GEO DataSets

(Submitter supplied) RpoD is a houskeeping sigma factor and RpoN is an alternative one. It was identified their intragenic and intergenic binding sites and association with the RNA polymerase.

Organism:

Escherichia coli str. K-12 substr. MG1655; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17439 GPL22503

8 Samples

Download data: GFF

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

Organism:

Escherichia coli str. K-12 substr. MG1655; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL17439 GPL22503

10 Samples

Download data: GFF

(Submitter supplied) RpoD is a houskeeping sigma factor and RpoN is an alternative one. It was identified their intragenic and intergenic binding sites and association with the RNA polymerase.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22503

2 Samples

Download data: GFF, TXT

(Submitter supplied) We have shown that mitomycin C induces expression of the rsr-yrlBA-rtcBA operon in Salmonella Typhimurium in a manner that is dependent on the activator for this operon, RtcR. As such, treatment with mitomycin C generates the ligand or other cellular conditions that activate RtcR and likely generates the substrates on which the components of this RNA repair operon act. We performed an RNA-seq analysis on WT cells and cells with components of the RNA repair operon, or the activator of the operon, deleted with and without mitomycin C. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21220

24 Samples

Download data: XLSX

(Submitter supplied) ChIP-on-chip analysis of RNAP and RpoD binding to the Salmonella enterica serovar Typhimurium chromosome demonstrated a high degree of overlap between RNAP and RpoD binding and provided us with important insights into the global distribution of these factors. Furthermore this data was correlated with information on the location of 1873 transcription start sites identified by RNA-Seq technology, thereby providing a detailed transcriptional map of Salmonella Typhimurium.

Organism:

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

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10008

5 Samples

Download data: TXT

(Submitter supplied) Bacterial transcription networks typically consist of hundreds of transcription factors and thousands of promoters. However, current attempts to map bacterial promoters have failed to report the true complexity of bacterial transcription. The differential RNA-seq (dRNA-seq) approaches only identified a subset of promoters because they involved few growth conditions. Here, we present a simplified approach for global promoter identification in bacteria, based upon the analysis of RNA-seq data from multiple environmental conditions. more...

Organism:

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

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17562

34 Samples

Download data: GR

(Submitter supplied) When performed at single bp resolution, the genome-wide location, occupancy level, and structural organization of DNA binding proteins provides mechanistic insights into genome regulation. Here we use ChIP-exo to provide the first high resolution view of the epigenomic organization of the E. coli transcription machinery and nucleoid structural proteins when cells are growing exponentially and upon rapid reprogramming (acute heat shock). more...

Organism:

Escherichia coli

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21222

50 Samples

Download data: GFF

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

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20056

21 Samples

Download data: BW

(Submitter supplied) The Fis nucleoid-associated protein controls the expression of a large and diverse regulon of genes in Gram-negative bacteria. Fis production is normally maximal in bacteria during the early exponential phase of batch culture growth, becoming almost undetectable by the onset of stationary phase. We tested the effect of rewiring the Fis regulatory network in Salmonella by moving the complete fis gene from its usual location near the origin of chromosomal replication to the position normally occupied by the dps gene in the Right macrodomain of the chromosome, creating the strain GX. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20056

12 Samples

Download data: BW, XLSX

(Submitter supplied) The Fis nucleoid-associated protein controls the expression of a large and diverse regulon of genes in Gram-negative bacteria. Fis production is normally maximal in bacteria during the early exponential phase of batch culture growth, becoming almost undetectable by the onset of stationary phase. We tested the effect of rewiring the Fis regulatory network in Salmonella by moving the complete fis gene from its usual location near the origin of chromosomal replication to the position normally occupied by the dps gene in the Right macrodomain of the chromosome, creating the strain GX. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20056

9 Samples

Download data: BW, XLSX

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

Organism:

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

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL5780 GPL9091

40 Samples

Download data: GPR, TXT

(Submitter supplied) We used ChIP-chip analysis to identify where the nucleoid associated protein StpA binds on the Salmonella Typhimurium genome. We identified 285 chromosomal regions bound by StpA, ranging in size from 400 to 3500 base pairs and containing 572 genes. Comparison of the ChIP data revealed that StpA displayed an identical binding profile to H-NS; all genomic regions associated with StpA were also bound by H-NS. more...

Organism:

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

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL5791

8 Samples

Download data: TXT

(Submitter supplied) StpA is a paralogue of the nucleoid associated protein H-NS that is conserved in a range of enteric bacteria and had no known function in Salmonella enterica serovar Typhimurium. Here, we show that 5% of the Salmonella genome is regulated by StpA, which contrasts with the situation in Escherichia coli where deletion of stpA only had minor effects on gene expression. The StpA-dependent genes of S. Typhimurium are a specific subset of the H-NS regulon that are predominantly under the positive control of sigma38 (RpoS), CRP-cAMP and PhoP. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL9091

12 Samples

Download data: GPR

(Submitter supplied) StpA is a paralogue of the nucleoid associated protein H-NS that is conserved in a range of enteric bacteria and had no known function in Salmonella enterica serovar Typhimurium. Here, we show that 5% of the Salmonella genome is regulated by StpA, which contrasts with the situation in Escherichia coli where deletion of stpA only had minor effects on gene expression. The StpA-dependent genes of S. Typhimurium are a specific subset of the H-NS regulon that are predominantly under the positive control of sigma38 (RpoS), CRP-cAMP and PhoP. more...

Organism:

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

Type:

Expression profiling by array

Platforms:

GPL5780 GPL9091

28 Samples

Download data: GPR, TXT

(Submitter supplied) Transcriptional profiling of three sequenced S. enterica strains: S. Typhimurium LT2, S. Typhi CT18, and S. Typhi Ty2 in PhoP-inducing and non-inducing conditions in vitro, and compared these results to profiles of phoP-/Q- mutants derived from S. Typhimurium LT2 and S. Typhi Ty2.

Organism:

Salmonella enterica subsp. enterica serovar Typhi str. Ty2; Salmonella enterica subsp. enterica serovar Typhi str. CT18; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Expression profiling by array

Platform:

GPL9043

12 Samples

Download data: TXT