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Omics score: 6

NGS based viability screening using haploid cell line

ABSTRACT: 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.

PROVIDER: EGAS00001001095 | EGA |

REPOSITORIES: EGA

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EGAS00001001095-sc-20150702 - samples

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.

| EGAD00001001428 | EGA

Gene expression in wild type and Cagal102 knockout Candida albicans strains.

2011-03-15 | GSE20883 | GEO

Homo sapiens

Project description:Identifying Novel Predictors of Resistance to DNA Damaging Agents

| PRJNA108541 | ENA

Mixed colonies of Aspergillus niger and Aspergillus oryzae cooperatively degrading wheat bran

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

Gene expression in wild type and Cagal102 knockout Candida albicans strains.

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

Systematic profiling of lysine lactylation proteome reveals distinct changes in lactylation between the parental AGS cells and cisplatin-resistant AGS cells

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 | iProX

Tissue/Cell DNaseI sensitivity/hypersensitivity screening

Project description:DNaseI hypersensitivity using DNase-array method on Affy platform overall design Per DNase-array method (Sabo et al Nature Methods 3:511,2006) PMID: 15782197 Keywords: genomic

2007-09-30 | GSE8962 | GEO

Systematic profiling of lysine lactylation proteome reveals distinct changes in lactylation between the parental AGS cells and cisplatin-resistant AGS cells

2024-05-09 | PXD050906 | Pride

Genome-wide profiling of γH2AX in Arabidopsis

Project description:The R-loop, composed of a DNA-RNA hybrid and the displaced single-stranded DNA, regulates diverse cellular processes. However, how cellular R-loops are sensed remain poorly understood. Here we report the discovery of the evolutionally conserved ALBA proteins (AtALBA1&2) functioning as the R-loops sensor of genic regions in higher plant Arabidopsis thaliana. AtALBA1 and 2 form a heterodimer protein complex and localize in the nucleus. While AtALBA1 binds to the DNA-RNA hybrid strand, AtALBA2 associates with single-stranded DNA in the R-loops. AtALBA1&2 preferentially binds to the genic R-loop regions that are associated with active epigenetic marks. Depletion of AtALBA1 or AtALBA2 results in hypersensitivity of plants to DNA damaging agents. Our results demonstrate the unprotected R-loops by loss of AtALBA1&2 are main source of DNA damage through γH2AX ChIP-seq.

2019-04-17 | GSE124943 | GEO

ALBA protein complex reads genic R-loops to maintain genome stability in Arabidopsis

Project description:The R-loop, composed of a DNA-RNA hybrid and the displaced single-stranded DNA, regulates diverse cellular processes. However, how cellular R-loops are sensed remain poorly understood. Here we report the discovery of the evolutionally conserved ALBA proteins (AtALBA1&2) functioning as the R-loops sensor of genic regions in higher plant Arabidopsis thaliana. AtALBA1 and 2 form a heterodimer protein complex and localize in the nucleus. While AtALBA1 binds to the DNA-RNA hybrid strand, AtALBA2 associates with single-stranded DNA in the R-loops. AtALBA1&2 preferentially binds to the genic R-loop regions that are associated with active epigenetic marks. Depletion of AtALBA1 or AtALBA2 results in hypersensitivity of plants to DNA damaging agents. Our results demonstrate the AtALBA1&2 protein complex is the Arabidopsis genic R-loops sensor for maintaining genome stability in Arabidopsis.

2019-04-17 | GSE121683 | GEO

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