Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA924229 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23109666_1.fastq.gz | Fastqsanger.gz | |||
| SRR23109666_2.fastq.gz | Fastqsanger.gz | |||
| SRR23109667_1.fastq.gz | Fastqsanger.gz | |||
| SRR23109667_2.fastq.gz | Fastqsanger.gz | |||
| SRR23109668_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcription profile of sorted Escherichia coli cells was compared to that of non-sorted cells to evaluate the effect of sorting process on transcriptome of E. coli. E. coli cells were harvest from planktonic cultures in annular reactor and stored in RNAlater. Sorting includes 2-min homogenization with OMNI TH homogenizer on ice for E. coli cells pre-stored in RNAlater and then resuspended in nuclease free phosphate buffered saline for sorting with one-step immuno-magnetic separation with anti-E. coli antibody and microbeads on a MACS separator (Miltenyi, Auburn, CA).
2010-07-13 | GSE22885 | GEO
Project description:Transcription profile of sorted Escherichia coli cells was compared to that of non-sorted cells to evaluate the effect of sorting process on transcriptome of E. coli. E. coli cells were harvest from planktonic cultures in annular reactor and stored in RNAlater. Sorting includes 2-min homogenization with OMNI TH homogenizer on ice for E. coli cells pre-stored in RNAlater and then resuspended in nuclease free phosphate buffered saline for sorting with one-step immuno-magnetic separation with anti-E. coli antibody and microbeads on a MACS separator (Miltenyi, Auburn, CA). Two condition experiments: sorted vs non-sorted. Two biological replicates with individually grown and harvested E. coli cells. Each biological replicate has two technical replicates of labeling and hybridization on microarray slides. Each slide has three built-in replicates for each probe.
2010-07-13 | E-GEOD-22885 | biostudies-arrayexpress
Project description:RiboFACSeq: A new method for investigating metabolic and transport pathways in bacterial cells by combining a riboswitch-based sensor, fluorescence-activated cell sorting and next-generation sequencing
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Project description:Transcriptional profiling of Escherichia coli TB1 cells under (-)-Roemerine treatment. The genome reprograming in the bacterial cells at transcription level was analyzed through treatment of the bacteria with plant-derived alkaloid, (-)-Roemerine, to elucidate the response of bacteria to the antibacterial drug.
2017-06-21 | GSE80827 | GEO
Project description:The invasive bacteria recognition by host cells through autophagy is a key factor for determining bacterial infection. Enteroinvasive Escherichia coli (EIEC) express a protein IcsB, which in Shigella, is known for inactivating the bacterial degradation process. Once EIEC showed less expression of icsB when compared to S. flexneri, we proposed to investigate the autophagy caused by EIEC infection. Our results showed that IcsB protein is an important virulence factor in EIEC because it causes a camouflage of the bacteria in the eukaryotic cell. When there is low or none expression of the protein, the cell recognition of the invasive bacteria is high, decreasing the bacteria dissemination. This found confirms the importance of the gene transcription and the sequence, since the strain E. coli SM124/13, complemented with icsB from Shigella, showed higher dissemination efficiency inside of the host cell. Additionally, our results revealed that eukaryotic cell infected by EIEC or Shigella flexneri showed distinguish responses. In EIEC infection, the autophagy was activated in human cells, but not in a conventional mode. Our hypothesis is that EIEC is recognized by autophagy, being an important cell process for bacterial recognition.
2020-01-11 | GSE93588 | GEO
Project description:The invasive bacteria recognition by host cells through autophagy is a key factor for determining bacterial infection. Enteroinvasive Escherichia coli (EIEC) express a protein IcsB, which in Shigella, is known for inactivating the bacterial degradation process. Once EIEC showed less expression of icsB when compared to S. flexneri, we proposed to investigate the autophagy caused by EIEC infection. Our results showed that IcsB protein is an important virulence factor in EIEC because it causes a camouflage of the bacteria in the eukaryotic cell. When there is low or none expression of the protein, the cell recognition of the invasive bacteria is high, decreasing the bacteria dissemination. This found confirms the importance of the gene transcription and the sequence, since the strain E. coli SM124/13, complemented with icsB from Shigella, showed higher dissemination efficiency inside of the host cell. Additionally, our results revealed that eukaryotic cell infected by EIEC or Shigella flexneri showed distinguish responses. In EIEC infection, the autophagy was activated in human cells, but not in a conventional mode. Our hypothesis is that EIEC is recognized by autophagy, being an important cell process for bacterial recognition.
2020-01-11 | GSE93587 | GEO
Project description:The invasive bacteria recognition by host cells through autophagy is a key factor for determining bacterial infection. Enteroinvasive Escherichia coli (EIEC) express a protein IcsB, which in Shigella, is known for inactivating the bacterial degradation process. Once EIEC showed less expression of icsB when compared to S. flexneri, we proposed to investigate the autophagy caused by EIEC infection. Our results showed that IcsB protein is an important virulence factor in EIEC because it causes a camouflage of the bacteria in the eukaryotic cell. When there is low or none expression of the protein, the cell recognition of the invasive bacteria is high, decreasing the bacteria dissemination. This found confirms the importance of the gene transcription and the sequence, since the strain E. coli SM124/13, complemented with icsB from Shigella, showed higher dissemination efficiency inside of the host cell. Additionally, our results revealed that eukaryotic cell infected by EIEC or Shigella flexneri showed distinguish responses. In EIEC infection, the autophagy was activated in human cells, but not in a conventional mode. Our hypothesis is that EIEC is recognized by autophagy, being an important cell process for bacterial recognition.
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Project description:Defining the cellular factors that drive growth rate and proteome composition is essential for understanding and manipulating cellular systems. In bacteria, ribosome concentration is known to be a constraining factor of cell growth rate, while gene concentration is usually assumed not to be limiting. Here, using single-molecule tracking, quantitative single-cell microscopy, and modeling, we show that genome dilution in Escherichia coli cells arrested for DNA replication results in a decrease in the concentration of active RNA polymerases and ribosomes. The resulting sub-linear scaling of total active RNA polymerases and ribosomes with cell size leads to sub-exponential growth, even within physiological cell sizes. Cell growth rate scales proportionally with the total number of active ribosomes in a DNA concentration-dependent manner. Tandem-mass-tag mass spectrometry experiments further revealed that a decrease in DNA-to-cell-volume ratio also incrementally remodels proteome composition with cell size. Altogether, our findings indicate that genome concentration is an important driver of exponential cell growth and a global modulator of proteome composition in E. coli. Comparison with studies on eukaryotic cells suggests DNA concentration-dependent scaling principles of gene expression across domains of life.
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Project description:We replaced the natural pnp locus with the human cDNA and studied the transcriptomes of 3 strains, namely the wt pnp+ (C-1a), the mutant with pnp ORF deletion (C-5691) and the strain with the substitution of the bacterial ORF with the human one (C-6001).
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Project description:Bacterial transcription factors (TFs) regulate gene expression to adapt to changing environments; when combined, the TF’s regulatory actions comprise transcriptional regulatory networks (TRNs). The chromatin immunoprecipitation (ChIP) assay is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It enables the genome-wide study of transcription factor binding sites (TFBSs) and gene regulation. Here, we present the genome-wide binding for major TFs in E. coli K-12 MG1655.
2021-08-15 | GSE181993 | GEO