Similar studies for GEO DataSets (Select 200196834) - GEO DataSets

Links from GEO DataSets

Items: 20

Select item 2001968341.

The role of the RNA chaperone protein ProQ in Pasteurella multocida

(Submitter supplied) The Gram-negative pathogen Pasteurella multocida is responsible for many important animal diseases. While a number of P. multocida virulence factors have been identified, very little is known about how gene expression and protein production is regulated in this organism. One mechanism by which bacteria regulate transcript abundance and protein production is riboregulation, which involves the interaction of a small RNA (sRNA) with a target mRNA to alter transcript stability and/or translational efficiency. more...

Organism:: Pasteurella multocida

Type:: Expression profiling by high throughput sequencing

Platform:: GPL31945
9 Samples

Download data: CSV

Series

Accession:: GSE196834

ID:: 200196834

PubMed Full text in PMC Similar studies

Select item 2000777212.

Comparison of the transcriptomes of a Pasteurella multocida VP161 wild-type strain with a Pasteurella multocida VP161 hfq mutant

(Submitter supplied) Objectives: To determine the transcripts that are differentially expressed in a hfq mutant. Hfq is an RNA chaperone that mediates many interactions between regultory RNAs and their mRNA targets. Analysis of the transcriptomes of the Pasteurella multocida wild-type strain and the Pasteurella multocida hfq mutant will allow for identification of genes controlled by hfq and the sRNAs with which it interacts.

Organism:: Pasteurella multocida

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21442
6 Samples

Download data: CSV, FA, GFF

Series

Accession:: GSE77721

ID:: 200077721

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001230503.

Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation

(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:: GPL26592 GPL24659
30 Samples

Download data: FA, GTF

Series

Accession:: GSE123050

ID:: 200123050

PubMed Full text in PMC Similar studies

Select item 2001230494.

Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation [CLASH]

(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

Series

Accession:: GSE123049

ID:: 200123049

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001230485.

Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation [RNA-seq]

Organism:: Escherichia coli str. K-12 substr. MG1655

Type:: Expression profiling by high throughput sequencing

Platform:: GPL26592
14 Samples

Download data: XLSX

Series

Accession:: GSE123048

ID:: 200123048

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001315206.

RNA-RNA interactomes of Hfq and ProQ reveal overlapping and competing roles for RNA chaperones

(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

Series

Accession:: GSE131520

ID:: 200131520

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001066337.

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:: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Escherichia coli str. K-12 substr. MG1655

Type:: Other

Platforms:: GPL20056 GPL21117
10 Samples

Download data: WIG

Series

Accession:: GSE106633

ID:: 200106633

PubMed Similar studies SRA Run Selector

Select item 2001253688.

Polynucleotide phosphorylase promotes the stability and function of Hfq-binding sRNAs by degrading target mRNA-derived fragments

(Submitter supplied) In many gram-negative and some gram-positive bacteria small regulatory RNAs (sRNAs) that bind the RNA chaperone Hfq have a pivotal role in modulating virulence, stress responses, metabolism, and biofilm formation. These sRNAs recognize transcripts through base-pairing, and sRNA-mRNA annealing consequently alters the translation and/or stability of transcripts leading to changes in gene expression. We have previously found that the highly conserved 3'-to-5' exoribonuclease polynucleotide phosphorylase (PNPase) has an indispensable role in paradoxically stabilizing Hfq-bound sRNAs and promoting their function in gene regulation in Escherichia coli. more...

Organism:: Escherichia coli str. K-12 substr. MG1655

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL15010
12 Samples

Download data: TXT, XLSX

Series

Accession:: GSE125368

ID:: 200125368

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001172569.

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:: GPL20051 GPL20056
42 Samples

Download data

Series

Accession:: GSE117256

ID:: 200117256

PubMed Full text in PMC Similar studies

Select item 20011725510.

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

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20011725211.

Role of ProQ in Salmonella virulence - pulse expression

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

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20011723612.

Role of ProQ in Salmonella virulence - dual RNA-Seq

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

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20023519413.

A novel acetyltransferase regulates the RNA binding capacity of the RNA chaperone Hfq in Escherichia coli

(Submitter supplied) Bacterial small regulatory RNAs (sRNAs) regulate gene expression by base-pairing to their target mRNAs. In Escherichia coli and many other bacteria, this process is dependent on the RNA chaperone Hfq, which binds sRNAs and mRNAs on different faces. YhbS (renamed here as HqbA), a putative Gcn5-related N-acetyltransferase (GNAT), was identified as a novel silencer of sRNA signaling in a genomic library screen. more...

Organism:: Escherichia coli str. K-12 substr. MG1655

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18956
24 Samples

Download data: XLSX

Series

Accession:: GSE235194

ID:: 200235194

PubMed Similar studies

Select item 20025001414.

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

PubMed Full text in PMC Similar studies

Select item 20011936415.

Characterize the regulon of 6C sRNA in Mycobacteria smegmatis

(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

Series

Accession:: GSE119364

ID:: 200119364

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20004612016.

Small RNAs and RNA chaperone Hfq in enterohemorrhagic E. coli

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

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

Series

Accession:: GSE46120

ID:: 200046120

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20004611817.

UV-crosslinking and high throughput sequencing of cDNAs (CRAC) of the RNA chaperone Hfq in enterohaemorhaggic E. coli

(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 GPL17024 GPL17025
11 Samples

Download data: GTF

Series

Accession:: GSE46118

ID:: 200046118

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20004611318.

Transcriptional profile of pulsed AsxR in Escherichia coli O157:H7 str. TUV93-0

(Submitter supplied) Transcript abundance in Escherichia coli O157:H7 was determined in the presence or absence of pulsed expression of the small RNA, AsxR.

Organism:: Escherichia coli; Escherichia coli O157:H7

Type:: Expression profiling by array

Platform:: GPL3051
1 Sample

Download data: GPR, TXT

Series

Accession:: GSE46113

ID:: 200046113

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20022777219.

PhrS pulse expression RNA-seq

(Submitter supplied) A key challenge for understanding the role(s) played by short, non-coding RNAs (sRNAs) in bacteria is identifying the mRNA targets regulated by the sRNAs. Because the Hfq protein mediates the interactions between many sRNAs and the corresponding target mRNAs, one apporach to identify the mRNA targets of sRNAs is to capture sRNA:mRNA interactions occuring on Hfq by exposing cells to UV-irradiation, which forms cross-links between nucleic acids and proteins. more...