U.S. flag

An official website of the United States government

Format
Items per page
Sort by

Send to:

Choose Destination

Search results

Items: 1 to 20 of 15104

1.

RNA-guided RNA silencing by an 1 Asgard archaeal Argonaute

(Submitter supplied) The dataset contains small RNAs that associated with HrAgo1 during heterologous expression in E. coli. The goal of the study was to determine what type of small RNAs associate with HrAgo1 and from what RNA transcripts these small RNAs are derived
Organism:
Escherichia coli
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL25368
1 Sample
Download data: XLSX
Series
Accession:
GSE267550
ID:
200267550
2.

RNAP stalling-derived genome instability underlies ribosomal antibiotics efficacy and resistance evolution (ChIP-seq data)

(Submitter supplied) Bacteria often evolve antibiotic resistance through mutagenesis. However, the processes causing the mutagenesis have not been fully resolved. Here we found that a broad range of ribosome-targeting antibiotics caused mutations through an underexplored pathway. Focusing on the clinically important aminoglycoside gentamicin, we found that the translation inhibitor caused genome-wide premature stalling of RNA polymerase (RNAP) in a loci-dependent manner. more...
Organism:
Escherichia coli
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL25368
12 Samples
Download data: BED, TXT
Series
Accession:
GSE267245
ID:
200267245
3.

RNA Post-transcriptional Modifications of an Early-Stage Large Subunit Ribosomal Intermediate

(Submitter supplied) Protein production by the ribosomes is fundamental to life and proper assembly of the ribosome is required for protein production. The RNA, which is post-transcriptionally modified, provides the platform for ribosome assembly. Thus, a complete understanding of ribosome assembly requires the determination of the RNA post-transcriptional modifications in all the ribosome assembly intermediates and on each pathway. more...
Organism:
Escherichia coli
Type:
Other
Platform:
GPL16085
3 Samples
Download data: CSV
Series
Accession:
GSE232539
ID:
200232539
4.

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:
Caulobacter sp. Root343; Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL34341 GPL32081
12 Samples
Download data: XLSX
Series
Accession:
GSE262579
ID:
200262579
5.

Interrogation of RNA-protein interaction dynamics in bacterial growth

(Submitter supplied) RNA-protein interactions are fundamental for bacterial homeostasis. However, we lack a system-wide understanding of their dynamics upon environmental perturbation. In this study, we have characterised the dynamics of 91% of the Escherichia coli proteome and the RNA-interaction properties of 271 RNA-binding proteins (RBPs) at different growth phases. We find that 68% of RBPs differentially bind RNA across growth phases and reveal novel RBP functions for proteins like the chaperone HtpG, a new tRNA-binding protein. more...
Organism:
Escherichia coli
Type:
Other
Platform:
GPL16085
8 Samples
Download data: BEDGRAPH
Series
Accession:
GSE235661
ID:
200235661
6.

Transcriptome analysis of Escherichia coli TO114 under salt stress

(Submitter supplied) Here, we treated Escherichia coli strain TO114 expressing a halotolerant cyanobacterium Halothece sp. PCC7418-derived NhaC Na+/H+ antiporter (H2569) with salt stress (0.4 M NaCl) and performed RNA sequencing analysis.
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25368
3 Samples
Download data: XLSX
Series
Accession:
GSE264731
ID:
200264731
7.

Antagonistic conflict between transposon-encoded introns and guide RNAs

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Clostridium senegalense; Escherichia coli
Type:
Other; Expression profiling by high throughput sequencing
Platforms:
GPL21222 GPL34292
8 Samples
Download data: BW
Series
Accession:
GSE261344
ID:
200261344
8.

Antagonistic conflict between transposon-encoded introns and guide RNAs (RNA-Seq)

(Submitter supplied) TnpB nucleases represent the evolutionary precursors to CRISPR-Cas12 and are widespread in all domains of life. IS605-family TnpB homologs function in bacteria as programmable RNA-guided homing endonucleases driving transposon maintenance through DSB-stimulated homologous recombination. Here we uncover molecular mechanisms of transposition lifecycle of IS607-family elements that, remarkably, also encode group I introns. more...
Organism:
Clostridium senegalense; Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL21222 GPL34292
4 Samples
Download data: BW
Series
Accession:
GSE261343
ID:
200261343
9.

Antagonistic conflict between transposon-encoded introns and guide RNAs (RIP-Seq)

(Submitter supplied) TnpB nucleases represent the evolutionary precursors to CRISPR-Cas12 and are widespread in all domains of life. IS605-family TnpB homologs function in bacteria as programmable RNA-guided homing endonucleases driving transposon maintenance through DSB-stimulated homologous recombination. Here we uncover molecular mechanisms of transposition lifecycle of IS607-family elements that, remarkably, also encode group I introns. more...
Organism:
Escherichia coli
Type:
Other
Platform:
GPL21222
4 Samples
Download data: BW
Series
Accession:
GSE261342
ID:
200261342
10.

The genetic architecture of protein interaction affinity and specificity

(Submitter supplied) Proteins function in crowded cellular environments in which they must bind to specific target proteins but also avoid binding to many other off-target proteins. In large protein families this task is particularly challenging because many off-target proteins have very similar structures. How this specificity of physical protein-protein interactions in cellular networks is encoded and evolves is not very well understood. more...
Organism:
Saccharomyces cerevisiae; Escherichia coli
Type:
Other
Platforms:
GPL17342 GPL21222
19 Samples
Download data: TXT
Series
Accession:
GSE245326
ID:
200245326
11.

Functional CRISPR-Cas9 knockout screening of the genetic determinants of human fibroblast migration propensity

(Submitter supplied) Directional cell migration plays a central role in a wide range of physiological and pathological conditions, such as inflammation and cancer. Steps involved in cell migration include cell polarization, formation of membrane protrusions at the cell front side and adhesion disassembly at the rear side, and a general cytoskeletal rearrangement. However, there are cell-specific and context-specific molecular events acting in the process. more...
Organism:
Escherichia coli; Homo sapiens
Type:
Other
Platforms:
GPL11154 GPL14548
11 Samples
Download data: TXT
Series
Accession:
GSE266226
ID:
200266226
12.

Adenine effect on Enterohemorraghic E.coli

(Submitter supplied) Previous experiments have shown that E. feacalis increases EHEC virulence by secreting adenine, this RNAseq aims to understand the molecular mechanism underlaying adenine role on EHEC
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25368
20 Samples
Download data: TXT
Series
Accession:
GSE244178
ID:
200244178
13.

TnpB homologs exapted from transposons are RNA-guided transcription factors

(Submitter supplied) Transposon-encoded tnpB and iscB genes encode RNA-guided DNA nucleases that promote their own selfish spread through targeted DNA cleavage and homologous recombination. These widespread gene families were repeatedly domesticated over evolutionary timescales, leading to the emergence of diverse CRISPR-associated nucleases including Cas9 and Cas12. We set out to test the hypothesis that TnpB nucleases may have also been repurposed for novel, unexpected functions other than CRISPR-Cas. more...
Organism:
Enterobacter cloacae; Escherichia coli; Enterobacter sp. BIDMC93
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
4 related Platforms
51 Samples
Download data: BED, BW, XLSX
Series
Accession:
GSE245749
ID:
200245749
14.

Robust Host Engineering: Enhancing Escherichia coli´s Abiotic Stress Resistance through Ornithine Lipid Membrane Modification

(Submitter supplied) Transcriptome analysis revealed that strains had differentially expressed stress and membrane-related genes compared to the control strain
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25368
8 Samples
Download data: TXT, XLSX
Series
Accession:
GSE233657
ID:
200233657
15.

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
16.

A cell-free pipeline for recreating methylation patterns radically enhances DNA transformation in bacteria

(Submitter supplied) The bacterial world offers diverse strains for understanding medical and environmental processes and for engineering synthetic-biology chasses. However, genetically manipulating these strains has faced a long-standing bottleneck: how to efficiently transform DNA. Here we report IMPRINT, a generalized, rapid and scalable approach to overcome DNA restriction, a prominent barrier to transformation. IMPRINT utilizes cell-free systems to express DNA methyltransferases from the bacterial host’s restriction-modification systems. more...
Organism:
Escherichia coli; Bifidobacterium breve
Type:
Other
Platforms:
GPL25368 GPL33564
7 Samples
Download data: TSV
Series
Accession:
GSE240651
ID:
200240651
17.

RpoS acts as a global repressor of virulence gene expression in Escherichia coli O104:H4 and enteroaggregative E. coli

(Submitter supplied) In 2011, in Germany, Escherichia coli O104:H4 caused the enterohemorrhagic E. coli (EHEC) outbreak with the highest incidence rate of hemolytic uremic syndrome. This pathogen carries an exceptionally potent combination of EHEC- and enteroaggregative E. coli (EAEC)-specific virulence factors. Here, we identified an E. coli O104:H4 isolate that carried a single nucleotide polymorphism (SNP) in the start codon (ATG>ATA) of rpoS, encoding the alternative sigma factor S. more...
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21222
12 Samples
Download data: CSV
Series
Accession:
GSE243699
ID:
200243699
18.

Dual Barcode is Essential for the Specificity of DSB Repair Capture

(Submitter supplied) We discovered that PCR-mediated template switching poses a significant challenge in ensemble tagged PCR, particularly in the template sequences with high similarities, which we successfully addressed by introducing a dual barcode. Template switching presents in repair sequencing (repair seq) and severely interfere the interpretation of the association between repair outcomes and the sgRNA in the vicinity. more...
Organism:
Homo sapiens; Escherichia coli
Type:
Other
Platforms:
GPL15520 GPL25368 GPL16085
30 Samples
Download data: TXT
Series
Accession:
GSE253191
ID:
200253191
19.

A bioinformatic pipeline for analysis of M.EcoGII methylation footprint PacBio long-read sequence data

(Submitter supplied) Recent studies have combined DNA methyltransferase footprinting of genomic DNA in nuclei with long-read sequencing, resulting in detailed chromatin maps for multi-kilobase stretches of genomic DNA from one cell. Nucleosome footprints and nucleosome-depleted regions can be identified, yielding unprecedented information concerning their degree of correlation within the same cell. The enzyme of choice is M.EcoGII, which methylates adenines in any sequence context, potentially resulting in very high resolution. more...
Organism:
Escherichia coli; Saccharomyces cerevisiae
Type:
Other
Platforms:
GPL32099 GPL29643
12 Samples
Download data: BAM, BED, BIGWIG
Series
Accession:
GSE243114
ID:
200243114
20.

Epithelial relay of microbial signals coordinates intestinal macrophage supported barrier repair [E. coli strains]

(Submitter supplied) The gastrointestinal tract is colonized by trillions of microorganisms collectively known as the gut microbiota. These microbes provide essential signals to support healthy gut function. The microbiota is separated from internal tissue by a single layer of intestinal epithelial cells that not only provides a physical barrier but also relays luminal signals to underlying gut immune cells. Altered microbiota composition including loss of anti-inflammatory microbes or outgrowth of mucosa-associated bacteria such as adherent-invasive E. more...
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14548
34 Samples
Download data: TXT
Series
Accession:
GSE261061
ID:
200261061
Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

db=gds|term=txid562[Organism:noexp]|query=1|qty=297|blobid=MCID_6655acae6c05354989d09f8e|ismultiple=true|min_list=5|max_list=20|def_tree=20|def_list=|def_view=|url=/Taxonomy/backend/subset.cgi?|trace_url=/stat?
   Taxonomic Groups  [List]
Tree placeholder
    Top Organisms  [Tree]

Find related data

Search details

See more...

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...
Support Center