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Items: 1 to 20 of 473

1.

Predicting off-target effects of antisense oligomers targeting bacterial mRNAs with the MASON webserver

(Submitter supplied) Antisense oligomers (ASOs) such as peptide nucleic acids (PNAs), designed to inhibit the translation of essential bacterial genes, have emerged as attractive sequence- and species-specific programmable RNA antibiotics. Yet, potential drawbacks include unwanted side effects caused by their binding to transcripts other than the intended target. To facilitate the design of PNAs with minimal off-target effects, we developed MASON (Make AntiSense Oligomers Now), a webserver for the design of PNAs that target bacterial mRNAs. more...
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20056
28 Samples
Download data: CSV
Series
Accession:
GSE199542
ID:
200199542
2.

Hfq RIL-seq in Salmonella

(Submitter supplied) We have used the RIL-seq technique to map the global RNA-RNA interactome on the sRNA chaperone Hfq in Salmonella enterica.
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Type:
Other
Platform:
GPL20056
4 Samples
Download data: TXT
Series
Accession:
GSE163336
ID:
200163336
3.

MAPS integrates regulation of actin-targeting effector SteC into the virulence control network of Salmonella small RNA PinT

(Submitter supplied) In this study we take an integrative approach to capturing targets of the Hfq- associated sRNA PinT, a known post-transcriptional timer of the two major virulence programs of Salmonella enterica, using MS2 affinity purification and RNA- sequencing (MAPS).
Organism:
Mus musculus; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL20056 GPL20064
15 Samples
Download data: WIG
Series
Accession:
GSE157499
ID:
200157499
4.

Structure-based analysis of the gene network controlled by the Salmonella RcsB response regulator

(Submitter supplied) RcsB is a transcriptional regulator that controls expression of numerous genes in Enterobacteriaceae. RcsB accomplishes this role alone or in combination with auxiliary transcriptional factors independently or dependently of phosphorylation. To understand the mechanisms by which RcsB regulates such a large number of genes, we performed structural and in vitro and in vivo functional studies with different RcsB variants. more...
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27045
24 Samples
Download data: TSV
Series
Accession:
GSE154668
ID:
200154668
5.

Improved bacterial RNA-seq by Cas9-based depletion of ribosomal RNA reads

(Submitter supplied) A major challenge for RNA-seq analysis of gene expression is to achieve sufficient coverage of informative non-ribosomal transcripts. In eukaryotic samples, this is typically achieved by selective oligo(dT)-priming of messenger RNAs to exclude ribosomal RNA (rRNA) during cDNA synthesis. However, this strategy is not compatible with prokaryotes in which functional transcripts are generally not polyadenylated. more...
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Bacteroides thetaiotaomicron VPI-5482
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL20056 GPL28278
40 Samples
Download data: CSV, WIG
Series
Accession:
GSE147155
ID:
200147155
6.

Transcriptomic analysis of swarm motility phenotype of Salmonella enterica serovar Typhimurium mutant defective in periplasmic glucan synthesis

(Submitter supplied) Movement of food-borne pathogens on moist surfaces enables them to migrate towards more favorable niches and facilitate their survival for extended periods of time. Salmonella enterica serovar Typhimurium mutants defective in OPG synthesis are unable to exhibit motility on moist surfaces (swarming) however their mobility in liquid (swim motility) remains unaffected. In order to understand the role of OPG in swarm motility, transcriptomic analysis was performed using cells growing on a moist agar surface. more...
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL17070 GPL18823
9 Samples
Download data: TXT
Series
Accession:
GSE86311
ID:
200086311
7.

MS2-affinity purification coupled with RNA sequencing (MAPS) reveals SraL sRNA targetome in Salmonella Typhimurium

(Submitter supplied) Recently, we developed an in vivo technology to draw the interacting map of a specific small regulatory RNA (sRNA). We called it MAPS for MS2-affinity purification coupled with RNA sequencing. In this study, we performed MAPS with SraL sRNA (Salmonella Typhimurium SL1344).
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL22775
2 Samples
Download data: TXT
Series
Accession:
GSE108234
ID:
200108234
8.

Role of ProQ in Salmonella virulence

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL20056 GPL20051
42 Samples
Download data
Series
Accession:
GSE117256
ID:
200117256
9.

Role of ProQ in Salmonella virulence - in vitro

(Submitter supplied) FinO-domain proteins such as ProQ of the model pathogen Salmonella enterica have emerged as a new class of major RNA-binding proteins in bacteria. ProQ has been shown to target hundreds of transcripts including mRNAs from many virulence regions but its role, if any, in bacterial pathogenesis has not been studied. Here, using a Dual RNA-seq approach to profile ProQ-dependent gene expression changes as Salmonella infects human cells, we reveal dysregulation of bacterial motility, chemotaxis and virulence genes which is accompanied by altered mitogen-activated protein kinase signaling in the host. more...
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20056
24 Samples
Download data: CSV
Series
Accession:
GSE117255
ID:
200117255
10.

Role of ProQ in Salmonella virulence - pulse expression

(Submitter supplied) FinO-domain proteins such as ProQ of the model pathogen Salmonella enterica have emerged as a new class of major RNA-binding proteins in bacteria. ProQ has been shown to target hundreds of transcripts including mRNAs from many virulence regions but its role, if any, in bacterial pathogenesis has not been studied. Here, using a Dual RNA-seq approach to profile ProQ-dependent gene expression changes as Salmonella infects human cells, we reveal dysregulation of bacterial motility, chemotaxis and virulence genes which is accompanied by altered mitogen-activated protein kinase signaling in the host. more...
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20056
6 Samples
Download data: CSV
Series
Accession:
GSE117252
ID:
200117252
11.

Role of ProQ in Salmonella virulence - dual RNA-Seq

(Submitter supplied) FinO-domain proteins such as ProQ of the model pathogen Salmonella enterica have emerged as a new class of major RNA-binding proteins in bacteria. ProQ has been shown to target hundreds of transcripts including mRNAs from many virulence regions but its role, if any, in bacterial pathogenesis has not been studied. Here, using a Dual RNA-seq approach to profile ProQ-dependent gene expression changes as Salmonella infects human cells, we reveal dysregulation of bacterial motility, chemotaxis and virulence genes which is accompanied by altered mitogen-activated protein kinase signaling in the host. more...
Organism:
Homo sapiens; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20051
12 Samples
Download data: CSV
Series
Accession:
GSE117236
ID:
200117236
12.

Global maps of ProQ binding in vivo reveal target recognition via RNA structure and stability control at mRNA 3' ends

(Submitter supplied) In this study binding sites for the RNA-binding protein ProQ was determined in Salmonella and Escherichia coli
Organism:
Escherichia coli str. K-12 substr. MG1655; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Type:
Other
Platforms:
GPL21117 GPL20056
10 Samples
Download data: WIG
Series
Accession:
GSE106633
ID:
200106633
13.

speG affects intracellular replication, polyamine metabolism, and transcriptomes of Salmonella

(Submitter supplied) The speG gene has been reported to regulate polyamine metabolism in Escherichia coli and Shigella, but its role in Salmonella remains unknown. Our preliminary studies have revealed that speG widely affects the transcriptomes of infected in vitro M and Caco-2 cells and that it is required for the intracellular replication of Salmonella enterica serovar Typhimurium (S. Typhimurium) in HeLa cells. In this study, we demonstrated that speG plays a time-dependent and cell type-independent role in the intracellular replication of S. more...
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Type:
Expression profiling by array
Platform:
GPL23939
8 Samples
Download data: TXT
Series
Accession:
GSE102885
ID:
200102885
14.

Salmonella Cascade assembles on both cis- and -trans encoded CRISPR RNAs

(Submitter supplied) CRISPR/Cas loci commonly encode both proteins and small guide RNAs (crRNAs) to assemble ribonucleoproteins particles (RNPs) that confer a sequence-based, adaptive immunity against viruses and plasmids in prokaryotes. However, it has not been established whether this conserved synteny of RNA and protein genes is needed for the efficient RNP production in vivo. We show that the pathogenic bacterium Salmonella Typhimurium harbours two physically unlinked loci, CRISPR01 and CRISPR02, both of which produce mature crRNAs, although CRISPR02 lacks the protein genes for the type I-specific Cascade complex. more...
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18823
16 Samples
Download data: WIG
Series
Accession:
GSE58602
ID:
200058602
15.

ChIP-chip analysis of RNAP and Sigma factor binding to the Salmonella enterica serovar Typhimurium chromosome

(Submitter supplied) ChIP-chip analysis of RNA Polymerase (RNAP), RpoD, RpoE, RpoH and RpoN in exponential phase (OD 0.2) and early stationary phase (OD 2.0) Salmonella enterica serovar Typhimurium SL1344 cultures
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Salmonella enterica subsp. enterica serovar Typhimurium
Type:
Genome binding/occupancy profiling by array
Platform:
GPL10008
20 Samples
Download data: TXT
Series
Accession:
GSE97283
ID:
200097283
16.

Salmonella enterica serovar Typhimurium gene expression in exponential and stationary phase cultures

(Submitter supplied) Transcriptional profiling of Salmonella Typhimurium strains SL1344 in exponential and stationary phase cultures
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Salmonella enterica subsp. enterica serovar Typhimurium
Type:
Expression profiling by array
Platform:
GPL11416
4 Samples
Download data: TXT
Series
Accession:
GSE97161
ID:
200097161
17.

REPARATION: Ribosome Profiling Assisted (Re-) Annotation of Bacterial genomes

(Submitter supplied) The delineation of genes in bacteria has remained an important challenge because prokaryotic genomes are often tightly packed frequently resulting in overlapping genes. We hereby present a de novo approach called REPARATION (RibosomeE Profiling Assisted (Re-)AnnotaTION) to delineate translated open reading frames (ORFs) in bacteria independent of (available) genome annotation. By deep sequencing of ribosome protected mRNA fragments (RPF) to map translating ribosomes across the entire genome, REPARATION takes advantage of the recently developed ribosome profiling (Ribo-seq) technique. more...
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL20056
4 Samples
Download data: BED, BEDGRAPH
Series
Accession:
GSE91066
ID:
200091066
18.

Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo

(Submitter supplied) The molecular roles of many RNA‐binding proteins in bacterial post‐transcriptional gene regulation are not well understood. Approaches combining in vivo UV crosslinking with RNA deep sequencing (CLIP‐seq) have begun to revolutionize the transcriptome‐wide mapping of eukaryotic RNA‐binding protein target sites. We have applied CLIP‐seq to chart the target landscape of two major bacterial post‐transcriptional regulators, Hfq and CsrA, in the model pathogen Salmonella Typhimurium. more...
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20056
12 Samples
Download data: WIG
Series
Accession:
GSE74425
ID:
200074425
19.

Targets of the small regulatory RNA DapZ

(Submitter supplied) To determine the targets of the small regulatory RNA DapZ in S. Typhimurium, we looked at the effect of a short pulse of DapZ over-expression on the Salmonella transcriptome, as well as a DapZ variant that lacks the GcvB-like R1 region. To achieve over-expression, the wild-type DapZ and its variant were cloned in the pBAD plasmid and induced with 0.2% L-arabinose for 10 min. We then extracted the total RNA for transcriptional profiling. more...
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Type:
Expression profiling by array
Platform:
GPL11416
6 Samples
Download data: TXT
Series
Accession:
GSE38523
ID:
200038523
20.

Analysis of bacterial and macrophage transcripts in ISRE-positive and negative infected macrophages

(Submitter supplied) To identify bacterial transcripts that may be associated with type I IFN production in Salmonella enterica subsp typhimurium (SL1344) infected macrophages we transformed macrophages with an ISRE-GFP reporter construct and sorted separate populations of GFP positive and GFP negative infected macrophages. We then did whole transcriptome profiling, collecting both host and bacterial transcripts, for differential expression analysis
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Mus musculus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL17021 GPL19729
9 Samples
Download data: TXT
Series
Accession:
GSE65531
ID:
200065531
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