidis and meningococcal disease associated filamentous phage MDAΦ as model, we show that RNA free apoCas9 dramatically enhances adaptation efficiency and that tracrRNA and crRNA together repress rather than enhance adaptation through interacting with Cas9. more...

Organism:: Neisseria meningitidis

Type:: Other

Platform:: GPL32230
79 Samples

Download data: CSV, FA

Series

Accession:: GSE245754

ID:: 200245754

PubMed Full text in PMC

Select item 2001603488.

Genome-wide transcriptional profiling of Bacillus subtilis in response to Hermetia illucens larvae extract

(Submitter supplied) The black soldier fly, Hermetia illucens, is a promising source for sustainable production of proteins, lipids and bioactive substances. Feeding on a variety of decomposing organic substrates which are typically inhabited by a range of different microorganisms like bacteria and fungi, H. illucens larvae is expected to be able to strongly produce antimicrobial peptides (AMPs) and other substances possessing antibiotic activity. more...

Organism:: Bacillus subtilis

Type:: Expression profiling by high throughput sequencing

Platform:: GPL29318
6 Samples

Download data: BW, TXT, XLSX

Series

Accession:: GSE160348

ID:: 200160348

SRA Run Selector

Select item 2001603479.

Transcriptomic study of Bacillus subtilis lacking seven extracytoplasmic function (ECF) σ factors

(Submitter supplied) Bacillus subtilis encodes seven extracytoplasmic function (ECF) σ factors, σM, σW, σX, σY, σZ, σV and σYlaC, that mediate response to cell envelop-active compounds. In this study, we aimed to define the transcriptomic differences between B. subtilis W168 wild type and the derivative 168 Δ7ECF mutant lacking seven ECF sigma factors under unstressed condition, which allows to identify the genes under control of these seven ECF sigma factors. more...

Organism:: Bacillus subtilis

Type:: Expression profiling by high throughput sequencing

Platform:: GPL29318
12 Samples

Download data: BW, TXT, XLSX

Series

Accession:: GSE160347

ID:: 200160347

SRA Run Selector

Select item 20016034610.

Genome-wide Transcriptional Profiling of Bacillus subtilis in response to valinomycin and CCCP

(Submitter supplied) Valinomycin is a cyclic depsipeptide antibiotic produced by Streptomyces fulvissimus, and also known as K+ ion-selective ionophore, that has been studied and used in research for over half of century. The broad antimicrobial activity of valinomycin is reported as an effect of the disturbance of ionic equilibrium and transmembrane potential that may influence the whole organism and then cause fatal consequences. more...

Organism:: Bacillus subtilis

Type:: Expression profiling by high throughput sequencing

Platform:: GPL29318
15 Samples

Download data: BW, TXT, XLSX

Series

Accession:: GSE160346

ID:: 200160346

SRA Run Selector

Select item 20027568211.

Diel expression dynamics in filamentous cyanobacteria

(Submitter supplied) Filamentous cyanobacteria of the Nostocaceae family are able to differentiate into multicellular forms to adapt to environmental stresses, and members can establish symbiosis with various embryophytes. Representative laboratory strains are typically grown under continuous light to maintain stable metabolic conditions, however, this departure from a natural diel cycle can result in extended stress. Early genomic examination of Nostoc punctiforme suggests the genetic potential for a circadian clock, but we lack insight into global cellular dynamics through the natural diel cycle for this model organism. more...

Organism:: Nostoc punctiforme PCC 73102

Type:: Expression profiling by high throughput sequencing

Platform:: GPL30445
36 Samples

Download data: CSV

Series

Accession:: GSE275682

ID:: 200275682

Select item 20028597112.

Overlooked contributions of ionic strength to cell envelope dynamics modulating outer membrane vesiculation and metal mineralization

(Submitter supplied) Electrically active Geobacter bacteria assemble conductive pili and release redox-active outer membrane vesicles to drive metal transformations critical to environmental and energy systems. Mechanistic understanding of these processes largely derives from studies of Geobacter sulfurreducens cultivated in mineral media that mimic natural geochemical conditions. Here, we show that modest drops (90 to 80 mM) in sodium ionic strength of common media did not impact cell permeability, but stimulated vesiculation, growth, and covalent anchoring of the outer membrane to the cell wall via a long Lpp peptide to accommodate cell wall expansions and periplasmic enlargement. more...

Organism:: Geobacter sulfurreducens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL35267
6 Samples

Download data: TSV, XLSX

Series

Accession:: GSE285971

ID:: 200285971

Select item 20029339413.

Structural mechanism of the Retron-Eco7 anti-phage defense system

(Submitter supplied) Retrons are prokaryotic genetic elements involved in anti-phage defense and consist of a non-coding RNA, a reverse transcriptase (RT), and various effector proteins. Retron-Eco7 (previously known as Retron-Ec78) from Escherichia coli encodes two effector proteins (a PtuA ATPase and a PtuB nuclease) and degrades host tRNATyr upon phage infection, thereby protecting host cells against invading phages. more...

Organism:: Escherichia coli str. K-12 substr. DH10B

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL35303
8 Samples

Download data: XLSX

Series

Accession:: GSE293394

ID:: 200293394

Select item 20028459414.

Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome

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

Organism:: Escherichia coli; Thermoplasma acidophilum; Planococcus halocryophilus; Bacillus subtilis; Pyrococcus furiosus; Saccharomyces cerevisiae; Salmonella enterica; Pseudomonas aeruginosa; Homo sapiens; Pyrodictium abyssi; Acetivibrio thermocellus; Haloferax volcanii; Sulfolobus acidocaldarius; Thermococcus kodakarensis

Type:: Expression profiling by high throughput sequencing

16 related Platforms
1540 Samples

Download data: TAB

Series

Accession:: GSE284594

ID:: 200284594

Select item 20029389515.

Identification of Three New Rugose Small Colony Variants from the Pseudomonas aeruginosa PA14 Biofilm

(Submitter supplied) Pseudomonas aeruginosa is a gram-negative, pathogenic, bacterium that produces biofilms containing phenotypically distinct subpopulations (Dodson et al., 2022). It was discovered that rugose small colony variants (RSCVs) were isolated with the biofilm subpopulations. RSCVs are hyper-biofilm producing bacterial mutants with increased antibiotic tolerance and are often found in chronic infections. When separating and characterizing the three biofilm cell subpopulations from a single P. more...

Organism:: Pseudomonas aeruginosa

Type:: Expression profiling by high throughput sequencing

Platform:: GPL34956
9 Samples

Download data: CSV

Series

Accession:: GSE293895

ID:: 200293895

Select item 20030003716.

Specific targeting of transcriptional T-box riboswitches leads to effective inhibition of S. aureus

(Submitter supplied) T-box riboswitches belong to a specific class of RNA regulatory elements that control gene expression in Gram-positive bacteria, including prominent human pathogens. They sense the availability of amino acids by detecting the aminoacylation status of their cognate tRNAs and regulate the expression of genes involved in aminoacylation, amino acid transport, and metabolism. Recent advances on the structures and mechanisms of several regulatory non-coding RNAs among pathogenic bacteria have garnered attention for the development of a new generation of species-specific antibacterials. more...

Organism:: Staphylococcus aureus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL35257
4 Samples

Download data: XLSX

Series

Accession:: GSE300037

ID:: 200300037

PubMed

Select item 20030555617.

Mechanisms of assembly and function of the Hsp70-Hsp40 chaperone machinery

(Submitter supplied) The orchestration of protein folding and maintenance by molecular chaperones is crucial for cellular homeostasis. Among them, Hsp70 and its co-chaperone Hsp40 form a central machinery that remodels client proteins involved in numerous biological processes. Despite their essential role, how Hsp70 and Hsp40 assemble into a functional complex has remained elusive. Here, we integrated cryo-electron microscopy and nuclear magnetic resonance spectroscopy to determine the architecture of the full-length Hsp70-Hsp40 machinery. more...

Organism:: Escherichia coli str. K-12 substr. MG1655

Type:: Other

Platform:: GPL29216
12 Samples

Download data: H5

Series

Accession:: GSE305556

ID:: 200305556

Select item 20027597218.

Pseudomonas aeruginosa clinical isolates can encode functional plastic degrading enzymes that allow survival on plastic and augment biofilm formation

(Submitter supplied) Several environmental bacteria encode plastic-degrading enzymes, a potential evolutionary response to the rapid introduction of plastic across global ecosystems. Given the widespread use of plastic in healthcare, we hypothesised that clinical bacterial isolates may also degrade plastic, rendering plastic-containing medical devices susceptible to degradation and failure and potentially offering these pathogens a carbon source that could be used to persist in the hospital-built environment. more...

Organism:: Pseudomonas aeruginosa

Type:: Expression profiling by high throughput sequencing

Platform:: GPL33271
6 Samples

Download data: TSV

Series

Accession:: GSE275972

ID:: 200275972

Select item 20030890719.

Challenge agent strain selection and characterization for a first-in-human Salmonella Typhimurium controlled human infection model

(Submitter supplied) Nontyphoidal Salmonella (NTS) infections cause significant illness worldwide, particularly in sub-Saharan Africa, where invasive NTS (iNTS) disease leads to life-threatening bloodstream infections. Developing vaccines to prevent iNTS is a public health priority, but progress has been slow due to gaps in understanding how these bacteria cause disease and how the immune system responds. Controlled human infection models (CHIMs) can accelerate vaccine development by allowing detailed investigation of infection biology in a controlled setting. more...

Organism:: Salmonella enterica subsp. enterica serovar Typhimurium

Type:: Expression profiling by high throughput sequencing

Platform:: GPL30218
12 Samples

Download data: XLSX

Series

Accession:: GSE308907

ID:: 200308907

Select item 20028213320.

Targeted protein evolution in the gut microbiome by diversity-generating retroelements

(Submitter supplied) Diversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, suggesting they play adaptive roles in this environment. We identified >1,100 unique DGRs among human-associated Bacteroides species and discovered a subset that diversify adhesive components of Type V pili and related proteins. more...

Organism:: Bacteroides uniformis ATCC 8492; Bacteroides fragilis 638R; Bacteroides finegoldii CL09T03C10; Bacteroides thetaiotaomicron VPI-5482; Bacteroides ovatus ATCC 8483