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High Depth sequencing for somatic mutations identification in DNA repair Knockout lines in Arabidopsis thaliana

dataset
posted on 2024-01-26, 22:36 authored by UC Davis
Purpose: To explore the distribution and effects of somatic mutations in DNA repair gene knockouts in Arabidopsis thaliana, with a focus on understanding their role in mutation biases observed in prior studies.Scope: The project involves the systematic identification and comparison of somatic mutation profiles in both mutant lines with knocked-out DNA repair genes and wild-type controls.Methods: Sample preparation involves grinding whole rosettes in liquid nitrogen, with DNA extraction performed using the Qiagen DNeasy Plant Mini Kit. Sequencing will be conducted via the Illumina platform, utilizing the NovaSeq system for high-depth whole-genome sequencing to achieve approximately 250x coverage.Expected Outcomes: The study aims to uncover patterns of mutation across the Arabidopsis genome, particularly in regions with genomic constraints, comparing MSH6 knockout lines to wild-type controls. The insights gained may shed light on the mechanisms of mutation bias and DNA repair pathways in plants.Project Data: The project will generate high-coverage genomic datasets, which will be made available in public repositories following standard data sharing policies and upon completion of the study.

Funding

National Institute of Food and Agriculture, 108681-Z5327202

Compact Pro High Bay, HG-2022-35

Foundation for Food and Agriculture Research, ICRC20-0000000014

History

Data contact name

BioProject Curation Staff

Publisher

National Center for Biotechnology Information

Temporal Extent Start Date

2023-11-11

Theme

  • Non-geospatial

ISO Topic Category

  • biota

National Agricultural Library Thesaurus terms

sequence analysis

Pending citation

  • No

Public Access Level

  • Public

Accession Number

PRJNA1039302

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