EGAS00001001095-sc-20150702 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001001428 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Identification of human deubiquitylating enzymes whose knock out result in hypersensitivity to DNA damaging agents, by comparing the sequence reads of ‘barcode region’ from mixed cell culture.
| EGAS00001001095 | EGA
Project description:RNA-Seq of round spermatids comparing WT (FVBNJ) to H2A.B3 knock-out mice
2019-01-16 | E-MTAB-7277 | ExpressionAtlas
Project description:CaGAL102 is a sequence homolog of Rmlb. In Candida knock out of this gene causes abnormal hyphal morphogenesis and increased sensitivity to cell wall damaging agents. The knock out strain is also avirulent in mouse model of systemic infection. To get a larger insight into the function of the protein product of this gene we carried out global transcription analysis through micro array experiment. The gene is expressed under normal growth conditions and the knock out causes the cells to become hyphal under these conditions. Many of the cell wall proteins were upregulated recapitulating the cell morphology. Keywords: Candida albicans, Gene knockout, genome wide transcription profiling study
2011-03-15 | GSE20883 | GEO
Project description:Homologous recombination (HR) deficiency enhances sensitivity to DNA damaging agents commonly used to treat cancer. In HR-proficient cancers, metabolic mechanisms driving response or resistance to DNA damaging agents remain unclear. Here we identified that depletion of alpha-ketoglutarate (αKG) sensitizes HR-proficient cells to DNA damaging agents by metabolic regulation of histone acetylation. αKG is required for the activity of αKG-dependent dioxygenases (αKGDDs), and prior work has shown that changes in αKGDD affect demethylases. Using a targeted CRISPR knockout library consisting of 64 αKGDDs, we discovered that Trimethyllysine Hydroxylase Epsilon (TMLHE), the first and rate-limiting enzyme in de novo carnitine synthesis, is necessary for proliferation of HR-proficient cells in the presence of DNA damaging agents. Unexpectedly, αKG-mediated TMLHE-dependent carnitine synthesis was required for histone acetylation, while histone methylation was affected but dispensable. The increase in histone acetylation via αKG-dependent carnitine synthesis promoted HR-mediated DNA repair through site- and substrate-specific histone acetylation. These data demonstrate for the first time that HR-proficiency is mediated through αKG directly influencing histone acetylation via carnitine synthesis and provide a metabolic avenue to induce HR-deficiency and sensitivity to DNA damaging agents.
2025-02-26 | GSE289735 | GEO
Project description:Identifying Novel Predictors of Resistance to DNA Damaging Agents
| PRJNA108541 | ENA
Project description:A. niger and A. oryzae are two filamentous fungi widely used in industry to produce various enzymes (e.g. pectinases, amylases) and metabolites (e.g. citric acid). Using proteomics, the co-cultivation of these two fungi in wheat bran showed an equal distribution of the two strains forming mixed colonies with a broad range of carbohydrate active enzymes produced. This stable mixed microbial system seems suitable for subsequent commercial processes such as enzyme production. XlnR knock-out strains for both aspergilli were used to study the influence of plant cell wall degrading enzyme production on the fitness of the mixed culture.
2017-02-27 | PXD005532 | Pride
Project description:Neuropathic pain is one of the most intractable pain conditions associated with tumor growth compressing and damaging nerves. A troublesome hallmark symptom of neuropathic pain is hypersensitivity to innocuous stimuli, known as “tactile allodynia,” which is often refractory to currently available analgesics. Diurnal variations in pain hypersensitivity are common in patients with cancer, but the underlying mechanisms are enigmatic. Herein, we report that spinal expression of lipocalin-2 (LCN2) enhances pain sensitivity of NCTC2472 fibrosarcoma-implanted male mice during specific stages of the diurnal cycle. As the tumor grew, interleukin-6 (IL-6) levels increased in the spinal cord of the mice. Increased IL-6 levels stimulated LCN2 expression in spinal microglia, but this expression was periodically repressed by the circadian clock components REV-ERBα and REV-ERBβ. Notably, intra-spinal dorsal horn injection of lentiviral vectors expressing REV-ERBα or REV-ERBβ in tumor-bearing mice alleviated tactile allodynia. Furthermore, intrathecal injection of SR9009, a synthetic agonist of REV-ERBs, also attenuated cancer-induced pain hypersensitivity, accompanied by suppressing spinal LCN2 expression. These results suggest that temporal elevation of LCN2 expression decreases the threshold of tactile pain hypersensitivity induced by tumor growth. We propose that the circadian clock component of REV-ERBs is an effective target for alleviation of cancer-induced tactile allodynia, identifying a new class of analgesic agents.
2025-04-27 | GSE255355 | GEO
Project description:CaGAL102 is a sequence homolog of Rmlb. In Candida knock out of this gene causes abnormal hyphal morphogenesis and increased sensitivity to cell wall damaging agents. The knock out strain is also avirulent in mouse model of systemic infection. To get a larger insight into the function of the protein product of this gene we carried out global transcription analysis through micro array experiment. The gene is expressed under normal growth conditions and the knock out causes the cells to become hyphal under these conditions. Many of the cell wall proteins were upregulated recapitulating the cell morphology. Keywords: Candida albicans, Gene knockout, genome wide transcription profiling study Wild type Sc5314 cells and the mutant CAS12 were grown in YPD till (OD 600nm) 1 following which total RNA was extracted using hot phenol method. The RNA was checked using Bioanalyser (Agilent). Single dye experiment was carried out using Cy3 labelled pooled wild type samples and two independent mutant RNA samples.
2011-03-15 | E-GEOD-20883 | biostudies-arrayexpress
Project description:Lactate enable to cause a novel post-translational modification, lactylation of proteins. We are interested in exploring whether lactate modulates DNA-damaging agents resistance in the form of lactylation. To gain a global view of DNA-damaging agents resistance-related lactylation, especially Kla of nonhistone substrates, we used 4D-Label free high-resolution LC-MS/MS, quantitative lysine lactylation analysis to investigate Kla substrates in cisplatin-resistant AGS cells.
2022-12-16 | PXD038880 |
Project description:Eukaryotic cells respond to DNA damage by arresting the cell cycle and modulating gene expression to ensure efficient DNA repair. The human ATR kinase and its homolog in yeast, MEC1, play central roles in transducing the damage signal. To characterize the role of the Mec1 pathway in modulating the cellular response to DNA damage, we used DNA microarrays to observe genomic expression in Saccharomyces cerevisiae responding to two different DNA-damaging agents. We compared the genome-wide expression patterns of wild-type cells and mutants defective in Mec1 signaling, including mec1, dun1, and crt1 mutants, under normal growth conditions and in response to the methylating-agent methylmethane sulfonate (MMS) and ionizing radiation. Here, we present a comparative analysis of wild-type and mutant cells responding to these DNA-damaging agents, and identify specific features of the gene expression responses that are dependent on the Mec1 pathway. Among the hundreds of genes whose expression was affected by Mec1p, one set of genes appears to represent an MEC1-dependent expression signature of DNA damage. Other aspects of the genomic responses were independent of Mec1p, and likely independent of DNA damage, suggesting the pleiotropic effects of MMS and ionizing radiation. The complete data set as well as supplemental materials is available at http://www-genome.stanford.edu/mec1 Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Using regression correlation
2005-09-24 | E-GEOD-3358 | biostudies-arrayexpress