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Items: 1 to 20 of 18745

1.

Genome-wide distribution of Tus-GFP in KRX E. coli

(Submitter supplied) We examined the chromosomal distribution of GFP-tagged Tus (Tus-GFP) in exponentially growing E. coli (KRX) using chromosome immunoprecipitation (ChIP)-Seq. Our ChIP-seq allowed delineation of a refined minimal replication fork trap within E. coli comprising two clusters of three Ter sites
Organism:
Escherichia coli KRX
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL29521
2 Samples
Download data: FASTA, TXT
Series
Accession:
GSE163680
ID:
200163680
2.

YciR, a specific 3′-phosphodiesterases, plays a role in the pathogenesis of Uropathogenic Escherichia coli CFT073

(Submitter supplied) Uropathogenic Escherichia coli are a prevailing causation of urinary tract infections infections and characterized by recurrence and resistance to antibiotics due to their misuse, causing a large economic burden to individuals and countries. An early determinant of the pathogenicity of UPEC is its ability to form intracellular bacterial communities in the cytoplasm of bladder epithelial cells after its invasion for evading immune response. more...
Organism:
Escherichia coli CFT073
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20323
2 Samples
Download data: TXT
Series
Accession:
GSE189294
ID:
200189294
3.

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
4.

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
5.

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
6.

A comparison between two Escherichia coli K-12 MG1655 substrains possessing different swimming motility

(Submitter supplied) Substrains in Escherichia coli K-12 MG1655 can possess various swimming motility, which is mostly resulted from different expression levels of flhDC. Here, we studied the swimming motility of two MG1655 substrains, CY562 and CY570. Our results showed that CY562 had no insertion at the promoter region of flhDC and possessed no swimming motility. In contrast, CY570 had an IS-element insertion at the promoter region of flhDC and showed a hyper-motile phenotype. more...
Organism:
Escherichia coli str. K-12 substr. MG1655
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26592
4 Samples
Download data: TXT
Series
Accession:
GSE165438
ID:
200165438
7.

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
8.

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
9.

Transcriptional profiling to elucidate processes regulated by 2',3'-cyclic nucleotide phosphodiesterase (CNPase) in Escherichia coli K12 BW25113 (E. coli)

(Submitter supplied) The impact of 2',3'-cyclic nucleotide phosphodiesterase (CNPase) on global gene expression in E. coli was investigated by heterologous expression of mammalian CNPase in a strain containing a deletion of the 'rna' gene. 'rna' encodes an endoribonuclease capable of hydrolyzing RNA into 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) such that deletion of 'rna' drastically reduces 2',3'-cNMPs levels to undetectable levels. more...
Organism:
Escherichia coli K-12
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30519
6 Samples
Download data: TSV
Series
Accession:
GSE182184
ID:
200182184
10.

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
11.

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
12.

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
13.

Transcriptomic study of E. coli 042 with a variant of aggR gene with a FRT sequence inserted in its 3´UTR by RNA-seq

(Submitter supplied) A common genomic feature of most EAEC strains is the presence of a virulence plasmid termed pAA. Plasmid-encoded virulence determinants are, among others, a transcriptional activator termed AggR, a member of the AraC-XylS family of transcription factors. We have previously determined the direct correlation between (p)ppGpp, expression of AggR and biofilm development in strain EAEC 042 (https://0-doi-org.brum.beds.ac.uk/10.3389/fmicb.2018.00717). more...
Organism:
Escherichia coli 042
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24145
2 Samples
Download data: XLSX
Series
Accession:
GSE160448
ID:
200160448
14.

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
15.

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:
Escherichia coli; Homo sapiens; Schizosaccharomyces pombe
Type:
Other
4 related Platforms
44 Samples
Download data: XLSX
Series
Accession:
GSE145685
ID:
200145685
16.

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
17.

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
18.

RNA sequencing of E. coli NCM3722 over the course of glucose to acetate growth transition

(Submitter supplied) To understand the gene response during the glucose to acetate diauxic transition, we grew E. coli in minimal media with acetate and a small amount of glucose. Cells were collected and RNA was purified at different time points during the growth transition, including pre-shift (growth on glucose), 5 minutes, 15 minutes, 60 minutes and 120 minutes after glucose run-out, and steady state growth on acetate (post-shift).
Organism:
Escherichia coli K-12
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24377
6 Samples
Download data: TXT
Series
Accession:
GSE185426
ID:
200185426
19.

IPOD-HR, ChIP-seq, RNA-seq of E. coli nucleoid associated protein deletions

(Submitter supplied) There is increasing evidence that microbes maintain a structured chromosome, which in turn impacts gene expression. However tools to profile the genome landscape and binding of key architectural proteins have been limited. We recently discovered densely occupied, multi-kilobase regions in E. coli that are transcriptionally silent, similar to eukaryotic heterochromatin. These regions, termed EPODs, overlap metabolic pathways and parasitic elements such as prophages. more...
Organism:
Escherichia coli str. K-12 substr. MG1655
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18956
124 Samples
Download data
Series
Accession:
GSE164796
ID:
200164796
20.

sRNA-mRNA pairing in absence of the RNA chaperone Hfq

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Escherichia coli K-12
Type:
Other
Platform:
GPL24020
12 Samples
Download data
Series
Accession:
GSE113593
ID:
200113593
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