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Items: 1 to 20 of 11168

1.

Bacterial ribosome pause sites surveyed by an integration of ribosome profiling and nascent chain profiling II

(Submitter supplied) Ribosome pauses are associated with diverse co-translational events and determine the fate of mRNAs and proteins. Thus the identification of the precise pause sites across transcriptome is a key, however, the landscape in bacterial has remained ambiguous. Here, we harnessed the multiple ribosome profiling strategies (standard, high-salt-wash, and disome) to survey the robust ribosome pause sites in E. more...
Organism:
Escherichia coli
Type:
Non-coding RNA profiling by high throughput sequencing; Other
Platform:
GPL25368
2 Samples
Download data: TXT
Series
Accession:
GSE180482
ID:
200180482
2.

Bacterial ribosome pause sites surveyed by an integration of ribosome profiling and nascent chain profiling

(Submitter supplied) Ribosome pauses are associated with diverse co-translational events and determine the fate of mRNAs and proteins. Thus the identification of the precise pause sites across transcriptome is a key, however, the landscape in bacterial has remained ambiguous. Here, we harnessed the multiple ribosome profiling strategies (standard, high-salt-wash, and disome) to survey the robust ribosome pause sites in E. more...
Organism:
Escherichia coli
Type:
Other; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL21433
7 Samples
Download data: TXT
Series
Accession:
GSE160623
ID:
200160623
3.

A multi-omics study of bacterial growth arrest in a synthetic biology application

(Submitter supplied) Scaling up the functioning of synthetic circuits from microplates to bioreactors is far from trivial to achieve. We here test the scalability performance of a previously developed growth switch for increasing product yields in bacteria, based on external control of RNA polymerase expression. We show that, in liter-scale bioreactors operating in fed-batch mode, growth-arrested Escherichia coli cells are able to convert glucose to glycerol at an increased yield. more...
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25140
18 Samples
Download data: CSV, TXT
Series
Accession:
GSE168336
ID:
200168336
4.

The strategy of a novel way to enhance bacterial motility

(Submitter supplied) Bacterial motility shows a strong evolvable feature depending on the environment. Hyper-motile E. coli could be isolated by evolving non-motile E. coli due to the mutations that enhanced transcriptional expression of the master regulator of the flagellum biosynthesis, FlhDC. These hyper-motile isolates showed reduced growth fitness but with the molecular mechanisms unrevealed. Here we obtained a novel type of hyper-motile isolates by evolving a weakly-motile E. more...
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25368
21 Samples
Download data: TXT
Series
Accession:
GSE165151
ID:
200165151
5.

A single-cell massively parallel reporter assay detects cell type specific cis-regulatory activity

(Submitter supplied) We developed a single-cell massively parallel reporter assay (scMPRA) to measure the activity of libraries of cis-regulatory sequences (CRSs) across multiple cell-types simultaneously. As a proof of concept, we assayed a library of core promoters in a mixture of HEK293 and K562 cells and showed that scMPRA is a reproducible, highly parallel, single-cell reporter gene assay. Our results show that housekeeping promoters and CpG island promoters have lower activity in K562 cells relative to HEK293, which likely reflects developmental differences between the cell lines. more...
Organism:
Homo sapiens; Escherichia coli
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL16085 GPL18573
13 Samples
Download data: CSV, MTX, TSV
Series
Accession:
GSE188639
ID:
200188639
6.

Ferric Citrate Uptake is a Virulence Factor in Uropathogenic Escherichia coli

(Submitter supplied) More than half of women will experience a urinary tract infection (UTI) with uropathogenic Escherichia coli (UPEC) causing ~80% of uncomplicated cases. Iron acquisition systems are essential for uropathogenesis, and UPEC encode functionally redundant iron acquisition systems, underlining their importance. However, a recent UPEC clinical isolate, HM7 lacks this functional redundancy and instead encodes a sole siderophore, enterobactin. more...
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21222
6 Samples
Download data: CSV, FASTA, GFF
Series
Accession:
GSE188170
ID:
200188170
7.

Selective recruitment of the AAA+ ATPase TnsC increases the fidelity of Type I-F CRISPR RNA-guided transposition

(Submitter supplied) Bacterial transposons are pervasive mobile genetic elements that exploit distinct DNA binding proteins for their horizontal spread. For example, E. coli Tn7 homes to a specific attachment site using a TniQ family protein, whereas diverse Tn7-like transposons employ Type I or Type V CRISPR-Cas systems to insert downstream of target sites specified by a guide RNA. Despite this targeting pathway diversity, transposition invariably requires TnsB, a DDE superfamily transposase that catalyses DNA excision and insertion, and TnsC, a AAA+ ATPase that is thought to communicate between the transposase and targeting proteins. more...
Organism:
Escherichia coli
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL29469 GPL21222
31 Samples
Download data: BED, BW, XLSX
Series
Accession:
GSE183114
ID:
200183114
8.

Spatial alanine metabolism determines local growth dynamics of Escherichia coli colonies

(Submitter supplied) By using transcriptomics, we studied the spatiotemporal transcriptional changes in Escherichia coli biofilm colonies
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26155
48 Samples
Download data: TXT
Series
Accession:
GSE175768
ID:
200175768
9.

Transcription-wide distribution of dihydrouridine (D) into mRNAs reveals its requirement for meiotic chromosome segregation.

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Escherichia coli; Schizosaccharomyces pombe; Homo sapiens
Type:
Expression profiling by high throughput sequencing; Other
4 related Platforms
60 Samples
Download data
Series
Accession:
GSE145686
ID:
200145686
10.

Transcription-wide distribution of dihydrouridine (D) into mRNAs reveals its requirement for meiotic chromosome segregation. [Rho-Seq]

(Submitter supplied) Here we have developed Rho-seq, an integrated pipeline detecting a range of modifications through differential modification-dependent Rhodamine labeling. Using Rho-seq, we report that the reduction of uridine to dihydrouridine by the Dus reductase family targets tRNAs in E. coli but expands to mRNAs is yeast. The modified mRNAs are enriched for cytoskeleton related encoded protein. We show that the a-tubulin encoding mRNA nda2 undergoes dihydrouridination, which affects its protein expression level. more...
Organism:
Homo sapiens; Escherichia coli; Schizosaccharomyces pombe
Type:
Other
4 related Platforms
44 Samples
Download data: XLSX
Series
Accession:
GSE145685
ID:
200145685
11.

E. coli SymE-SPA binds DNA in a wide variety of genomic locations in vivo [ChIP-seq]

(Submitter supplied) The purpose of this experiment was to demonstrate that SymE-SPA binds DNA in vivo when overexpressed, and identify where in the genome SymE-SPA binds. To do this SymE-SPA and an untagged SymE control were expressed, and areas of the genome enriched for SymE-SPA binding were identified.
Organism:
Escherichia coli
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL16085
8 Samples
Download data: WIG
Series
Accession:
GSE185893
ID:
200185893
12.

There is no evidence that E. coli SymE cleaves RNA [RNA-seq]

(Submitter supplied) The purpose of this experiment was to determine whether or not we could detect cleavage in mRNA extracted from cells that expressed high levels of the E. coli protein SymE. This was done by comparing read density across transcripts from +symE and empty vector samples after 0, 30 and 90 minutes of induction.
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21222
18 Samples
Download data: CSV
Series
Accession:
GSE185892
ID:
200185892
13.

Time series (T= 0-4 hours) for E. coli K-12 MC4100 after a shift from 23˚C to 37˚C (M9 minimal glycerol medium, exponential phase growth)

(Submitter supplied) We investigated the effect of a temperature shift from 23˚C to 37˚C, mimicking the temperature transition experienced by a microbe as it enters a human host. This strategy allowed the exploration of the kinetics of gene expression changes in immediate response to a temperature upshift and to characterize the suite of genes required to respond to 37˚C in the first few hours. We demonstrate that a significant number of genes are rapidly altered in expression within minutes to hours after a temperature shift. more...
Organism:
Escherichia coli
Type:
Expression profiling by array
Platform:
GPL6540
9 Samples
Download data: GPR, XLSX
Series
Accession:
GSE165794
ID:
200165794
14.

Multidimensional PTEN missense variant analysis reveals variant subgroups including potential dominant negatives

(Submitter supplied) Determining the pathogenicity of human genetic variants is a critical challenge, and functional assessment is often the only option. Experimentally characterizing millions of possible missense variants in thousands of clinically important genes will likely require generalizable, scalable assays. We previously developed Variant Abundance by Massively Parallel Sequencing (VAMP-seq), which measures the effects of thousands of missense variants of a protein on intracellular abundance in a single experiment. more...
Organism:
Escherichia coli; Homo sapiens
Type:
Other
Platforms:
GPL18573 GPL21222 GPL24462
9 Samples
Download data: CSV
15.

Inactivation of RNase P in Escherichia coli significantly changes post-transcriptional RNA metabolism

(Submitter supplied) Ribonuclease P (RNase P) is the only ribonuclease responsible for 5'-end maturation of tRNAs in all kingdoms of life. In Escherichia coli, it is also essential for separation of pre-tRNAs from multiple polycistronic transcripts. Using RNA sequencing (RNA-seq), we show here that RNase P affects the abundance of ~44% of the expressed mRNAs demonstrating a much more widespread role in mRNA decay than previously thought. more...
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21222
12 Samples
Download data: CSV
Series
Accession:
GSE149024
ID:
200149024
16.

The global transcriptomic profile in the spermidine-stressed E. coli

(Submitter supplied) To achieve extreme spermidine stress we used DspeG E. coli strain. We identified the pathways that are altered under spermidine stress. Among many changes spermidine altered the iron-sulfur cluster metabolism and redox balance in the cells. Therefore, we have shown that superoxide quencher, NAC and ascorbate mitigates spermidine stress. Overall our data explains the importaance of tight spermidine homeostasisin the cell.
Organism:
Escherichia coli
Type:
Expression profiling by array
Platform:
GPL22574
4 Samples
Download data: TXT
Series
Accession:
GSE154618
ID:
200154618
17.

CRP(T168P) and AC(S254R) mutant strain of E. coli W

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL28126 GPL29469 GPL21433
14 Samples
Download data: GFF, HTML, TXT
Series
Accession:
GSE162597
ID:
200162597
18.

Genome resequencing data of adaptive laboratory evolved E. coli W

(Submitter supplied) Using a synthetic biosensor to couple production of a specific metabolite with cell growth, we spontaneously evolved cells under the selective condition toward the acquisition of genotypes that optimally reallocated cellular resources. Using 3-hydroxypropionic acid (3-HP) production from glycerol in Escherichia coli as a model system, we found spontaneous mutations in the conserved regions of AC and CRP.
Organism:
Escherichia coli
Type:
Other
Platform:
GPL29469
3 Samples
Download data: HTML, TXT
Series
Accession:
GSE162596
ID:
200162596
19.

Transcriptomic data of CRP(T168P) and AC(S254R) mutant strain of E. coli W

(Submitter supplied) Using a synthetic biosensor to couple production of a specific metabolite with cell growth, we spontaneously evolved cells under the selective condition toward the acquisition of genotypes that optimally reallocated cellular resources. Using 3-hydroxypropionic acid (3-HP) production from glycerol in Escherichia coli as a model system, we determined that spontaneous mutations in the conserved regions of proteins involved in global transcriptional regulation altered the expression of several genes associated with central carbon metabolism. more...
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21433
6 Samples
Download data: GFF
Series
Accession:
GSE162595
ID:
200162595
20.

Genome-wide maps of CRP(T168P)-binding change in Escherichia coli W

(Submitter supplied) Using a synthetic biosensor to couple production of a specific metabolite with cell growth, we spontaneously evolved cells under the selective condition toward the acquisition of genotypes that optimally reallocated cellular resources. Using 3-hydroxypropionic acid (3-HP) production from glycerol in Escherichia coli as a model system, we determined that spontaneous mutations in the conserved regions of proteins involved in global transcriptional regulation altered the expression of several genes associated with central carbon metabolism. more...
Organism:
Escherichia coli
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL28126
5 Samples
Download data: GFF
Series
Accession:
GSE162594
ID:
200162594
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