GEO DataSets

(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

(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

(Submitter supplied) Strain engineering for industrial production requires the improvement of tolerance to multiple unfavorable conditions. Here, we report using global regulator libraries based on the CRISPR-enabled trackable genome engineering (CREATE) method to engineer tolerance against multiple inhibitors in Escherichia coli. Deep mutagenesis libraries were rationally designed, constructed, and screened to target 34,340 mutations across 23 global regulators. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14548

6 Samples

Download data: TXT, XLSX

(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:

Homo sapiens; Escherichia coli

Type:

Other

Platforms:

GPL14548 GPL24676 GPL32081

478 Samples

Download data: BED, TXT, XLSX

(Submitter supplied) Guanidine DNA quadruplex (G4-DNA) structures convey a distinctive layer of epigenetic information that is critical for the regulation of key biological activities and processes as genome transcription regulation, replication and repair. Despite several works that have been published recently, the information regarding their role and possible use as therapeutic drug targets in bacteria is still scarce. more...

Organism:

Staphylococcus aureus; Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17452 GPL14548

8 Samples

Download data: RPKM

(Submitter supplied) RNA-seq based transcriptome analysis was employed to understand the genome-wide expression patterns under the phytotoxin treatment. To identify differentially expressed genes, we compared phytotoxins (toxoflavin and tropolone) transcriptome to methanol transcriptome as the solvent of phytotoxins. The expression of 2327 and 830 genes was differentially changed by toxoflavin and tropolone, respectively.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14548

9 Samples

Download data: TXT

(Submitter supplied) Bacterial mRNAs have short life cycles, in which transcription is rapidly followed by translation and degradation within seconds to minutes. The resulting diversity of mRNA molecules across different life-cycle stages impacts their functionality but has remained unresolved. Here we quantitatively map the 3’ status of cellular RNAs in Escherichia coli during steady-state growth and report a large fraction of molecules (median>60%) that are fragments of canonical full-length mRNAs. more...

Organism:

Escherichia coli; synthetic construct; Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

5 related Platforms

37 Samples

Download data: BEDGRAPH

(Submitter supplied) We identified two new lethal stresses whose depletion results in bacterial cell death at least partially through incomplete BER. We confirmed that this pathway is causal to cell death and compared the various physiological changes that occur as a consequence of depletion of these two essentially proteins.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14548

14 Samples

Download data: XLSX

(Submitter supplied) N6-methyladenine (6mA) is a natural DNA modification and functions primarily in restriction-modification (R-M) systems in prokaryotes. Recent studies uncovered the existence and revealed the genome-wide distribution of 6mA in eukaryotes. Specifically, it was reported that 6mA was mainly enriched in mammalian mitochondrial DNA (mtDNA) and could regulate mitochondrial activity. we achieved the genome-wide mapping of 6mA in E. more...

Organism:

Escherichia coli; Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL14548 GPL11154

9 Samples

Download data: TSV

(Submitter supplied) Purpose:Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived E.coli transcriptome profiling (RNA-seq) of Wild type and ΔrecA with or without antibiotics treatment. Methods:libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument, Sequencing was carried out using a 2x150bp paired-end (PE) configuration, image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14548

8 Samples

Download data: XLSX

(Submitter supplied) In bacteria, adaptive regulation of gene expression occurs through the precise interactions of hundreds of DNA binding proteins across the chromosome. Decades of research has revealed the identity and functions of many of these regulators. However, a systems-level understanding of gene expression requires simultaneous, comprehensive monitoring of these interactions as a function of genetic and environmental perturbations. more...

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

52 Samples

Download data: GR, TSV

(Submitter supplied) In large-scale production processes, metabolic control is typically achieved by limited supply of essential nutrients like ammonia. With increasing bioreactor dimensions, microbial producers such as Escherichia coli are exposed to changing substrate availabilities due to limited mixing. In turn, cells sense and respond to these dynamic conditions leading to frequent activation of their regulatory programs which result in production yield losses. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14548

20 Samples

Download data: XLSX

(Submitter supplied) We develop a model for ribosome-protected fragment (RPF) spectra that accounts for the local codon context-dependent variation of peptide elongation times and fragment processing biases. We use a Marquardt algorithm for non-linear regression with maximum likelihood (ML) like statistics to fit the RPF sequencing data. Taking advantage of the factorial character of the present model, we reconstruct the parameters adhering to an ideal, unbiased RPF spectrum.

Organism:

Escherichia coli

Type:

Other

Platform:

GPL14548

3 Samples

Download data: TAB

(Submitter supplied) Effect of three different antimicrobial compounds, trimethoprim(TMP), cis-tetra-ortho-chloroazobenzene-trimethoprim (TCATa) and trans-tetra-ortho-chloroazobenzene-trimethoprim (TCATd) , on the resistance development and transcriptome of the E. coli strain CS1562. In addition, acontrol sample was taken along of the propagated parent strain (CS1562) without the addition of any compounds.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14548

4 Samples

Download data: TXT

(Submitter supplied) We used next generation sequencing to sequence the transcriptome of AIEC str. NRG857c and identify the genes that are differentially regulated in the gut.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14548

6 Samples

Download data: TXT

(Submitter supplied) In a given bacterial population, antibiotic treatment kills a large portion of the population, while a small, tolerant subpopulation survives. Tolerant cells disrupt the efficacy of antibiotic treatment and increase the likelihood that a population gains antibiotic resistance. Antibiotic tolerance is different from resistance because tolerant cells cannot grow and replicate in the presence of the antibiotic, but when the antibiotic is removed, they begin to propagate. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14548

18 Samples

Download data: CSV

(Submitter supplied) Purpose: We investigate the evolutionary footprints of a bacteria-plasmid association consisting of Escherichia coli K-12 MG1655 and plasmid RP4 undergoing a long-term sub-MIC antibiotic stress. Methods: Bacterial mRNA profiles of evolved RP4-carrying strains (E:H:p) and ancestral RP4-carrying strains (A:H:p) were generated by deep sequencing on an Illumina Hiseq platform. The sequence reads that passed quality filters were analyzed by Burrows–Wheeler Aligner (BWA), followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14548

2 Samples

Download data: TXT

(Submitter supplied) Probe rRNA structural changes during assembly with dimethyl sulfate

Organism:

Escherichia coli

Type:

Other

Platform:

GPL14548

13 Samples

Download data: TSV, TXT

(Submitter supplied) When performing a computation, genetic circuits change states through a symphony of genetic parts that turn regulator expression on and off. Debugging is frustrated by an inability to measure part function and identify the origins of failures. Here, we take “snapshots” of a large genetic circuit in different states. RNA-seq is used to visualize circuit function as a changing pattern of RNA polymerase (RNAP) flux along the DNA. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14548

18 Samples

Download data: WIG, XLS

(Submitter supplied) Ribosome profiling analysis of phage T4 infected E. coli yielded protected mRNA fragments within the normal size range derived from ribosomes stalled at the take-off codon. Ribosomes at this position also yielded some 53 nucleotide fragments, 16 longer. These were due to protection of the nucleotides that form the 5’ stem loop.

Organism:

Escherichia coli; Tequatrovirus T4

Type:

Other

Platforms:

GPL14548 GPL28207

4 Samples

Download data: TXT