Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31612102_1.fastq.gz | Fastqsanger.gz | |||
| SRR31612102_2.fastq.gz | Fastqsanger.gz | |||
| SRR31612103_1.fastq.gz | Fastqsanger.gz | |||
| SRR31612103_2.fastq.gz | Fastqsanger.gz | |||
| SRR31612104_1.fastq.gz | Fastqsanger.gz |
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Project description:The control of cellular processes by direct electronic interface will facilitate the development of biosensors, synthetic biology, and nanobiotechnology by providing the means to pass information from synthetic to living elements of hybrid systems. To investigate the potential of manipulating cellular gene expression by means of electric current, Escherichia coli cultures were screened for electric current inducible genes using global gene expression profiling. Cells in stationary phase were subjected to a DC current density of 2.5 mA/cm2 for 2 min after which the cells were lysed and the total RNA extracted. Of the 4290 expressed genes in E. coli , 432 genes were found to be significantly differentially expressed at an effective alpha value of 5.8 X 10-6. Of these, 333 genes were induced and 99 repressed. Several genes were verified as differentially expressed by quantitative real-time RT-PCR. The set of differentially expressed genes were examined for the presence of regulatory factors, subsidiary regulon genes, and biological function, particularly redox functions. Transcripts for the regulatory proteins fnr, sspB, soxS, oxyR, creB and yeiL were found to be up-regulated, and crp was down regulated. While soxS and oxyR were up-regulated, the downstream genes controlled by these regulatory proteins were not differentially expressed, suggesting that the oxidative stress level of low-current electric exposure is small. Genes controlled by FNR and CRP, many of which have redox function, were found to be differentially expressed suggesting modulation by direct reduction that can only be partially explained as a response to the reducing environment created by the electrolytic generation of H2 at the cathode. Genes associated with phosphate metabolism and membrane proteins were also differentially expressed. Three biological replicates were exposed to electric current along with three biological replicate controls.
2010-06-25 | E-GEOD-5192 | biostudies-arrayexpress
Project description:The control of cellular processes by direct electronic interface will facilitate the development of biosensors, synthetic biology, and nanobiotechnology by providing the means to pass information from synthetic to living elements of hybrid systems. To investigate the potential of manipulating cellular gene expression by means of electric current, Escherichia coli cultures were screened for electric current inducible genes using global gene expression profiling. Cells in stationary phase were subjected to a DC current density of 2.5 mA/cm2 for 2 min after which the cells were lysed and the total RNA extracted. Of the 4290 expressed genes in E. coli , 432 genes were found to be significantly differentially expressed at an effective alpha value of 5.8 X 10-6. Of these, 333 genes were induced and 99 repressed. Several genes were verified as differentially expressed by quantitative real-time RT-PCR. The set of differentially expressed genes were examined for the presence of regulatory factors, subsidiary regulon genes, and biological function, particularly redox functions. Transcripts for the regulatory proteins fnr, sspB, soxS, oxyR, creB and yeiL were found to be up-regulated, and crp was down regulated. While soxS and oxyR were up-regulated, the downstream genes controlled by these regulatory proteins were not differentially expressed, suggesting that the oxidative stress level of low-current electric exposure is small. Genes controlled by FNR and CRP, many of which have redox function, were found to be differentially expressed suggesting modulation by direct reduction that can only be partially explained as a response to the reducing environment created by the electrolytic generation of H2 at the cathode. Genes associated with phosphate metabolism and membrane proteins were also differentially expressed. Keywords: electric current induced gene expression
2008-02-12 | GSE5192 | GEO
Project description:Electric current induced genes in Escherichia coli
| PRJNA96533 | ENA
Project description:Study on changes in gene expression in primary cultures of neonatal rat ventricular cardiomyocytes to electric stimulation. Through comparing non-stimulated, stimulated and blebbistatin supplemented and stimulated cultures we set out to identify the genes that are specifically activated by electric pulsing separate from cardiomyocyte contractions. After initial recovery phase, primary cultures of neonatal rat ventricular cardiomyocytes were cultured for 3 days without pulsing, with electric pulsing or with electric pulsing combined with blebbistatin. Per treatment: 3 arrays, with samples obtained from 3 separate series of cardiomyocyte isolation and culturing. Per array: sample prepared from pooled (1:1) RNA from duplicate experiments.
2009-12-10 | E-GEOD-15856 | biostudies-arrayexpress
Project description:We use a human whole genome microarray to analyze the effects of nanosecond pulsed electric fields on Jurkat cells with the focus on early response genes to DNA damage. Keywords: nanosecond pulsed electric fields, jurkat cells, DNA damage
2006-02-01 | GSE4106 | GEO
Project description:The scarcity of effective treatment options for high grade brain tumours has led to a wide ranging search for alternative means of therapy for these difficult to treat tumours. Electrical field therapy is one such area that has been considered. The OptuneTM system is an FDA approved novel anti-mitotic device that delivers continuous alternating electric fields to the patient for the treatment of primary and recurrent Glioblastoma multiforme (GBM) (tumor treating fields - TTFields). Alternative electric fields delivery systems are also being investigated for the treatment of various cancers.To further explore alternative potential mechanisms of electric fields as a whole, we ran Optune, DBS electric fields treated and control untreated KNS42, U87 and GIN-31 (primary) cell lines on Clariom S Human Assays to produce genome-wide expression data.
2020-10-01 | E-MTAB-9043 | biostudies-arrayexpress
Project description:Study on changes in gene expression in primary cultures of neonatal rat ventricular cardiomyocytes to electric stimulation. Through comparing non-stimulated, stimulated and blebbistatin supplemented and stimulated cultures we set out to identify the genes that are specifically activated by electric pulsing separate from cardiomyocyte contractions.
2009-12-10 | GSE15856 | GEO
Project description:Cortical neurons exhibit astounding diversity in gene expression as well as in morphological and electrophysiological properties. Most existing neural taxonomies are based on either transcriptomic or morpho-electric criteria, as it has been technically challenging to study both aspects of neuronal diversity in the same set of cells. Here we used Patch-seq to combine patch-clamp recording, biocytin staining, and single-cell RNA sequencing of over 1300 neurons in adult mouse motor cortex, providing a comprehensive morpho-electric annotation of almost all transcriptomically defined neural cell types. We found that, although broad families of transcriptomic types (Vip, Pvalb, Sst, etc.) had distinct and essentially non-overlapping morpho-electric phenotypes, individual transcriptomic types within the same family were not well-separated in the morpho-electric space. Instead, there was a continuum of variability in morphology and electrophysiology, with neighbouring transcriptomic cell types showing similar morpho-electric features, often without clear boundaries between them. Our results suggest that neural types in the neocortex do not always form discrete entities. Instead, neurons follow a hierarchy consisting of distinct non-overlapping branches at the level of families, but can form continuous and correlated transcriptomic and morpho-electrical landscapes within families.
2020-12-24 | GSE163764 | GEO
Project description:Catheter ablation is an effective treatment to prevent recurrence of Atrial fibrillation (AF) and can be used to maintain sinus rhythm and improve symptoms of AF, but to some extent it can cause a range of adverse effects associated with catheter ablation. Pulsed electric field is a newer treatment modality to replace catheter ablation for atrial fibrillation due to its fewer side effects. Different from radiofrequency ablation, which destroys diseased myocardial tissue by thermal energy, pulsed electric field ablation achieves the purpose of atrial fibrillation ablation by inducing damage to diseased myocardial cells through irreversible electroporation. However, some experimental parameters and mechanism of pulsed electric fields remain unclear.
2023-11-30 | GSE214387 | GEO
Project description:Hybridization can act as a catalyst for rapid phenotypic evolution by introducing novel allelic combinations, which can affect hybrid phenotype through changes in gene expression. The African weakly electric fish use their muscle-derived electric organ to produce electric organ discharge (EOD) for electrocommunication and electrolocation. The EOD in genus Campylomormyrus and cross-species hybrids is usually species-specific and varies during ontogeny. We compared the gene expression patterns and allele specific expression between juvenile and adult individuals in C. compressirostris (EOD duration 0.4 ms in juvenile and 0.4 ms in adult), C. rhynchophorus (EOD duration 5 ms in juvenile and 40 ms in adult) and their hybrid (EOD duration 0.4 ms in juvenile and 4 ms in adult). Differentially expressed genes between juveniles and adults were highly enriched in “membrane”, “plasma membrane” and “cytoplasm” Go Ontogeny terms. We detected several potassium channel-related genes (e.g. KCNJ2, ADCYAP1) that are potentially involved in the EOD development during ontogeny. The alleles from C. compressirostris show dominant expression in the hybrid at juvenile and adult life stages. KCNJ2 is the only gene that exhibits allelic dominance of C. rhynchophorus allele, and has an increasing expression during ontogeny in this allele. This suggests that the EOD development in hybrids could be related to the increasing allelic expression of the C. rhynchophorus allele under the scenario of overall dominance of C. compressirostris alleles. Our study sheds light in the evolution of the electric organ discharge in electric fishes and on the role of introgressive hybridization in complex phenotypic traits.
2023-08-31 | GSE240784 | GEO