U.S. flag

An official website of the United States government

Format
Items per page
Sort by

Send to:

Choose Destination

Search results

Items: 1 to 20 of 639

1.

The transcriptional response to low temperature is weakly conserved across Enterobacteriales

(Submitter supplied) Bacteria respond to changes in their external environment like temperature by changing the transcription of their genes, but we know little about how these regulatory patterns evolve. We used RNA-seq to study the transcriptional response of a shift from 37°C to 15°C in wild-type Escherichia coli, Salmonella enterica, Citrobacter rodentium, Enterobacter cloacae, Klebsiella pneumoniae, and Serratia marcescens, as well as ∆rpoS strains of E. more...
Organism:
Enterobacter cloacae; Escherichia coli; Klebsiella pneumoniae; Serratia marcescens; Citrobacter rodentium; Salmonella enterica
Type:
Expression profiling by high throughput sequencing
6 related Platforms
64 Samples
Download data: TXT
Series
Accession:
GSE267531
ID:
200267531
2.

Impact of Multiple Antimicrobial Exposures on the Transfer Efficiency of Multidrug Resistance Plasmids in Salmonella enteric

(Submitter supplied) Antimicrobial exposure can potentially lead to increased antimicrobial resistance plasmid transfer. RNA sequencing data was collected from conjugal pairs of Salmonella enterica and Escherichia coli exposed or not exposed to tetracycline over a time course to determine differences in transcript numbers associated with conjugation and tetracycline exposure. The samples were sequenced on the Illumina HiSeq X10 platform with the 150-bp paired-end kit. more...
Organism:
Salmonella enterica; Escherichia coli J53
Type:
Expression profiling by high throughput sequencing
Platform:
GPL34283
24 Samples
Download data: XLSX
Series
Accession:
GSE261094
ID:
200261094
3.

CLIP-seq of Salmonella ProQ in intracellular-like conditions

(Submitter supplied) The aim of the project is to identify transcriptome-wide binding sites for the global RNA-binding protein ProQ in Salmonella during intracellular-like conditions.
Organism:
Salmonella enterica
Type:
Other
Platform:
GPL27048
4 Samples
Download data: WIG
Series
Accession:
GSE250014
ID:
200250014
4.

An intracellular phosphorus-starvation signal activates the PhoB/PhoR two-component system in Salmonella enterica

(Submitter supplied) Bacteria acquire P primarily as inorganic orthophosphate (Pi, PO43-). Once internalized, Pi is rapidly assimilated into biomass during the synthesis of ATP. Because Pi is essential, but excessive ATP is toxic, the acquisition of environmental Pi is tightly regulated. In the bacterium Salmonella enterica (Salmonella), growth in Pi-limiting environments activates the membrane sensor histidine kinase PhoR, leading to the phosphorylation of its cognate transcriptional regulator PhoB and subsequent transcription of genes involved in adaptations to low Pi. more...
Organism:
Salmonella enterica
Type:
Expression profiling by high throughput sequencing
Platform:
GPL33267
16 Samples
Download data: TSV
Series
Accession:
GSE227715
ID:
200227715
5.

Reconstruction of a Pan-regulon for Fur uncovers the conservation of its transcriptional regulation in E. coli

(Submitter supplied) Regulons for many transcription factors have been elucidated in model strains leading to an understanding of their role in producing physiological states. Comparative analysis of a regulon and its target genes between different strains of the same species is lacking. Ferric uptake regulator (Fur), involved in iron homeostasis, is one of the most conserved TFs, and is present in a wide range of bacteria. more...
Organism:
Escherichia coli; Escherichia coli K-12; Salmonella enterica; Escherichia coli O157:H7
Type:
Expression profiling by high throughput sequencing
4 related Platforms
36 Samples
Download data: CSV
Series
Accession:
GSE150501
ID:
200150501
6.

The Fur Pan-regulon in E. coli shows diversity in strain-specific sets of target genes

(Submitter supplied) Regulons for many transcription factors have been elucidated in model strains leading to an understanding of their role in producing physiological states. Comparative analysis of a regulon and its target genes between different strains of the same species is lacking. Ferric uptake regulator (Fur), involved in iron homeostasis, is one of the most conserved TFs, and is present in a wide range of bacteria. more...
Organism:
Salmonella enterica; Escherichia coli; Escherichia coli K-12; Escherichia coli O157:H7
Type:
Genome binding/occupancy profiling by high throughput sequencing
4 related Platforms
36 Samples
Download data: GFF
Series
Accession:
GSE150240
ID:
200150240
7.

RNA degradation analysis reveals ribosome dynamics in complex microbiome samples

(Submitter supplied) The microbiome has revealed itself as a key player in health and disease. To better understand its role, in addition to microbial diversity, it is important to understand species-specific activity and gene expression. While metatranscriptomics investigates mRNA abundance2, it does not inform about faster post-transcriptional regulation3. Although prokaryotic translation is a common target for antibiotics, a direct measurement of microbiome ribosome dynamics remains inaccessible. more...
Organism:
Enterococcus faecalis; Bacillus subtilis; Limosilactobacillus reuteri; Limosilactobacillus fermentum; human feces metagenome; Listeria monocytogenes; Saccharomyces cerevisiae; Salmonella enterica; Parabacteroides merdae; Escherichia coli; Synechocystis sp. PCC 6803; Staphylococcus aureus; Bacillus amyloliquefaciens; Lactiplantibacillus plantarum; Cryptococcus neoformans; Caulobacter vibrioides; Segatella copri; Alistipes finegoldii; Hoylesella timonensis; compost metagenome
Type:
Other
17 related Platforms
199 Samples
Download data: BEDGRAPH, TXT, XLSX
Series
Accession:
GSE153497
ID:
200153497
8.

Typhoidal Salmonella Dendritic Cell Survival Mechanism Revealed by Dual RNA sequencing

(Submitter supplied) Salmonella enterica represent a major disease burden worldwide. While non-typhoidal Salmonella (NTS) serovars trigger self-limiting diarrhoea, leading to occasional secondary bacteraemia, S. enterica serovar Typhi is responsible for potentially life-threatening Typhoid fever. Dendritic cells (DCs) are key professional antigen presenting cells of the human immune system. The ability of pathogenic bacteria to subvert DC functions and prevent T cell recognition contributes to their survival and dissemination within the host. more...
Organism:
Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Salmonella enterica subsp. enterica serovar Typhi str. Ty2; Salmonella enterica subsp. enterica serovar Typhimurium str. D23580; Homo sapiens
Type:
Expression profiling by high throughput sequencing
7 related Platforms
93 Samples
Download data: TXT
Series
Accession:
GSE161854
ID:
200161854
9.

Differences between the global transcriptomes of Salmonella enterica serovars Dublin and Cerro during infection of bovine epithelial cells

(Submitter supplied) This study compares the global transcriptomes of highly pathogenic bovine-adapted S. enterica serovar Dublin and the less pathogenic bovine-adapted serovar Cerro during interactions with bovine epithelial cells, to identify genes that impact serovar-related outcomes of S. enterica infections in dairy animals
Organism:
Salmonella enterica
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27048
12 Samples
Download data: TXT
Series
Accession:
GSE182165
ID:
200182165
10.

A chromatin immunoprecipitation database for prokarytic organisms

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Escherichia coli; Klebsiella pneumoniae; Shigella flexneri; Staphylococcus aureus; Pseudomonas putida; Yersinia pseudotuberculosis; Escherichia coli K-12; Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Type:
Genome binding/occupancy profiling by high throughput sequencing
9 related Platforms
102 Samples
Download data: GFF
Series
Accession:
GSE182079
ID:
200182079
11.

A chromatin immunoprecipitation database for prokarytic organisms [fur]

(Submitter supplied) Bacterial transcription factors (TFs) regulate gene expression to adapt to changing environments; when combined, the TF’s regulatory actions comprise transcriptional regulatory networks (TRNs). The chromatin immunoprecipitation (ChIP) assay is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It enables the genome-wide study of transcription factor binding sites (TFBSs) and gene regulation. more...
Organism:
Escherichia coli; Klebsiella pneumoniae; Shigella flexneri; Yersinia pseudotuberculosis; Salmonella enterica
Type:
Genome binding/occupancy profiling by high throughput sequencing
5 related Platforms
14 Samples
Download data: GFF
Series
Accession:
GSE181770
ID:
200181770
12.

Niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica

(Submitter supplied) Salmonella enterica serovar Typhimurium (S. Typhimurium) is a zoonotic pathogen that causes diarrheal disease in humans and animals. During salmonellosis, S. Typhimurium colonizes epithelial cells lining the gastrointestinal tract. S. Typhimurium has an unusual lifestyle in epithelial cells that begins within an endocytic-derived Salmonella-containing vacuole (SCV), followed by escape into the cytosol, epithelial cell lysis and bacterial release. more...
Organism:
Salmonella enterica
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19226
4 Samples
Download data: TSV
Series
Accession:
GSE179103
ID:
200179103
13.

Transcriptomic comparison of WT and yebEFG mutant of Salmonella enterica ATCC 14028 strains grown in LB and in the presence of sublethal concentration of nalidixic acid

(Submitter supplied) RNA-sequencing of two Salmonella enterica strains (WT, ∆yebEFG) in standard laboratory conditions (LB to ESP), and in SOS-response inducing conditions (LB+nalidixic acid)
Organism:
Salmonella enterica
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27048
12 Samples
Download data: TXT
Series
Accession:
GSE159310
ID:
200159310
14.

RNA Atlas of Bacterial Human Pathogens Uncovers Stress Dynamics Linked to Bacterial Infections

(Submitter supplied) Pathogenic bacteria encounter a variety of stressful host environments during infection. Their responses to meet these challenges protect them from deadly damages and aid in adaption to harmful environments. Bacterial products critical for this protection are therefore interesting as suitable targets for new antimicrobials. To shed light on the complex array of molecular pathways involved in bacterial stress responses we challenged 32 diverse human pathogenic bacteria to 11 infection related stress conditions and catalogued their transcriptomes. more...
Organism:
Helicobacter pylori; Enterococcus faecalis; Neisseria meningitidis; Staphylococcus epidermidis; Streptococcus pyogenes; Listeria monocytogenes; Salmonella enterica; Achromobacter xylosoxidans; Campylobacter jejuni; Francisella tularensis; Acinetobacter baumannii; Neisseria gonorrhoeae; Escherichia coli; Shigella flexneri; Aggregatibacter actinomycetemcomitans; Haemophilus influenzae; Staphylococcus aureus subsp. aureus MRSA252; Staphylococcus aureus subsp. aureus MSSA476; Borreliella burgdorferi; Pseudomonas aeruginosa; Legionella pneumophila; Klebsiella pneumoniae; Yersinia pseudotuberculosis; Vibrio cholerae; Streptococcus suis; Streptococcus agalactiae; Streptococcus pneumoniae; Mycobacterium tuberculosis; Burkholderia pseudomallei
Type:
Expression profiling by high throughput sequencing
30 related Platforms
1122 Samples
Download data: TXT
Series
Accession:
GSE152295
ID:
200152295
15.

The role of Salmonella Genomic Island 4 in metal tolerance of Salmonella enterica serovar I 4,[5],12:i:- pork outbreak isolate USDA15WA-1

(Submitter supplied) Multidrug-resistant (MDR; resistance to >3 antimicrobial classes) Salmonella enterica serovar I 4,[5],12:i:- strains were linked to a 2015 foodborne outbreak from pork. Strain USDA15WA-1, associated with the outbreak, harbors an MDR module and the metal tolerance element Salmonella Genomic Island 4 (SGI-4). Characterization of SGI-4 revealed that conjugational transfer of SGI-4 resulted in the mobile genetic element (MGE) replicating as a plasmid or integrating into the chromosome. more...
Organism:
Salmonella enterica
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29222
12 Samples
Download data: TXT
Series
Accession:
GSE159054
ID:
200159054
16.

Salmonella Typhimurium uses smooth swimming to increase invasion in the mammalian gut

(Submitter supplied) The enteric pathogen Salmonella enterica serovar Typhimurium infects humans and animals. Invasion of intestinal epithelial cells is an important step in gut colonization. Both the Salmonella invasion-associated Type III Secretion System 1 (T3SS1) and motility are required for efficient invasion. The master regulator HilD induces expression of T3SS1 and flagella genes, thus coordinating expression of invasion and motility. more...
Organism:
Salmonella enterica
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29062
6 Samples
Download data: TXT
Series
Accession:
GSE156765
ID:
200156765
17.

Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Escherichia coli BW25113; Salmonella enterica; Escherichia coli K-12
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing
5 related Platforms
39 Samples
Download data: TDF, TXT
Series
Accession:
GSE135949
ID:
200135949
18.

Mapping PT modifications in bacteria

(Submitter supplied) One microbial organism always contains multiple DNA modification systems as defense strategies or epigenetic controls. Here, we describe crosstalk between two distinct DNA modifications with different target sequence motif: DNA phosphorothioation (PT, GPSAAC/GPSTTC by DndACDE proteins) and N6-methyl-adenine methylation (m6A, G6mATC by Dam protein). By using a newly developed DNA modification sequencing method PT nick-seq, we found that half of PT modifications change from GAAC/GTTC to GATC sites after bacteria have lost Dam.
Organism:
Salmonella enterica; Escherichia coli K-12
Type:
Other
Platforms:
GPL27120 GPL27121
12 Samples
Download data: TXT
Series
Accession:
GSE135910
ID:
200135910
19.

ChIP-seq study on Dnd proteins

(Submitter supplied) Tto get the DNA PT modification proteins binding regions on the genome, ChIP with anti-Flag antibody followed by Illumina sequencing was applied.
Organism:
Salmonella enterica
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL27048
24 Samples
Download data: TDF
Series
Accession:
GSE135768
ID:
200135768
20.

Salmonella enterica serovar Typhimurium strain 14028s transcriptome response to tomato media

(Submitter supplied) Summary: Salmonella enterica serovar Typhimurium strain 14028s transcriptome response to tomato medium (TM) and tomato root exudates (TX) compared to minimal medium (MM). Purpose: Salmonella mRNA profile, when grown in different media was compared to minimal medium to reveal environment specific transcriptional changes. Methods: mRNA profiles were generated using Illumina HiSeq in triplicates. The sequences were analysed using Bowtie2 followed by Cufflinks.
Organism:
Salmonella enterica
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19226
9 Samples
Download data: CXB, TXT
Series
Accession:
GSE132634
ID:
200132634
Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

db=gds|term=txid28901[Organism:noexp]|query=1|qty=100|blobid=MCID_667af55e8c5d4760e228e053|ismultiple=true|min_list=5|max_list=20|def_tree=20|def_list=|def_view=|url=/Taxonomy/backend/subset.cgi?|trace_url=/stat?
   Taxonomic Groups  [List]
Tree placeholder
    Top Organisms  [Tree]

Find related data

Search details

See more...

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...
Support Center