txid90371[Organism:noexp] - GEO DataSets

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Select item 2002340101.

Improved RNA stability estimation through Bayesian modeling reveals most bacterial transcripts have sub-minute half-lives

(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:: GPL17070 GPL21220
132 Samples

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Series

Accession:: GSE234010

ID:: 200234010

Select item 2002340092.

Improved RNA stability estimation through Bayesian modeling reveals most bacterial transcripts have sub-minute half-lives [RIF-seq]

(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

Series

Accession:: GSE234009

ID:: 200234009

Select item 2002340073.

Improved RNA stability estimation through Bayesian modeling reveals most bacterial transcripts have sub-minute half-lives [CLIP-seq]

Organism:: Salmonella enterica subsp. enterica serovar Typhimurium

Type:: Other

Platform:: GPL21220
12 Samples

Download data: CSV, GFF

Series

Accession:: GSE234007

ID:: 200234007

Select item 2002614804.

Peeling back the layers of competitive exclusion using Salmonella as a model

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

Type:: Expression profiling by array

Platform:: GPL14855
11 Samples

Download data: XYS

Series

Accession:: GSE261480

ID:: 200261480

Analyze with GEO2R

Select item 2002328195.

A side-by-side comparison of peptide-delivered antisense antibiotics employing different nucleotide mimics

(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

Series

Accession:: GSE232819

ID:: 200232819

Select item 2002186336.

Improved bacterial single-cell RNA-seq through automated MATQ-seq

(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

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Series

Accession:: GSE218633

ID:: 200218633

PubMed Full text in PMC Similar studies

Select item 2002186327.

Improved bacterial single-cell RNA-seq through automated MATQ-seq [scRNA-seq]

(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

Series

Accession:: GSE218632

ID:: 200218632

PubMed Full text in PMC Similar studies

Select item 2002186318.

Improved bacterial single-cell RNA-seq through automated MATQ-seq [bulk RNA-seq]

Organism:: Salmonella enterica subsp. enterica serovar Typhimurium

Type:: Expression profiling by high throughput sequencing

Platform:: GPL30637
12 Samples

Download data: TSV

Series

Accession:: GSE218631

ID:: 200218631

PubMed Full text in PMC Similar studies

Select item 2001392089.

Host succinate is a signal for activation of Salmonella virulence during intracellular infection

(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:: GPL27640 GPL19057 GPL24107
72 Samples

Download data: TXT

Series

Accession:: GSE139208

ID:: 200139208

PubMed Similar studies

Select item 20013920710.

Host metabolic reprogramming during immune activation promotes intracellular bacterial survival (glycerol or succinate)

(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

Series

Accession:: GSE139207

ID:: 200139207

PubMed Similar studies SRA Run Selector

Select item 20013920611.

Host metabolic reprogramming during immune activation promotes intracellular bacterial survival (2DG)

Organism:: Salmonella enterica subsp. enterica serovar Typhimurium

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27640
12 Samples

Download data: TXT

Series

Accession:: GSE139206

ID:: 200139206

PubMed Similar studies SRA Run Selector

Select item 20013920512.

Host metabolic reprogramming during immune activation promotes intracellular bacterial survival (host and bacteria)

Organism:: Salmonella enterica subsp. enterica serovar Typhimurium; Mus musculus

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL19057 GPL24107
54 Samples

Download data: TXT

Series

Accession:: GSE139205

ID:: 200139205

PubMed Similar studies SRA Run Selector

Select item 20021418413.

Effect of disruption of tonB, exbB, exbD and MccY treatment on gene expression in Salmonella enterica subsp. enterica serovar Typhimurium

(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

Series

Accession:: GSE214184

ID:: 200214184

PubMed Full text in PMC Similar studies

Select item 20021057014.

Host Acid Signal Controls Salmonella Flagella Biogenesis through CadC-YdiV Axis

(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

Series

Accession:: GSE210570

ID:: 200210570

Select item 20014634715.

Spaceflight analogue culture enhances the host-pathogen interaction between Salmonella and a 3-D biomimetic intestinal co-culture model

(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:: GPL28223 GPL21697 GPL28222
72 Samples

Download data: TXT

Series

Accession:: GSE146347

ID:: 200146347

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20020075816.

RNA sequencing unveils very small RNAs with potential regulatory functions in bacteria

(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:: synthetic construct; Salmonella enterica subsp. enterica serovar Typhimurium; Pseudomonas aeruginosa PA7; Legionella pneumophila; 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

Series

Accession:: GSE200758

ID:: 200200758

PubMed Full text in PMC Similar studies

Select item 20019747517.

A trade-off for maintenance of multidrug-resistance IncHI2 plasmids in Salmonella Typhimurium through co-evolution

(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

Series

Accession:: GSE197475

ID:: 200197475

PubMed Full text in PMC Similar studies

Select item 20018042518.

Transcriptional Sequencing of Salmonella enterica serovar Typhimurium wild typle and DsrA-deletion mutant Survival unfer LB or H2O2 conditions

(Submitter supplied) To elucidated the regulatory effect of DsrA on the oxidative resistance in Salmonella enterica serovar Typhimurium. RNA sample of wild-type and DsrA-deletion strain that grown in LB medium or H2O2 stress were extracted. Three biological replicates were carried out per sample. RNA sample was sequenced with Illumina HiSeq 4000 System. DESeq2 method was used to calculate the differentially expressed genes. more...

Organism:: Salmonella enterica subsp. enterica serovar Typhimurium

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27471
12 Samples

Download data: XLS

Series

Accession:: GSE180425

ID:: 200180425

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20018557819.

PacBio SMRT-seq of wild-type, ∆metJ, and ∆dam Salmonella enterica serovar Typhimurium (14028s)

(Submitter supplied) PacBio SMRT-seq of wild-type, ∆metJ, and ∆dam Salmonella enterica serovar Typhimurium grown under SPI-1-inducing and SPI-2-inducing conditions.