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Guardians of the genome protecting DNA from endogenous sources of damage

ABSTRACT: Analysis of mutational signatures caused by DNA repair defects in human induced pluripotent stem (iPS) cells. A reference human iPS cell line will be used for genetic manipulation to introduce homozygous knockouts of 100 genes known to be involved in or connected to DNA repair or DNA editing. Following a defined period of growth after homozygous knockout of each gene, sub clones will be generated and sequenced. The progenitor Ã¢Â€ÂœparentalÃ¢Â€Â IPS cell line will be used to generate reference sequence data, in order to determine the mutational signature acquired due to the gene knockout. This is a pilot study to investigate the effects of oxygen conditions and growth period on mutations acquired

PROVIDER: EGAS00001000874 | EGA |

REPOSITORIES: EGA

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Guardians of the genome protecting DNA from endogenous sources of damage

Project description:Analysis of mutational signatures caused by DNA repair defects in human induced pluripotent stem (iPS) cells. A reference human iPS cell line will be used for genetic manipulation to introduce homozygous knockouts of 100 genes known to be involved in or connected to DNA repair or DNA editing. Following a defined period of growth after homozygous knockout of each gene, sub clones will be generated and sequenced. The progenitor Ã¢Â€ÂœparentalÃ¢Â€Â IPS cell line will be used to generate reference sequence data, in order to determine the mutational signature acquired due to the gene knockout.

| EGAS00001000800 | EGA

The dynamics of Atm signalling dictate cellular fate decisions after DNA damage

Project description:DNA damage activates diverse cellular responses â€“ either protective or deleterious â€“that ultimately promote or inhibit proliferation. How the distinct responses conferring crucial cell fate decisions are chosen is unclear. Using a systems approach, we demonstrate that the dynamic features of Atm dependent DNA double-strand break (DSB) signalling response dictate cellular outcome. Combining temporal phosphoproteome and nascent transcriptome analyses after low or high DNA-damage-load, we discovered that some responses, such as Tp53 activation, have an activation threshold and others arise independently of DNA-damage-load. Using DSB repair deficient cells, we show that persistent DSBs alter the kinetics â€“ but not the amplitude â€“ of Atm signalling. Thus, we demonstrate that pathway choices are dictated by the signalling dynamics and hence cell fate decisions are responsive to DNA-damage-load and repair capacity of the cells.

2023-01-18 | PXD013620 | Pride

Transcription profiling of Arabidopsis Hsa32 mutant and wild type plants subjected to heat shock

Project description:Plants and animals share similar mechanisms in the heat-shock (HS) response, such as synthesis of the conserved HS proteins (Hsps). However, because plants are confined to a growing environment, in general they require unique features to cope with heat stress. We have analyzed the function of a novel Hsp, heat-stress-associated 32-kD protein (Hsa32), which is highly conserved in land plants but absent in most other organisms. The gene responds to HS at the transcriptional level in moss, Arabidopsis, and rice. Like other Hsps, Hsa32 protein accumulates greatly in Arabidopsis seedlings after HS treatment. Disruption of Hsa32 by T-DNA insertion does not affect growth and development under normal conditions. However, the acquired thermotolerance in the knockout line was compromised following a long recovery period (> 24 h) after an acclimation HS treatment, when a severe HS challenge killed the mutant but not the wild-type plants, but no significant difference was observed if they were challenged within a short recovery period. Microarray analysis of the knockout mutant indicates that only the expression of Hsa32 was significantly altered in HS response. Taken together, our results suggest that Hsa32 is not required for the induction but maintenance of acquired thermotolerance. This report provides direct evidence that a plant-specific Hsp plays an important role in thermotolerance.

2007-06-27 | E-GEOD-4062 | biostudies-arrayexpress

Single-cell transcriptome profiling of Sox2-low iPS cells

Project description:Single-cell RNA-seq was performed on homozygous Sox2 knockout induced pluripotent stem (iPS) cells, where residual Sox2 expression is observed from incompletely silenced retroviral transgenes. These were compared to Sox2-low iPS cells rescued by exogenous Sox2 transgenic expression, and wild-type iPS cells to assess the lineage expression profile of Sox2-low cells and degree of transcriptional heterogeneity in each population.

2020-12-28 | E-MTAB-9931 | biostudies-arrayexpress

RNA-Seq of isogenic human iPS cell-derived cardiomyocytes with RBM20 mutations created by genome editing [RNA-Seq]

Project description:RBM20 heterozygous (Het) and homozygous (Homo) R636S and homozygous 8-bp deletion (which causes nonsense-mediated decay) mutations were created by genome editing in an iPS cell line generated from a healthy male patient. Those cells were differentiated into cardiomyocytes by modulating the WNT signaling pathway, and then are subjected to the lactate purification method.

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RNA-Seq of isogenic human iPS cell-derived cardiomyocytes with RBM20 mutations created by genome editing (RiboMinus RNA-Seq)

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EGAS00001002060-sc-2019-09-24T10:04:42Z - samples

Project description:Analysis of mutational signatures caused by exposure to known mutagens in human induced pluripotent stem (iPS) cells. A reference human iPS cell-line will be exposed to 100 chemicals known or proposed to be mutagenic. Following exposure to mutagen, cells will undergo a period of recovery before sub clones are generated and sequenced. The progenitor "parental" IPS cell-line will be used to generate reference sequence data, in order to determine the mutational signatures acquired as a result of exposure to different mutagens.

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A compendium of mutational signatures due to environmental exposures

Project description:Analysis of mutational signatures caused by exposure to known mutagens in human induced pluripotent stem (iPS) cells. A reference human iPS cell-line will be exposed to 100 chemicals known or proposed to be mutagenic. Following exposure to mutagen, cells will undergo a period of recovery before sub clones are generated and sequenced. The progenitor “parental” IPS cell-line will be used to generate reference sequence data, in order to determine the mutational signatures acquired as a result of exposure to different mutagens.

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Heat shock response in Arabidopsis Hsa32 knockout mutant

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Multi-omics analysis into the molecular mechanisms underlying the up-regulation of HBG1/2 expression induced by HBB deletion

Project description:A multi-omics study examining chromatin accessibility, transcriptome, proteome and phosphorylation patterns in the HBB homozygous knockout of the HUDEP2 cell line (HBB-KO)

2022-04-04 | PXD030182 | Pride

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