GEO DataSets

(Submitter supplied) Bacterial transcription is controlled by many transcription factors and promoters. Currently many promoters are mapped only in in vitro conditions. We use an intra-macrophage model to map the promoters and their expression in vivo. InSPI2 is an in vitro growth condition mimicking intra-macrophage condition. We also characterize the transcriptome of Salmonella during growth in an in vitro intra-macrophage growth condition.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17562

6 Samples

Download data: GR

(Submitter supplied) New tools for studying bacterial transcripts at the single nucleotide level offer an unparalleled opportunity to understand the bacterial transcriptome. For the model pathogen Salmonella enterica serovar Typhimurium, it is necessary to identify the regulatory inputs for all RNA transcripts, including small RNAs (sRNAs) and coding genes. Here, we use RNA-seq to define the transcriptomes of mutants lacking 18 global regulatory systems that, among other functions, modulate the expression of the SPI1 and SPI2 Type Three secretion systems in S. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17562

28 Samples

Download data: WIG

(Submitter supplied) Culture was split into halves and 500 uM dipyridyl was added to one half. Samples were collected after the indicated times. Groups of assays that are related as part of a time series. Keywords: time_series_design

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by array

Platform:

GPL3048

6 Samples

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(Submitter supplied) Background: Biofilm formation by Salmonella species enhances the capacity of these pathogenic bacteria to survive stresses that are commonly encountered within food processing and during host infection. The persistence of Salmonella within the food chain has become a major health concern, as biofilms can serve as a reservoir to contaminate food products. While the molecular mechanisms required for the survival of bacteria on surfaces are not fully understood, transcriptional studies of other bacteria have demonstrated that biofilm growth triggers the expression of specific sets of genes, compared with planktonic cells. more...

Organism:

Salmonella enterica

Type:

Expression profiling by array

Platform:

GPL8849

21 Samples

Download data: GPR, TXT

(Submitter supplied) Here, we report global gene expression of S. enterica serovar Typhimurium within Acanthamoeba castellanii by Cappable-Seq

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20792

6 Samples

Download data: CSV, XLSX

(Submitter supplied) Bacteria possess many small noncoding RNAs whose regulatory roles in pathogenesis are little understood due to a paucity of macroscopic phenotypes in standard virulence assays. Here, we use a novel Dual RNA-seq approach for a single-step simultaneous RNA profiling in both pathogen and host to reveal molecular phenotypes of sRNAs during infection with Salmonella Typhimurium. We identify a new PhoP/Q-activated small RNA which upon bacterial internalization acts to temporally control the expression of both, invasion-associated effectors and virulence genes required for intracellular survival. more...

Organism:

Homo sapiens; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20051 GPL20050

42 Samples

Download data: CSV

(Submitter supplied) Bacteria possess many small noncoding RNAs whose regulatory roles in pathogenesis are little understood due to a paucity of macroscopic phenotypes in standard virulence assays. Here, we use a novel Dual RNA-seq approach for a single-step simultaneous RNA profiling in both pathogen and host to reveal molecular phenotypes of sRNAs during infection with Salmonella Typhimurium. We identify a new PhoP/Q-activated small RNA which upon bacterial internalization acts to temporally control the expression of both, invasion-associated effectors and virulence genes required for intracellular survival. more...

Organism:

Homo sapiens; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20050

8 Samples

Download data: CSV

(Submitter supplied) Bacteria possess many small noncoding RNAs whose regulatory roles in pathogenesis are little understood due to a paucity of macroscopic phenotypes in standard virulence assays. Here, we use a novel Dual RNA-seq approach for a single-step simultaneous RNA profiling in both pathogen and host to reveal molecular phenotypes of sRNAs during infection with Salmonella Typhimurium. We identify a new PhoP/Q-activated small RNA which upon bacterial internalization acts to temporally control the expression of both, invasion-associated effectors and virulence genes required for intracellular survival. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20062 GPL20050

12 Samples

Download data: CSV

(Submitter supplied) Bacteria possess many small noncoding RNAs whose regulatory roles in pathogenesis are little understood due to a paucity of macroscopic phenotypes in standard virulence assays. Here, we use a novel Dual RNA-seq approach for a single-step simultaneous RNA profiling in both pathogen and host to reveal molecular phenotypes of sRNAs during infection with Salmonella Typhimurium. We identify a new PhoP/Q-activated small RNA which upon bacterial internalization acts to temporally control the expression of both, invasion-associated effectors and virulence genes required for intracellular survival. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21220

18 Samples

Download data: CSV

(Submitter supplied) Bacteria possess many small noncoding RNAs whose regulatory roles in pathogenesis are little understood due to a paucity of macroscopic phenotypes in standard virulence assays. Here, we use a novel Dual RNA-seq approach for a single-step simultaneous RNA profiling in both pathogen and host to reveal molecular phenotypes of sRNAs during infection with Salmonella Typhimurium. We identify a new PhoP/Q-activated small RNA which upon bacterial internalization acts to temporally control the expression of both, invasion-associated effectors and virulence genes required for intracellular survival. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20065

33 Samples

Download data: CSV

(Submitter supplied) Bacteria possess many small noncoding RNAs whose regulatory roles in pathogenesis are little understood due to a paucity of macroscopic phenotypes in standard virulence assays. Here, we use a novel Dual RNA-seq approach for a single-step simultaneous RNA profiling in both pathogen and host to reveal molecular phenotypes of sRNAs during infection with Salmonella Typhimurium. We identify a new PhoP/Q-activated small RNA which upon bacterial internalization acts to temporally control the expression of both, invasion-associated effectors and virulence genes required for intracellular survival. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Homo sapiens; Sus scrofa; Mus musculus

Type:

Expression profiling by high throughput sequencing

6 related Platforms

89 Samples

Download data: CSV

(Submitter supplied) Bacteria possess many small noncoding RNAs whose regulatory roles in pathogenesis are little understood due to a paucity of macroscopic phenotypes in standard virulence assays. Here, we use a novel Dual RNA-seq approach for a single-step simultaneous RNA profiling in both pathogen and host to reveal molecular phenotypes of sRNAs during infection with Salmonella Typhimurium. We identify a new PhoP/Q-activated small RNA which upon bacterial internalization acts to temporally control the expression of both, invasion-associated effectors and virulence genes required for intracellular survival. more...

Organism:

Homo sapiens; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20051

2 Samples

Download data: CSV

(Submitter supplied) Bacteria possess many small noncoding RNAs whose regulatory roles in pathogenesis are little understood due to a paucity of macroscopic phenotypes in standard virulence assays. Here, we use a novel Dual RNA-seq approach for a single-step simultaneous RNA profiling in both pathogen and host to reveal molecular phenotypes of sRNAs during infection with Salmonella Typhimurium. We identify a new PhoP/Q-activated small RNA which upon bacterial internalization acts to temporally control the expression of both, invasion-associated effectors and virulence genes required for intracellular survival. more...

Organism:

Homo sapiens; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL20051

51 Samples

Download data: CSV

(Submitter supplied) Bacteria possess many small noncoding RNAs whose regulatory roles in pathogenesis are little understood due to a paucity of macroscopic phenotypes in standard virulence assays. Here, we use a novel Dual RNA-seq approach for a single-step simultaneous RNA profiling in both pathogen and host to reveal molecular phenotypes of sRNAs during infection with Salmonella Typhimurium. We identify a new PhoP/Q-activated small RNA which upon bacterial internalization acts to temporally control the expression of both, invasion-associated effectors and virulence genes required for intracellular survival. more...

Organism:

Homo sapiens; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20050

24 Samples

Download data: CSV

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

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium; Homo sapiens; Sus scrofa; Mus musculus; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

8 related Platforms

279 Samples

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(Submitter supplied) Salmonella enterica var. Typhimurium (S. Typhimurium) is a Gram-negative, facultative intracellular pathogen that infects the intestinal tracts of humans and animals. In the host, S. Typhimurium encounters a wide range of oxygen concentrations going from oxic conditions in the stomach to near anoxic conditions in the distal sigmoid colon-rectal junction. In Escherichia coli, FNR (Fumarate Nitrate Reductase) is one of the main regulatory proteins involved in oxygen sensing and in controlling the transcription of the genes required for the aerobic/anaerobic transition.. more...

Organism:

Salmonella; Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by array

Platform:

GPL1835

6 Samples

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(Submitter supplied) Global expression profiles of Salmonella typhi grown in the supernatant of infection and within human macrophages at 0h, 2h, 8h and 24h were obtained. Stringent analytical methods were used to compare Salmonella typhi cDNAs and revealed that known virulence factors, such as the SPI-1 and SPI-2 encoded type III secretion systems, were found to be expressed as predicted during infection by Salmonella. more...

Organism:

Salmonella enterica; Salmonella; Salmonella enterica subsp. enterica serovar Typhi

Type:

Expression profiling by array

Platforms:

GPL1835 GPL548

30 Samples

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(Submitter supplied) The cDNA obtained before and after each round of SCOTS (first, second and third) from 2 h post-infection were hybridized to analyse the effect of SCOTS round on transcripts population. The number of detected genes increase with the numer of round of SCOTS. Because the cDNA prepared by 3 round of SCOTS gave the best results, three round of SCOTS were used in the preparation of the other samples. Keywords: Evaluation of SCOTS round

Organism:

Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhi

Type:

Expression profiling by array

Platform:

GPL548

24 Samples

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(Submitter supplied) Genomic DNA from Strain ISP1820 and CT18 were compared to identify missing genes in strain ISP1820. Keywords: Comparative Genomic Hybridization

Organism:

Salmonella enterica subsp. enterica serovar Typhi; Salmonella enterica

Type:

Genome variation profiling by array

Platform:

GPL548

3 Samples

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(Submitter supplied) An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. We have adapted a microarray-based transposon tracking strategy for use with a Salmonella enterica serovar Typhimurium cDNA microarray in order to identify genes important for survival and replication in RAW 264.7 mouse macrophage-like cells or in the spleens of BALB/cJ mice. A 50,000-CFU transposon library of S. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by array

Platform:

GPL2772

12 Samples

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