GEO DataSets

(Submitter supplied) UV-crosslining of protein-RNA complexes was employed to capture sRNA-mRNA interactions occuring on the RNA degradosome protein, RNase E, in enterohaemorhaggic E. coli. Abstract from associated mansucript: In many organisms small regulatory RNAs (sRNA) play important roles in the regulation of gene expression by base-pairing to specific target mRNAs. In enterohaemorrhagic E. coli (EHEC), sRNAs are encoded by both the “core” genome and in numerous horizontally acquired pathogenicity islands. more...

Organism:

Escherichia coli O157:H7 str. Sakai

Type:

Other

Platform:

GPL21393

2 Samples

Download data: GTF, HYB

(Submitter supplied) Enterohaemorrhagic E. coli is significant human pathogen that causes disease ranging from haemorrhagic colitis to haemolytic uremic syndrome. The later can lead to potentially fatal renal failure and is caused by the release of Shiga toxins that are encoded within lambdoid bacteriophages. The toxins are encoded within the late transcript of the phage and are regulated by anti-termination of the PR’ late promoter during lytic induction of the phage. more...

Organism:

Escherichia coli O157:H7 str. Sakai

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28004

8 Samples

Download data: BEDGRAPH, SGR

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

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli; Escherichia coli O157:H7; Escherichia coli O157:H7 str. Sakai

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

4 related Platforms

12 Samples

Download data: GPR, GTF, TXT

(Submitter supplied) UV-crosslinking and high througput sequencing of cDNAs (CRAC) was used to map the binding sites Hfq in enterohaemorhaggic E. coli (EHEC). Hfq was tagged with a His-FLAG dual affintiy tag and UV crosslinked after growth in the MEM-HEPES media essentailly as per Granneman et al (2009) PNAS. We additionally crosslinked Hfq in non-pathogenic E. coli K12 str. MG1655 grown in LE media. Hfq-RNA complexes were purified and trimmed using RNase A/T1. more...

Organism:

Escherichia coli O157:H7 str. Sakai; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17026 GPL17025 GPL17024

11 Samples

Download data: GTF

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

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24659 GPL26592

30 Samples

Download data: FA, GTF

(Submitter supplied) By shaping gene expression profiles, small RNAs (sRNAs) enable bacteria to efficiently adapt to changes in their environment. To better understand how Escherichia coli acclimatizes to nutrient availability, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) to uncover Hfq-associated RNA-RNA interactions at specific growth stages. We demonstrate that Hfq CLASH robustly captures bona fide RNA-RNA interactions identified hundreds of novel sRNA base-pairing interactions, including many sRNA-sRNA interactions and involving 3’UTR-derived sRNAs. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL24659

16 Samples

Download data: TXT

(Submitter supplied) By shaping gene expression profiles, small RNAs (sRNAs) enable bacteria to efficiently adapt to changes in their environment. To better understand how Escherichia coli acclimatizes to nutrient availability, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) to uncover Hfq-associated RNA-RNA interactions at specific growth stages. We demonstrate that Hfq CLASH robustly captures bona fide RNA-RNA interactions identified hundreds of novel sRNA base-pairing interactions, including many sRNA-sRNA interactions and involving 3’UTR-derived sRNAs. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26592

14 Samples

Download data: XLSX

(Submitter supplied) We report the transcriptomic profile of Escherichia coli when the small RNA RydC is overexpressedand how this can be used to identify putative mRNA targets. This technique allowed us to identify potential mRNA targets to further validate in vivo.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15010

6 Samples

Download data: TXT, WIG

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

Organism:

Staphylococcus aureus subsp. aureus str. JKD6008

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL31256 GPL34143

18 Samples

Download data: TXT

(Submitter supplied) Small RNAs have been found to control a broad range of bacterial phenotypes including tolerance to antibiotics. Vancomycin tolerance in multidrug resistance Staphylococcus aureus is correlated with dysregulation of small RNAs although their contribution to antibiotic tolerance in poorly understood. RNA-RNA interactome profiling techniques are expanding our understanding of sRNA-mRNA interactions in bacteria; however, determining the function of these interactions for hundreds of sRNA-mRNA pairs is a major challenge. more...

Organism:

Staphylococcus aureus subsp. aureus str. JKD6008

Type:

Other

Platform:

GPL34143

10 Samples

Download data: TXT

(Submitter supplied) Small RNAs have been found to control a broad range of bacterial phenotypes including tolerance to antibiotics. Vancomycin tolerance in multidrug resistance Staphylococcus aureus is correlated with dysregulation of small RNAs although their contribution to antibiotic tolerance in poorly understood. RNA-RNA interactome profiling techniques are expanding our understanding of sRNA-mRNA interactions in bacteria; however, determining the function of these interactions for hundreds of sRNA-mRNA pairs is a major challenge. more...

Organism:

Staphylococcus aureus subsp. aureus str. JKD6008

Type:

Other

Platform:

GPL34143

2 Samples

Download data: TXT

(Submitter supplied) Small RNAs have been found to control a broad range of bacterial phenotypes including tolerance to antibiotics. Vancomycin tolerance in multidrug resistance Staphylococcus aureus is correlated with dysregulation of small RNAs although their contribution to antibiotic tolerance in poorly understood. RNA-RNA interactome profiling techniques are expanding our understanding of sRNA-mRNA interactions in bacteria; however, determining the function of these interactions for hundreds of sRNA-mRNA pairs is a major challenge. more...

Organism:

Staphylococcus aureus subsp. aureus str. JKD6008

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31256

6 Samples

Download data: TXT

(Submitter supplied) Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen responsible for high levels of human morbidity and mortality. MRSA co-ordinates expression of an array of bacterial factors involved in antimicrobial resistance, nutrient acquisition and immune evasion in the host. Post-transcriptional regulation by small RNAs (sRNAs) has emerged as an important mechanism for the control of MRSA virulence. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29493 GPL27158

91 Samples

Download data: BEDGRAPH, FA, GTF, TXT, XLSX

(Submitter supplied) Understanding RNA processing and turnover requires knowledge of cleavages by major endoribonucleases within a living cell. We have employed TIER-Seq (transiently inactivating an endoribonuclease followed by RNA-Seq) to profile cleavage products of the essential endoribonuclease RNase E in Salmonella enterica. A dominating cleavage signature is the location of a uridine two nucleotides downstream in a single-stranded segment, which we rationalize structurally as a key recognition determinant that may favor RNase E catalysis. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19729

8 Samples

Download data: WIG

(Submitter supplied) The first goal of the study was to identify genes differentially regulated by MavR in EHEC strain 86-24. The second goal was to identify direct targets of MavR through the MAPS protocol.

Organism:

Escherichia coli O157:H7

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29711 GPL28511

10 Samples

Download data: TXT

(Submitter supplied) The polynucleotide phosphorylase (PNPase) is conserved among both Gram-positive and Gram-negative bacteria. As a core part of the degradosome, the PNPase is involved in maintaining proper RNA levels within the bacterial cell. It plays a major role in RNA homeostasis and decay since it acts as a 3’- to 5’-exoribonuclease. Furthermore PNPase can catalyze the reverse reaction by elongating RNA molecules in 5’- to 3’-end direction which finally has a destabilizing effect on the prolonged RNA molecule. more...

Organism:

Cereibacter sphaeroides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24048

9 Samples

Download data: BED, CSV, WIG

(Submitter supplied) Purpose: The goals of this study are to identify the putative mRNA targets that are regulated by the 6C sRNA. We constuct an inducible vector to transiently overexpressed the 6C sRNA in M. smegmatis, and then we perform RNA-Seq to look for genes that are differicently expressed upon the over-expression of 6C sRNA, which we think these genes are the potential targets of the 6C sRNA.

Organism:

Mycolicibacterium smegmatis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25523

2 Samples

Download data: TXT

(Submitter supplied) sRNAs play important roles in regulating gene expression post-transcriptionally. Here, we used RNA-seq to compare gene expression in a WT strain and a dicF1-4 deletion strain.

Organism:

Escherichia coli O157:H7 str. EDL933

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24005

6 Samples

Download data: TXT

(Submitter supplied) Hfq is a ubiquitous Sm-like RNA-binding protein in bacteria involved in physiological fitness and pathogenesis, while its in vivo binding nature remains elusive. Here we reported genome-wide Hfq-bound RNAs in Yersinia pestis, a causative agent of plague, by using cross-linking immunoprecipitation coupled with deep sequencing (CLIP-seq) approach. We show that the Hfq binding density is enriched in more than 80% mRNAs of Y. more...

Organism:

Yersinia pestis

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21403

8 Samples

Download data: TXT

(Submitter supplied) In many bacteria, the base pairing between most small regulatory RNAs (sRNAs) and their targets is facilitated by the Hfq RNA chaperone. However, recent studies have shown FinO-domain proteins also bind sRNAs. To compare the contributions of Hfq and the FinO-domain ProQ protein in Escherichia coli, we carried out RIL-seq, which allows global identification of two RNAs bound to the same protein. We detected hundreds of RNA pairs on ProQ. more...

Organism:

Escherichia coli K-12

Type:

Other

Platform:

GPL24570

56 Samples

Download data: BED, WIG