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Items: 13

1.

Bacteria conjugate ubiquitin-like proteins to interfere with phage assembly

(Submitter supplied) Multiple immune pathways in humans conjugate ubiquitin-like proteins to virus and host molecules as a means of antiviral defense. Here we studied an anti-phage defense system in bacteria, comprising a ubiquitin-like protein, ubiquitin-conjugating enzymes E1 and E2, and a deubiquitinase. We show that during phage infection, this system specifically conjugates the ubiquitin-like protein to the phage central tail fiber, a protein at the tip of the tail that is essential for tail assembly as well as for recognition of the target host receptor. more...
Organism:
Escherichia coli; Caulobacter sp. Root343
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL34341 GPL32081
12 Samples
Download data: XLSX
Series
Accession:
GSE262579
ID:
200262579

PubMed Similar studies

2.

A new reagent for in vivo structure probing of RNA G and U residues that improves RNA structure prediction alone and combined with DMS

(Submitter supplied) A key to understanding the roles of RNA in regulating gene expression is knowing their structures in vivo. One way to obtain this information is through probing structures of RNA with chemicals. To probe RNA structure directly in cells, membrane-permeable reagents that modify the Watson-Crick (WC) face of unpaired nucleotides can be used. While dimethyl sulfate (DMS) has led to substantial insight into RNA structure, it has limited nucleotide specificity in vivo, with WC face reactivity only at Adenine (A) and Cytosine (C) at neutral pH. more...
Organism:
Escherichia coli
Type:
Other
Platform:
GPL32081
33 Samples
Download data: TXT
Series
Accession:
GSE254895
ID:
200254895

PubMed Similar studies

3.

Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters [plasmid libraries subassembly, v2]

(Submitter supplied) The inability to scalably and precisely measure the activity of developmental enhancers in multicellular systems is a bottleneck in genomics. Here, we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. The resulting measurement of reporter expression is accurate over multiple orders of magnitude, with a precision approaching the limit set by Poisson counting noise. more...
Organism:
Escherichia coli
Type:
Other
Platforms:
GPL32081 GPL21222 GPL28771
42 Samples
Download data: TXT
Series
Accession:
GSE245260
ID:
200245260

PubMed Full text in PMC Similar studies

4.

Discovery of diverse DNA cytosine deaminases enables a single-enzyme method for base resolution methylation detection

(Submitter supplied) Cytosine deaminases have important uses in the detection of epigenetic modifications and in genome editing. However, the range of applications of deaminases is limited by their substrate preference. To expand the toolkit of deaminases, we developed an in-vitro approach that bypasses a major hurdle with their severe toxicity in expression hosts. We screened 175 putative cytosine deaminases, primarily from bacteria, and found enzymes with strong activity on double- and single-stranded DNA in various sequence contexts, including some without any sequence constraints. more...
Organism:
Escherichia coli; Homo sapiens
Type:
Other
Platforms:
GPL32081 GPL14548 GPL24676
478 Samples
Download data: BED, TXT, XLSX
Series
Accession:
GSE233932
ID:
200233932

5.

tRNA structure-seq in peptide-rich droplets

(Submitter supplied) Compartmentalization of RNA in biopolymer-rich membraneless organelles is now understood to be pervasive and critical for the function of extant biology, and has been proposed as a prebiotically-plausible way to accumulate RNA. Compartment-RNA interactions that drive encapsulation have the potential to influence RNA structure and function in compartment- and RNA sequence-dependent ways. Herein, we detail Next-Generation Sequencing (NGS) experiments performed for the first time in membraneless compartments called complex coacervates to characterize the fold of many different transfer RNAs (tRNAs) simultaneously under the potentially denaturing conditions of these compartments. more...
Organism:
Escherichia coli; synthetic construct
Type:
Other
Platforms:
GPL32628 GPL32081
60 Samples
Download data
Series
Accession:
GSE225730
ID:
200225730

PubMed Full text in PMC Similar studies

6.

Interplay between bacterial RNA 5'-termini deNADding protein NudC and DEAD-box RNA helicase CsdA in stress-responses

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32081
21 Samples
Download data: TSV
Series
Accession:
GSE224608
ID:
200224608

PubMed Full text in PMC Similar studies

7.

Whole transcriptome sequencing of E. coli BW25113 wt and nudC knockout strains

(Submitter supplied) In the present study we performed total RNA sequencing of E. coli BW25113 wt and nudC knockout strains. RNA-seq analysis revealed that the inactivation of nudC gene in bacteria shows alteration of level of sRNA and protein-coding transcripts mainly associated with bacterial chemotaxis and flagellar assembly pathways.
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32081
6 Samples
Download data: TSV
Series
Accession:
GSE224606
ID:
200224606

PubMed Full text in PMC Similar studies

8.

5’-NAD-RNA identification in E. coli BW25113 wt, nudC and csdA knockouts

(Submitter supplied) In the present study we applied NAD captureSeq to charecterize the 5'-NAD-RNA profile of E. coli BW25113 wt strain as well as nudC and csdA knockouts. The data obtained showed that both knockouts resulted in an increased number of identified 5’-NAD-RNA species, thus suggesting that CsdA might add a potentially new layer of control on NAD-epitranscriptomic landscape.
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32081
15 Samples
Download data: TSV
Series
Accession:
GSE224605
ID:
200224605

PubMed Full text in PMC Similar studies

9.

The distinct transcriptome of virulence-associated phylogenetic group B2 Escherichia coli

(Submitter supplied) Strains of urinary tract associated E. coli both recent isolates and from the ECOR collection and non pathogenic E. coli strains were analyzed. Replicates were performed to establish the reproduciblity, then single experiments were performed there on.
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL21222 GPL32081
45 Samples
Download data: FA, MATRIX
Series
Accession:
GSE235964
ID:
200235964

10.

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; Escherichia coli; Synechocystis sp. PCC 6803; Staphylococcus aureus; Bacillus amyloliquefaciens; Lactiplantibacillus plantarum; Cryptococcus neoformans; Caulobacter vibrioides; Segatella copri; Alistipes finegoldii; Hoylesella timonensis; compost metagenome; Listeria monocytogenes; Saccharomyces cerevisiae; Salmonella enterica; Parabacteroides merdae
Type:
Other
17 related Platforms
199 Samples
Download data: BEDGRAPH, TXT, XLSX
Series
Accession:
GSE153497
ID:
200153497

PubMed Full text in PMC Similar studies SRA Run Selector

11.

probe based bacterial single-cell RNA sequencing predicts toxin regulation

(Submitter supplied) Clonal bacterial populations rely on transcriptional variation across individual cells to commit to specialized states that increase the population’s fitness. Such heterogeneous gene expression is implicated in fundamental microbial processes including sporulation, cell communication, detoxification, substrate utilization, competence, biofilm formation, and motility1. To identify specialized cell states and determine the processes by which they develop, isogenic bacterial populations need to be studied at the single cell level2,3. more...
Organism:
Escherichia coli; Clostridium perfringens; Bacillus subtilis
Type:
Expression profiling by high throughput sequencing
4 related Platforms
8 Samples
Download data: H5
Series
Accession:
GSE223752
ID:
200223752

PubMed Full text in PMC Similar studies

12.

Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Escherichia coli; Homo sapiens; Mus musculus
Type:
Expression profiling by high throughput sequencing; Other
7 related Platforms
368 Samples
Download data
Series
Accession:
GSE217690
ID:
200217690

PubMed Full text in PMC Similar studies

13.

System-wide analyses reveal essential roles of N-terminal protein modification in bacterial physiology

(Submitter supplied) Removal of the N-terminal formyl group on nascent proteins by peptide deformylase (PDF) is the most prevalent protein modification in bacteria that impacts over 90% of the proteome. PDF is essential and a critical target of antibiotic development; however, its role in bacterial physiology remains a long-standing question. In this work, we used system-wide and time-resolved analyses of the E. coli translatome and proteome to investigate the consequences of PDF inhibition at different stages. more...
Organism:
Escherichia coli
Type:
Other
Platforms:
GPL18133 GPL32081
12 Samples
Download data: TXT
Series
Accession:
GSE199360
ID:
200199360

PubMed Full text in PMC Similar studies

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