Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A compendium of mutational signatures due to environmental exposures

ABSTRACT: 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.

PROVIDER: EGAS00001002060 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

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.

| EGAD00001005351 | EGA

Genetic and phenotypic changes to Venezuelan equine encephalitis virus following treatment with β-D-N4-hydroxycytidine, an RNA mutagen

Project description:The high mutation rate of RNA viruses provides viral populations with the ability to adapt to new environments but also makes them vulnerable to extinction due to the deleterious effects of mutations, which is the conceptual basis for the antiviral activity of RNA mutagens. However, there are still gaps in the quantitative understanding of the dynamics between the mutations induced by an RNA mutagen and its effects on viral fitness. To address this, we used Venezuelan Equine Encephalitis Virus (VEEV) and the potent RNA mutagen β-d-N4-hydroxycytidine (NHC) as a model to analyze virus replication competency and mutation frequency following treatment in the total and replication-competent viral populations separately. We found that NHC induced transition mutations in a concentration dependent manner in the total population, while the replication-competent population maintained itself within an increased, yet narrow, mutation spectrum. The incorporation of NHC mainly happened during the positive sense RNA synthesis of VEEV. A growth kinetic analysis of VEEV population treated with NHC pointed to a lower but more diverse distribution in mutational fitness, demonstrating that NHC-induced mutations negatively and broadly affect the fitness of the virus. Together, our study provides mechanistic insight into how RNA mutagens affect viral population landscape and the potential of RNA mutagens as an antiviral strategy for alphaviruses.

2024-10-25 | GSE207136 | GEO

EGAS00001000778-sc-20160302 - samples

Project description:Pilot study for mutagen exposure work to be carried out as part of mutational signatures project.

| EGAD00001001934 | EGA

Mutational signatures of DNA damage and repair processes Mutagen Exposure Pilot

Project description:Pilot study for mutagen exposure work to be carried out as part of mutational signatures project.

| EGAS00001000778 | EGA

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

Mus musculus

Project description:Analysis of mutational signatures by chemical mutagens in gpt delta mice

| PRJDB8227 | ENA

Guardians of the genome protecting DNA from endogenous sources of damage

| EGAS00001000874 | EGA

TBA

Project description:Analysis of mutational signatures arising in vivo in humans. iPS cells from control patients and 100 patients carrying known mutations in DNA repair/editing genes will be generated, and sequenced.Blood from the patients will also be used to generate reference 'germline' sequence data.

| EGAS00001000801 | EGA

TBA

| EGAS00001000802 | EGA

TBA

| EGAS00001000803 | EGA