GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Escherichia coli

Type:

Other; Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

4 related Platforms

118 Samples

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(Submitter supplied) Control of gene expression is fundamental to biology, and post transcriptional regulation is an important component of this process. In mammals, the 3′UTR in particular serves as a major source of regulatory information within the transcript. Here, we developed an accurate, high throughput, reporter based system to evaluate the impact of >1,400 full length human 3′UTRs on RNA stability, translational regulation, and total protein output. more...

Organism:

Escherichia coli

Type:

Other

Platforms:

GPL16085 GPL25346

4 Samples

Download data: TSV

(Submitter supplied) With the growing threat posed by emerging drug-resistant bacteria, the discovery of new antibiotics and the exploration of additional antimicrobial mechanisms of medicines currently used in the clinic are urgent. In this study, we found that disulfiram, a drug used for the treatment of alcohol addiction, inhibited the growth of multiple bacteria and quickly inhibited the growth of E. coli. When combined with kanamycin or polymyxins in vitro, disulfiram could augment the bactericidal effect against E. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

6 Samples

Download data: TXT, XLS

(Submitter supplied) Binding to RNA has been observed for an ever-increasing number of proteins, which often have other functions. The contributions of RNA binding to protein function are best discerned by studying “separation-of-function” mutants that hamper interaction with RNA without affecting other aspects of protein function. To design these mutants, we need precise knowledge of the residues that contribute to the affinity of the protein to its RNA ligands. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL30119

4 Samples

Download data: TSV

(Submitter supplied) Plasmids are widely used across molecular biology and are becoming increasingly valuable products, but robust plasmid replication is held back by stability issues in the host. This study investigated how Escherichia coli responds to plasmid stress at the transcriptional level by modulating plasmid copy number, plasmid size, selection marker and carbon source. This GEO contains controls from this study alone.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

4 Samples

Download data: CSV, TXT

(Submitter supplied) We report the genome-wide analysis from chromatin immunoprecipitated DNA (ChIP-sequencing) of the DNA binding pattern of ParBF (SopB) of plasmid F. This study, performed in E. coli, investigates the impact of mutations in the CTP binding motif BoxIII on ParBF DNA binding profiles in vivo. We found that ParBF-N153A allele binds to parS as WT but is impaired in clamp formation thus abolishing the long distance DNA binding on parS-proximal DNA. more...

Organism:

Escherichia coli

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25140

8 Samples

Download data: TXT

(Submitter supplied) The activity of DNA adenine methyltransferase (Dam) and DNA cytosine methyltransferase (Dcm) together account for nearly all methylated nucleotides in the Escherichia coli K-12 MG1655 genome. Previous studies have shown that perturbation of DNA methylation alters E. coli global gene expression, but it is unclear whether the methylation state of Dam or Dcm target sites regulates local transcription. We observed an underrepresentation of Dam sites in transcriptionally silent extended protein occupancy domains (EPODs), and we thus hypothesized that a methylation-deficient version of MG1655 would show large-scale aberrations in chromatin structure. To test our hypothesis, we cloned methyltransferase deletion strains and performed global protein occupancy profiling using high resolution in vivo protein occupancy display (IPOD-HR), chromatin immunoprecipitation for RNA polymerase (RNAP-ChIP), and transcriptome abundance profiling using RNA-Seq. Our results indicate that loss of DNA methylation does not result in large-scale changes in genomic protein occupancy such as the formation of EPODs. However, loci with dense clustering of Dam methylation sites show methylation-dependent changes in local RNA polymerase and total protein occupancy, but local transcription is unaffected. Our transcriptome profiling data indicates that deletion of dam and/or dcm results in significant expression changes within some functional gene categories including SOS response, flagellar synthesis, and translation, but these expression changes appear to result from indirect regulatory consequences of methyltransferase deletion. In agreement with the downregulation of genes involved in flagellar synthesis, dam deletion is characterized by a swimming motility-deficient phenotype. We thus conclude that DNA methylation does not control the overall protein occupancy landscape of the E. coli genome, and that observable changes in gene regulation are generally not resulting from regulatory consequences of local methylation state.

Organism:

Escherichia coli

Type:

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

Platform:

GPL32081

48 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Retrons are bacterial genetic retroelements that encode reverse transcriptase capable of producing multicopy single-stranded DNA (msDNA) and function as antiphage defense systems. Phages employ several strategies to counter the host defense systems, but no mechanisms for evading retrons are known. Here, we show that tRNATyr and Rad (retron anti defense) of T5 phage family inhibit the defense activity of retron 78 and a broad range of retrons, respectively. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

6 Samples

Download data: XLSX

(Submitter supplied) Microbes experience high cell density in many environments that come with diverse resource limitations and stresses. However, high density physiology remains poorly understood. We utilized well-controlled culturing systems to grow wild-type and metabolically engineered Escherichia coli strains into high cell densities (50–80 g Cdry cell weight L-1) and explore the associated transcriptional dynamics. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

470 Samples

Download data: CSV

(Submitter supplied) The heat-shock response is a cellular protection mechanism against sudden temperature upshifts extensively studied in Escherichia coli. However, the effects of thermal evolution on this response remain largely unknown. In this study, we investigated the early and late physiological and transcriptional responses to temperature upshift in a thermotolerant strain under continuous culture conditions. Adaptive laboratory evolution was performed on a metabolically engineered E. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL35385

4 Samples

Download data: TXT

(Submitter supplied) The insulin receptor (INSR) entrains tissue growth and metabolism to nutritional conditions. Complete loss of function in humans leads to extreme insulin resistance and infantile mortality, while loss of 80-90% function permits longevity of decades. Even low-level activation of severely compromised receptors, for example by anti-receptor monoclonal antibodies, thus offers the potential for decisive clinical benefit. more...

Organism:

Mus musculus; Escherichia coli

Type:

Other

Platforms:

GPL29643 GPL13112

69 Samples

Download data: CSV, TSV, TXT

(Submitter supplied) The aim of the study was to uncover the mechanism behind m6A methylation on E. coli mRNA, and to elude to its functional roles by characterising it and asessing its affects under stress. We carried out m6A sequencing under different conditions.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32081

2 Samples

Download data: TXT

(Submitter supplied) The aim of the study was to uncover the mechanism behind m6A methylation on E. coli mRNA, and to elude to its functional roles by characterising it and asessing its affects under stress. We carried out m6A sequencing to meet these aims, and conclude that there is no enzymatic mechanism acting directly on the mRNA responsible for m6A installation, and that the modification is most likely non-functional, and appears randomly throughout the transcriptome.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL21433

20 Samples

Download data: TAB

(Submitter supplied) Spontaneous cellular reprogramming is rare, but has been observed in adult cells. This is most evident in the mammalian liver, where hepatocytes undergo physiological reprogramming to generate functional biliary epithelial cells (BECs) in response to injury. The underlying mechanisms driving this cell fate switch remain unclear, however. Here, we characterize epigenetic changes occurring during this transition at the single cell level, and show that reprogramming occurs synchronously and deterministically, though reprogrammed cells retain epigenetic hepatocyte memory. more...

Organism:

Escherichia coli; Mus musculus

Type:

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

Platforms:

GPL28126 GPL21273 GPL21626

86 Samples

Download data: BROADPEAK, BW, TBI, TSV, TXT

(Submitter supplied) Investigating the evolution of Escherichia coli in microgravity offers valuable insights into microbial adaptation to extreme environments. Here the effects of simulated microgravity (SµG) on gene expression of E. coli REL606, a strain evolved terrestrially for 35 years is explored. We evaluated the transcriptomic changes for glucose-limited and glucose-replete conditions over 24 hours which illustrate that SµG increased the expression of stress response and cell membrane-related genes, particularly under glucose-limited conditions. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33919

64 Samples

Download data: CSV

(Submitter supplied) This dataset contains RNA-seq profiles of Escherichia coli K-12 MG1655 collected under a variety of conditions to enable transcriptional regulatory network (TRN) analysis using the iModulon framework.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

16 Samples

Download data: CSV

(Submitter supplied) We present a novel platform for high-resolution mapping of DNA polymerase activity and stability under the effects of harsh chemistries that are incompatible with most other mutational scanning methods. This approach pairs compartmentalized self-replication (CSR), a high-throughput method for polymerase directed evolution, with deep mutational scanning (DMS), a method of quantifying variant effect via next-generation sequencing of libraries that are subjected to a functional selection. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL32081

13 Samples

Download data: CSV

(Submitter supplied) This study demonstrates that Lpp (Braun’s lipoprotein), and L, D-transpeptidases are required for AggR activation. We found that deletion lpp in EAEC resulted in the downregulation of more than 100 genes involved in transport, metabolism, and virulence. Among those genes, fourteen transcriptional factors, including AggR, were differentially expressed in 042Dlpp.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

4 Samples

Download data: XLSX

(Submitter supplied) Thhe dataset contains small interfering DNAs (siDNAs) that associated with MaAgo during heterologous expression in E. coli in absence or presence of MaACE1. The goal of the study was to 1) determine what type of siDNAs associate with MaAgo 2) from what sequences these siDNAs are derived and 3) whether MaACE1 influences the length or type of the siDNAs associated with MaAgo.

Organism:

Escherichia coli

Type:

Other

Platform:

GPL25368

2 Samples

Download data: XLSX

(Submitter supplied) Bacterial gene networks have many operons, each coordinating the kinetics of a few genes in time and strength. In E. coli, nearly half of these operons also have internal promoters, which allow regulating the downstream genes, independently from upstream genes. We studied their role during genome-wide stresses targeting a few key elements of the transcription machinery, namely, RNAP and Gyrase. We show that absolute differences in response strength between genes in the same operon follow a sinusoidal function of the distance between them. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21433

15 Samples

Download data: CSV, XLSX